Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes)

The subfamily Crotalinae (pitvipers) contains over 190 species of venomous snakes distributed in both the Old and New World. We incorporated an extensive sampling of taxa (including 28 of 29 genera), and sequences of four mitochondrial gene fragments (2.3kb) per individual, to estimate the phylogeny of pitvipers based on maximum parsimony and Bayesian phylogenetic methods. Our Bayesian analyses incorporated complex mixed models of nucleotide evolution that allocated independent models to various partitions of the dataset within combined analyses. We compared results of unpartitioned versus partitioned Bayesian analyses to investigate how much unpartitioned (versus partitioned) models were forced to compromise estimates of model parameters, and whether complex models substantially alter phylogenetic conclusions to the extent that they appear to extract more phylogenetic signal than simple models. Our results indicate that complex models do extract more phylogenetic signal from the data. We also address how differences in phylogenetic results (e.g., bipartition posterior probabilities) obtained from simple versus complex models may be interpreted in terms of relative credibility. Our estimates of pitviper phylogeny suggest that nearly all recently proposed generic reallocations appear valid, although certain Old and New World genera (Ovophis, Trimeresurus, and Bothrops) remain poly- or paraphyletic and require further taxonomic revision. While a majority of nodes were resolved, we could not confidently estimate the basal relationships among New World genera and which lineage of Old World species is most closely related to this New World group.     

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

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

A revision of the genera Dirphys Howard and Encarsiella Hayat (Hymenoptera: Aphelinidae)

Abstract. Dirphys and Encarsiella are revised for the world, and include four and six species respectively. Three Dirphys and two Encarsiella species are described as new. Generic diagnoses and keys to world species of Dirphys and Encarsiella are provided, and their biology is reviewed. These genera are related to the large and economically very important genera Coccophagus and Encarsia , which between them contain about 400 currently valid species. Encarsiella was recently synonymized with Dirphys , and both have previously been confused with Coccophagus and Encarsia , adding to the difficulty surrounding the taxonomy of the latter genera. Computerized character analysis based on parsimony supports the reinstatement of Encarsiella as a valid genus and shows relationships between Dirphys, Encarsia and Encarsiella.     

Catalogue of genera and species of the family Chondracanthidae Milne Edwards, 1840 (Copepoda: Poecilostomatoida) with notes on morphology

The status of subfamilies and genera within Chondracanthidae Milne Edwards, 1840 has recently been revised. Forty four genera are currently recognised as valid for the Chondracanthidae and a comprehensive catalogue to the valid genera and species of the family is presented here. In addition, numerous supplementary observations are presented on existing taxa for which incomplete or inadequate data were previously available.     

In situ characterization of nitrifiers in an activated sludge plant: detection of Nitrobacter Spp

Aims: The purpose of this work was to investigate microbial ecology of nitrifiers at the genus level in a typical full-scale activated sludge plant. Methods and Results: Grab samples of mixed liquor were collected from a plug-flow reactor receiving domestic wastewater. Fluorescent in situ hybridization technique (FISH) was used to characterize both ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in combination with Confocal Scanning Laser Microscope (CSLM). Fluorescently labelled, 16S rRNA-targeted oligonucleotide probes were used in this study. Both Nitrosomonas and Nitrosospira genera as AOB and Nitrobacter and Nitrospira genera as NOB were sought with genus specific probes Nsm156, Nsv443 and NIT3 and NSR1156, respectively. Conclusions: It was shown that Nitrosospira genus was dominant in the activated sludge system studied, although Nitrosomonas is usually assumed to be the dominant genus. At the same time, Nitrobacter genus was detected in activated sludge samples. Significance and Impact of the Study: Previous studies based on laboratory scale pilot plants employing synthetic wastewater suggested that only Nitrospira are found in wastewater treatment plants. We have shown that Nitrobacter genus might also be present. We think that these kinds of studies may not give a valid indication of the microbial diversity of the real full-scale plants fed with domestic wastewater.     

