The colubrid radiation in Africa (Serpentes: Golubridae): phylogenetic relationships and evolutionary patterns based on immunological data

Phylogenetic relationships among genera of African colubrids were evaluated using estimates of divergence among serum albumins compared by microcomplement fixation. Representatives of about half of the extant genera of African colubrids, as well as the Elapidae, Atractaspis and the Madagascan colubrid Leioheterodon, were analysed. The tree of best fit to the data has an unresolved basal polychotomy comprising at least five lineages of colubrids, as well as Elapidae and Atractaspis; thus, colubrids were not demonstrably monophyletic with these data. Two cosmopolitan clades, colubrines and natricines, are represented in Africa by series of closely related genera, but divergence among other genera is relatively great. Rate tests show that this is apparently not due to higher rates of albumin evolution in these, relative to other colubrids. Among the other associations supported by the immunological data are: (1) Psammophis-(Rhamphiophis-Dipsina)-Malpolon-Psammophylax; (2) Amblyodipsas-Macrelaps; (3) (Lycodonomorphus-Lamprophis)-Mehelya; and (4) Colubrinae-Natricinae. Grayia is questionably associated with the colubrine-natricine lineage. Prosymna and Lycodon are clearly members of the colubrine clade, and Amplorhinus possibly associates with Leioheterodon. Gonionotophis, Duherria, Lycophidion and Pseudaspis show no strong association with any other genera, and represent other basal or near-basal clades within the colubrid/elapid radiation. The immunological data do not support a clade comprising the Elapidae, Atractaspis and some ‘aparallactines’ relative to Viperidae and other colubrids. The basal colubrid-elapid-Atractaspis divergence occurred more than 30 Myr ago, and the fossil record of colubrids in Africa greatly underestimates both the age and clade diversity of this group. In contrast to the pattern of radiation in the neotropics, where most colubrids belong to one of three major clades, in Africa only the colubrine lineage comprises a substantial portion of the extant generic diversity; most other genera stem from relatively ancient cladogenetic events and have few living representatives.     

叶蝉科昆虫分子系统发育的研究进展

从基因组DNA的提取、研究的基因片段、PCR引物选用、扩增条件以及叶蝉科不同阶元的分子系统发育分析等方面,综述叶蝉科(半翅目:叶蝉科)昆虫分子系统发育的研究进展。目前角顶叶蝉类的研究成果相对较多,大叶蝉亚科次之,其余类群的研究较少或无。线粒体基因与核基因序列联合分析以及线粒体全序列分析以及基因序列与形态数据相结合分析,分子鉴定叶蝉与共生菌之间的协同进化的研究,将是叶蝉分子系统学未来发展的主要研究手段。     

The Parvidrilidae – a diversified groundwater family: description of six new species from southern Europe,and clues for its phylogenetic position within Clitellata (Annelida)

The Parvidrilidae Erséus, 1999 constitute the most recently described family of oligochaete microdriles. Prior to this study, Parvidrilus strayeri Erséus, 1999, and Parvidrilus spelaeus Martínez‐Ansemil, Sambugar & Giani, 2002, found in groundwaters of the USA (Alabama) and Europe (Slovenia and Italy), respectively, were the only two species in this family. In this paper, six new species – Parvidrilus camachoi , Parvidrilus gianii , Parvidrilus jugeti , Parvidrilus meyssonnieri , Parvidrilus stochi , and Parvidrilus tomasini – and Parvidrilus gineti (Juget, 1959) comb. nov. are added to the family. With all species being stygobiont, the Parvidrilidae is unique in being the only family of oligochaetes worldwide comprising taxa that are restricted to groundwater habitats. Parvidrilids are exceedingly small worms whose principal morphological characteristics are the presence of hair setae in ventral bundles, the markedly posterior position of setae within the segments, the presence of mid‐dorsal glandular pouches in mesosomial segments, the lateral development of the clitellum, the presence of a single male pore in segment XII, and the presence (or absence) of a single spermatheca. The phylogenetic relationships of the Parvidrilidae within the Clitellata were investigated using the nuclear 18S rRNA gene, and the most representative and taxonomically balanced data set of clitellate families available to date. The data were analysed by parsimony, maximum likelihood, and Bayesian inference. Irrespective of the method used, Parvidrilidae were placed far from Capilloventridae, one family once suggested to be closely related to parvidrilids. Although closer to Enchytraeidae than Phreodrilidae, two other suggested putative sister families, the exact position of Parvidrilidae within Clitellata still remained uncertain in the absence of branch support. The examination of reproductive structures, together with the similarity of other important anatomical traits of the new species herein described, reinforced the idea that phreodrilids were the best candidate to be the sister group to parvidrilids on morphological grounds. A fragment of the mitochondrial cytochrome oxidase I gene, used as a barcode, also genetically characterized a few Parvidrilus species. The observation that two species diverge from each other by high genetic distances, even though their type localities are more or less only 100 km apart, is interpreted in the context of low dispersal abilities of inhabitants of the subterranean aquatic ecosystem, and habitat heterogeneity. The Parvidrilidae appear to be a diversified, Holarctic, and probably widely distributed family in groundwater, but very often overlooked because of the small size and external similarity with the polychaete family Aeolosomatidae of its members. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 530–558.     