Evolution and taxonomy in capitate hydroids and medusae (Cnidaria: Hydrozoa)

A cladistic analysis of Capitata groups the families in four suborders based on medusa characters (such as manubrium morphology, position of gonads, and position and number of marginal tentacles) and hydroid characters (such as presence or absence of an oral tentacle whorl, and the different development of the tentacles of the oral and aboral whorls). On the family and generic levels, the revision results in changes which unite the separate hydroid and medusa taxonomic systems, defining genera which are not based on characters solely relating to the reduction of medusae to fixed gonophores. In those families where the reduction of the medusa can be analysed, it is shown that the reduction occurred after all synapomorphies defining the genera had evolved and usually affected individual species within a genus rather than the original species from which the other species in the genus evolved. This supports the view that medusa reduction is not in itself a valid generic character. A discussion of the theories of 'inconsistent' or 'mosaic' evolution concludes that no difference in evolutionary rate or degree of specialization can be demonstrated among taxa with free medusae and taxa with gonophores.     

A revision of the genera Sipunculus and Xenosiphon (Sipuncula)

A critical analysis of historically used characters, based on a large series of specimens, is presented. Based on a comparative morphological analysis of type specimens, the 19 species of Sipunculus and four of Xenosiphon are reviewed. The genera and subgenera are redefined so that, after appropriate revisions arc made, Sipunculus (Sipunculus) has eight, Sipunculus (Contraporus) new subgenus has two, and Xenosiphon has only one remaining valid species. A zoogeographical note and a key to the species are included.     

An examination of the Phascolosotna subgenera Antillesoma, Rueppellisoma and Satonus (Sipuncula)

Three of the subgenera in the sipunculan genus Phascolosoma are reviewed, based on examination of type material. The presumed difference between the subgenera Antillesoma and Rueppellisoma (number of retractor muscles) is shown to be invalid and the taxa are therefore synonymous. The 15 species are either considered junior synonyms of P. antillarum (eight), transferred to other species or genera (six), or considered incertae sedis (one). Phascolosoma antillarum is redescribed. Of the eight species in the subgenus Satonus, only P. pectinatum remains valid: the others are considered either to belong to other taxa (four) or to be incertae sedis (three).     

A taxonomic revision of the genera Phrygionis Hübner and Pityeja Walker (Geometridae: Ennominae, Palyadini)

Phrygionis and Pityeja belong to the Palyadini, a tribe of neotropical Ennominae. The moths of both genera bear striking wing markings and mere variants were frequently described as species with the consequence that species diversity was overestimated. Numerous taxonomic changes are made in this work based on the study of primary types and much other material. Variation and distribution is recorded for each species and subspecies. Phylogenetic relationships within Phrygionis are examined, and comments are made on the evolution of wing pattern within this genus.
Fifteen full species are recognized in this study (13 in Phrygionis and two in Pityeja ), of which four (all in Phrygionis ) are described as new; 19 species-group (specific and subspecific) names refer to valid taxa. Twenty-four species-group names are synonymized (19 in Phrygionis and five in Pityeja ) and five are recombined with different genera (four with Phrygionis and one with Pityeja ). Three generic names are synonymized (one in Phrygionis and two in Pityeja ).     

Phylogenetic relationships among Heliconiinae genera based on morphology (Lepidoptera: Nymphalidae)

Abstract.  Phylogenetic relationships among Heliconiinae genera are proposed based on early-stage and adult morphology. Parsimony analyses of forty-nine species in twenty-nine genera indicate that Heliconiinae can be divided into four main groups: (1) Pardopsis , Acraea and Actinote ; (2) Cethosia plus Neotropical genera; (3) Oriental genera and (4) fritillaries. Analyses of adult characters suggested that Oriental genera form a monophyletic group, whereas those of adult plus early-stage characters artificially split this group into three separate lineages. Our character set does not contain enough phylogenetic information to resolve relationships among fritillary genera with confidence, and further studies of this group are needed. The classification of the Heliconiinae is revised based on our results.     

A cladistic analysis of the Trichostrongyloidea (Nematoda).

A morphologically based cladistic analysis of 40 genera included within the Trichostrongyloidea (Amidostomatidae, Dromaeostrongylidae and Trichostrongylidae) is proposed. Two genera were used as outgroups, one from the Strongylina and the other from the Ancylostomatina. Seven genera do not appear in the matrix because some significant morphological characters remain unknown for these genera. Nonetheless, except for Moguranema which is excluded as incertae sedis, a likely systematic position could be assigned to them based on the morphological characters that are known. The classification which best fits the consensus tree is composed of three families. In adding the genera not included in the tree, we obtain: (i) Trichostrongylidae with three sub-families, Amidostomatinae (four genera), Filarinematinae (three genera) and Trichostrongylinae (five genera); (ii) Haemonchidae with two sub-families: Ostertagiinae (eight genera) and Haemonchinae (five genera); (iii) Cooperiidae with three sub-families: Libyostrongylinae (five genera), Obeliscoidinae n. subfam. (five genera) and Cooperiinae (ten genera). Dromaeostrongylus and Ortleppstrongylus, whose females have a caudal spine, are excluded from the Trichostrongyloidea and are placed in the Molineoidea. The hypotheses relating to the evolutionary history of the Trichostrongyloidea are: the origin of the superfamily could have occurred during the upper Cretaceous period. The two most ancient sub-families (Amidostomatinae and Filarinematinae) would be of Gwondwanan origin and evolved during the Paleocene period within Neotropical aquatic birds and within the Australian marsupials. The Trichostrongylinae would have arisen during the Eocene period within birds and then adapted to diverse archaic mammals in the Neotropical region on one hand and in the Nearctic region, on the other hand and lastly adapted to the Lagomorpha and subsequently to the Ruminantia. In both families originating from the Trichostrongylidae, the adaptation to the Lagomorpha may have taken place during the Oligocene but in a different way. In the Haemonchidae, the Ostertagiinae may have passed directly from the Neartic region to Europe. In the Cooperiidae, the adaptation to Lagomorpha may have occurred either within the Libyostrongylinae which may have remained in the Ethiopian region since the Paleocene, or, more likely, by the passage of the Obeliscoidinae from the Nearctic region to the Asian, through the Bering strait. In all cases, the adaptation of the Trichostrongyloidea of Lagomorpha to Ruminants apparently took place during the Miocene, mainly in the Palearctic and the Ethiopian regions.     

中国与北美苔藓植物区系关系的探讨

关于中国和北美间苔藓植物区系关系的研究是在20世纪90年代开始的。研究表明中国和北美苔类和藓类的种间关系疏远,这一事实说明两个大陆在第三纪后期分离后,由于地质、地理、气候等因素的差异致使苔藓植物区系成分也产生明显分异。虽然它们在科、属方面差异较小,但两个大陆已各自形成地区特有的苔类和藓类的属。已知的中国特有及东亚特有的苔类属有5个,藓类属有22个;而已知北美地区特有的苔类属有4个、藓类属有5个。北美东部和西部形成于不同地质时期,在苔藓植物方面与中国共同分布的科、属和种存在一定差异。从神农架藓类植物研究表明,从共同分布的种来看,北美东部与中国比北美西部与中国的相似性系数高约6％。从两地区间苔类和藓类植物的雌雄同株或雌雄异株及孢子直径大小而论,这两个因素似乎并不是影响苔藓植物在两大地区间分布的主要原因,但对苔藓植物的分布仍然十分重要。本文作者认为结合中国和北美的地史、地理条件及苔藓植物自身的特点,可以认为白令海峡不是阻碍中国和北美苔藓植物交流的绝对自然屏障;中国和北美苔藓植物区系关系目前的状况,是长期多次交流融合和分异的结果。     

New species of eocene primates and the phylogeny of European adapidae.