Primary classification and phylogeny of the Polemoniaceae, with comments on molecular cladistics

The system of classification of the Polemoniaceae currently in use was published by Grant in 1959. Much new evidence concerning relationships in the family has been obtained by numerous workers since 1959, and the old system is in need of revision. A revised system down to the genus level, based on conventional and unconventional characters, including molecular evidence, is presented here. Nineteen genera are grouped into eight tribes and two subfamilies. Three new tribes are described: Acanthogilieae, Loeselieae, and Leptodactyloneae. Several genera are transferred to new groups. The phylogeny of the family is discussed in the light of both the older and new evidence. The approach used in constructing both the 1959 and new systems is that of evolutionary systematics. Two recent (1996, 1997) family-wide surveys of cpDNA and rDNA use cladistic methods of analysis to arrive at sets of major groups. Some of this molecular evidence has been adopted for the present revised system. However, much incongruence still exists between the new sets of clades, on the one hand, and the present revised system or the still-viable parts of the 1959 system on the other hand. The incongruences call for an examination and comparison of the contrasting methods of evolutionary systematics and molecular cladistics. A fundamental flaw in the 1996 and 1997 treatments is the attempt to classify plants on the basis of single-gene gene trees.     

Back to the future: A synthesis of strepsirrhine systematics

The stepsirrhine primates, defined here as living tooth-combed primates, their immediate ancestor, and all of its descendants, are a diverse assemblage of mammals, viewed by some as exemplars of the richness of evolutionary innovation and by others as uninteresting “primitive” primates. Fortunately, the former view has taken precedence in recent years. The Strepsirrhini have been central to numerous debates touching on key issues such as the congruence of phylogeny to biogeography, the reliability of morphological characters for phylogeny reconstruction, and the relationship of living lineages to fossil lineages. Thanks to important theoretical and methodological advances, particularly within the arena of genetics, a robust picture of strepsirrhine phylogeny is emerging that casts light on these and numerous other evolutionary questions. © 1997 Wiley-Liss, Inc.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

Examination of subfamilial phylogeny in Bromeliaceae using comparative sequencing of the plastid locus ndhF

Parsimony analysis of 31 sequences of the chloroplast locus ndhF was used to address questions of subfamilial phylogeny in Bromeliaceae. Results presented here are congruent with those from chloroplast DNA restriction site analysis in recognizing a clade containing Bromelioideae and Pitcairnioideae, and in resolving Tillandsioideae near the base of the family. Placements of several taxonomically difficult genera (e.g., Glomeropitcairnia and Navia) corroborate those of traditional treatments; however, these data suggest that Brocchinia (Pitcairnioideae) is the sister group to the remainder of Bromeliaceae. Further evidence for the paraphyly of Pitcairnioideae includes the resolution of Puya as the sister group to Bromelioideae. Implications for taxonomic realignment at the subfamily level are considered.     

Nomenclature in the dock. Overclassification leads to instability: a case study in the horticulturally important genus Cyclamen (Myrsinaceae)

Nine different classifications have been produced in the last 70 years for the horticulturally valuable genus Cyclamen , a small genus with fewer than 30 species. These classifications, generated by intuitive methods and cladistic analyses, incorporated a total of four infrageneric ranks above that of species and were based on data from morphology, cytology and DNA sequencing. Our results, based on cladistic analyses of three independent data sources − nrDNA ITS, cpDNA trn L intron and morphological data − reveal good resolution only in nrDNA sequence data. However, when these three data sources are combined they provide stronger resolution and support for three major clades, only one of which, subgenus Psilanthum , has been consistently supported in previous classifications. The differing infrageneric classifications produced in Cyclamen result from varying taxon sampling, differing interpretation of morphological data, changes in the sources and analysis of data, and inconsistent application of names. Extensive subdivision of small genera in the absence of adequate data that could provide evidence for consistent patterns of relationship is premature and leads to a proliferation of names.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 339–349.     

The two-horned chamaeleons of East Africa

There have been numerous attempts to resolve the taxonomy of the two-horned chamaeleons of East Africa. However, the high levels of intraspecific variation and reported sympatry of morphologically distinct taxa indicate that their current classification is unsatisfactory. Tissue samples were collected from specimens from most mountain massifs (excluding the Nguu) where two-horned chamaeleons are known to occur and were used to sequence partial 12S and 16S rRNA, as well as ND2 mtDNA genes. These specimens and further museum material were used to review morphological variation and to define discriminating characters for each taxon. Phylogenetic analyses of gene sequences show clear genetic divergence between allopatric populations, although two lineages occur in sympatry in the East Usambara Mountains, and is supported by divergent morphology. In light of these results a formal revision of the taxonomy of all East African two-horned chamaeleons is proposed and seven species are recognized ( Kinyongia boehmei , K. fischeri , K. matschiei , K. multituberculata , K. tavetana , K. uluguruensis and K. vosseleri ). These taxa form a monophyletic group except for K. uluguruensis , which seems to be more closely related to one-horned species. Most of these taxa have been previously described and subsequently reduced to synonyms. Two other previously described two-horned taxa are not recognized as valid: Chamaeleo tornieri is considered species inquiriendae , and C. fischeri werneri is placed in synonymy with K. multituberculata . A dichotomous key is provided for the identification of these taxa and some aspects of their conservation, ecology and evolutionary origins are also discussed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 367–391.     