Restudy of virtually all of the important collections of European Eocene primates of the family Adapidae indicates that 28 valid species in 8 genera are now known, spanning a time period of nearly 20 million years. The biostratigraphic distribution of each species has been studied in the context of established reference levels, and a maximum of four evolutionary lineages are known from any one locality. Ten new species are proposed in the genera Pelycodus (1 sp.), Protoadapis (4 sp.), Periconodon (2 sp.), Anchomomys (1 sp.), and Adapis (2 sp.). Phylogenetic relationships among the species, based on stratophenetic linking, are indicated whenever possible.     

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.     

Molecular systematics of the Cactaceae

Bayesian, maximum‐likelihood, and maximum‐parsimony phylogenies, constructed using nucleotide sequences from the plastid gene region trnK‐matK, are employed to investigate relationships within the Cactaceae. These phylogenies sample 666 plants representing 532 of the 1438 species recognized in the family. All four subfamilies, all nine tribes, and 69% of currently recognized genera of Cactaceae are sampled. We found strong support for three of the four currently recognized subfamilies, although relationships between subfamilies were not well defined. Major clades recovered within the largest subfamilies, Opuntioideae and Cactoideae, are reviewed; only three of the nine currently accepted tribes delimited within these subfamilies, the Cacteae, Rhipsalideae, and Opuntieae, are monophyletic, although the Opuntieae were recovered in only the Bayesian and maximum‐likelihood analyses, not in the maximum‐parsimony analysis, and more data are needed to reveal the status of the Cylindropuntieae, which may yet be monophyletic. Of the 42 genera with more than one exemplar in our study, only 17 were monophyletic; 14 of these genera were from subfamily Cactoideae and three from subfamily Opuntioideae. We present a synopsis of the status of the currently recognized genera.
© The Willi Hennig Society 2011.     

Chronological analysis of the species of Conus described during the 18th century

The 339 species-group names in the gastropod genus Conus proposed between 1758 and 1800 have been analyzed in chronological order, in order to (1) identify each nominal species, and (2) determine the correct name of each valid species. Additions and corrections are given to the author's series of papers on type specimens and identity of the described species of Conus. A table listing the 339 species-group names alphabetically indicates the present locations of the 124 known type specimens and the status of each name. At present, 123 valid species are recognized (118 Recent, 5 Tertiary), 159 names are synonyms of previously or simultaneously described species, 35 are nomina dubia, 19 are assigned to infrasubspecific rank, and 3 have been trandferred to genera in other families. Problems involving homonymy of 44 names have been resolved. The proportion of valid species to described species remained quite constant (about 80%) between 1758 and 1786, but then declined sharply to 40%. By 1800, although only 13% of all known species-group names in Conus had been introduced, they probably account for 25% of the known valid Recent species. Extension of the chronological study to species described through 1840 may establish the correct names of half the valid Recent species of Conus.     

Global diversity of true bugs (Heteroptera; Insecta) in freshwater

The aquatic and semi-aquatic Heteroptera, consisting of the infraorders Leptopodomorpha, Gerromorpha, and Nepomorpha, comprise a significant component of the world’s aquatic insect biota. Within these three infraorders as a whole there are currently 23 families, 343 genera and 4,810 species group taxa considered valid, of which 20 families, 326 genera and 4,656 species inhabit freshwater. In addition, more than 1,100 unequivocally diagnosed species remain to be described. Aquatic Heteroptera occur on all continents except Antarctica, and are most numerous in the tropical regions, although there are many distinctly cold-adapted genera. Overall species richness is highest in the Neotropical and Oriental regions, which harbor 1,289 and 1,103 species, respectively. In comparison to these core tropical regions, species richness is significantly lower in the Afrotropical (799 species), Australasian (654 species), Palearctic (496 species), Nearctic (424 species) and Pacific (37 species) regions. Aquatic Heteroptera are notable for utilizing an exceptionally broad range of habitats, from marine and intertidal to arctic and high alpine, across a global altitudinal range of 0–4,700 m. Species may be found in almost every freshwater biotope, and many exhibit striking morphological adaptations to their aquatic environment, making them excellent subjects for ecological and biogeographic studies. Guest editors: E. V. Balian, C. Lévêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment     

Molecular phylogenetics of soricid shrews (Mammalia) based on mitochondrial cytochrome b gene sequences: with special reference to the Soricinae

Molecular phylogeny of soricid shrews (Soricidae, Eulipotyphla, Mammalia) based on 1140 bp mitochondrial cytochrome b gene (cyt b ) sequences was inferred by the maximum likelihood (ML) method. All 13 genera of extant Soricinae and two genera of Crocidurinae were included in the analyses. Anourosorex was phylogenetically distant from the main groupings within Soricinae and Crocidurinae in the ML tree. Thus, it could not be determined to which subfamily Anourosorex should be assigned: Soricinae, Crocidurinae or a new subfamily. Soricinae (excluding Anourosorex ) should be divided into four tribes: Neomyini, Notiosoricini, Soricini and Blarinini. However, monophyly of Blarinini was not robust in the present data set. Also, branching orders among tribes of Soricinae and those among genera of Neomyini could not be determined because of insufficient phylogenetic information of the cyt b sequences. For water shrews of Neomyini ( Chimarrogale , Nectogale and Neomys ), monophyly of Neomys and the Chimarrogale – Nectogale group could not be verified, which implies the possibility of multiple origins for the semi-aquatic mode of living among taxa within Neomyini. Episoriculus may contain several separate genera. Blarinella was included in Blarinini not Soricini, based on the cyt b sequences, but the confidence level was rather low; hence more phylogenetic information is needed to determine its phylogenetic position. Furthermore, some specific problems of taxonomy of soricid shrews were clarified, for example phylogeny of local populations of Notiosorex crawfordi , Chimarrogale himalayica and Crocidura attenuata .     

冬虫夏草无性型研究概况*

文献调查结果表明与冬虫夏草有关的无性型菌种已报道有22个学名,涉及13个属。针对这些名称上存在的命名问题本文展开了讨论,并评述了不同名称与冬虫夏草的关系及其有关菌种的研究进展。在已报道的分离菌种中,作为新种正式描述的名称有8个,其中6个为合格发表,其余2个未能满足名称合格发表的条件;还有4个名称在文献中作为新种提到,但没有合格发表的出处,也有一例只提到名称而无其他要素;另有5个名称则只有属名,尚未鉴定到种的水平。中国被毛孢为多个独立的研究证明为冬虫夏草的无性型,还有3个无性型名称已被证明不可能是冬虫夏草的无性型。其他无性型名称与冬虫夏草的关系有待进一步验证。文中对与冬虫夏草有关的菌种定名、无性型分离和验证方法、复无性型现象,以及有关学名问题作了讨论。     

A cladistic analysis of wax scales (Hemiptera: Coccoidea: Coccidae: Ceroplastinae)

Seven genera of wax scales (Ceroplastinae) have been accepted as valid by some or all coecidologists: Ceroplastes Gray, Ceroplastidia Cockerell, Cerostegia De Lotto, Gascardia Targioni Tozzetti, Paracerostegia Tang, Vinsonia Signoret and Waxiella De Lotto. The status of most these genera is controversial. The present study reviews the taxonomic history of wax scales and presents a new classification based on cladistic analysis of morphological data from the adult females of eighty-three species. The analysis indicates that the wax scales form a monophyletic group, that Waxiella is monophyletic but that Ceroplastidia, Gascardia and Vinsonia are not, and fails to support the generic status of Cerostegia and Paracerostegia. Apart from the type species of Vinsonia , which was placed as a sister to the rest of wax scales, the only other species assigned to Vinsonia and most species of all other genera fall within Ceroplastes in the cladogram. Recognition of any of these genera renders Ceroplastes paraphyletic or polyphyletic. Thus, cladistically, the wax scales should be classified into one genus, Ceroplastes.