Polyphyly of Limoniastrum (Plumbaginaceae): evidence from DNA sequences of plastid rbcL, trnL intron and trnL-F intergene spacer

Phylogenetic relationships of Limoniastrum and other genera of subfamily Staticoideae (Plumb-aginaceae) were studied using parsimony analysis of the plastid gene rbc L, the intron of trn L and the intergene spacer of trnL-trn F. Our analysis showed that Limoniastrum was polyphyletic. Limoniastrum ifniense , in both rbc L and combined data analyses, is sister to Armeria and Psylliostachys , whereas in the trn L-F (intron and spacer combined) analysis it is sister to a clade composed of Acantholimon, Dictyolimon and the remaining species of Limoniastrum . In all analyses, the five remaining species of Limoniastrum (excluding Limoniatrum ifniense ) formed a clade with two groups of species: L. monopetalum+L. guyonianum and those sometimes considered as the segregate genus Bubania ( L.feei, L. weygandiorum and L. rechingeri ). Levels of sequence divergence among these three groups of Limoniatrum were greater than for other well supported genera in the family and, in combination with morphological differences and paucity of synapomorphies, led us to conclude that separate generic status for each of the three clades is warranted.     

Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies

Lepidoptera (butterflies and moths) represent one of the most diverse animals groups. Yet, the phylogeny of advanced ditrysian Lepidoptera, accounting for about 99 per cent of lepidopteran species, has remained largely unresolved. We report a rigorous and comprehensive analysis of lepidopteran affinities. We performed phylogenetic analyses of 350 taxa representing nearly 90 per cent of lepidopteran families. We found Ditrysia to be a monophyletic taxon with the clade Tischerioidea + Palaephatoidea being the sister group of it. No support for the monophyly of the proposed major internested ditrysian clades, Apoditrysia, Obtectomera and Macrolepidoptera, was found as currently defined, but each of these is supported with some modification. The monophyly or near-monophyly of most previously identified lepidopteran superfamilies is reinforced, but several species-rich superfamilies were found to be para- or polyphyletic. Butterflies were found to be more closely related to ‘microlepidopteran’ groups of moths rather than the clade Macrolepidoptera, where they have traditionally been placed. There is support for the monophyly of Macrolepidoptera when butterflies and Calliduloidea are excluded. The data suggest that the generally short diverging nodes between major groupings in basal non-tineoid Ditrysia are owing to their rapid radiation, presumably in correlation with the radiation of flowering plants.     

关于节肢动物系统分类与进化的分子佐证

从分子系统学方面就了肢动物系统进化及高级阶元分类研究中争论的关键问题进行比较分析。综述了该领域所取得的新进展,着重从分子水平来探讨节肢动物的起源与进化。     

Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phylogeny of oligochaetous Clitellata

Clitellata, with more than one third of all annelid species described, is briefly introduced, and an overview of the hypotheses of phylogenetic relationships among the groups traditionally referred to as oligochaetes is given. The presentation is placed in a historical context and describes the trend to move from intuitive, narrative approaches to more formal analyses of character patterns. Monophyly of the earthworms (the megadriles, or Metagynophora sensu Jamieson), or at least a major part of them (Crassiclitellata sensu Jamieson), and paraphyly of the ‘microdrile’ largely aquatic, groups are supported by both morphological and molecular data. Further, DNA sequences as well as spermatozoal ultrastructure corroborate that all leech-like taxa (Hirudinida, Acanthobdellida and Branchiobdellida) constitute a clade derived within ‘Oligochaeta’, closely related to the family Lumbriculidae. Molecular systematic studies also support relationships already identified on the basis of morphological data, e.g., the position of Naididae within Tubificidae, the position of Phreodrilidae close to, but outside, the same family, and the putative sistergroup relationship between the newly discovered Capilloventridae and the rest of Clitellata. A recent study using 18S rDNA suggests that Enchytraeidae is closely related to Metagynophora, and that these two taxa, which contain all terrestrial oligochaetous clitellates, form a clade derived from aquatic ‘microdriles’ This refutes a recent hypothesis proposing that the ancestor of Clitellata was terrestrial. To a great extent, however, the basal resolution of the oligochaetous clitellates remains unclear.     

系统发育研究中多重序列比对常见问题分析

在简单介绍序列比对原理的基础上,结合自己的经验,对经常出现的问题进行总结分析,以期在将来的序列比对工作中避免此类问题的发生.     

Revision of the systematics of algae in the order Laminariales (Phaeophyta) from the Far-Eastern Seas of Russia on the basis of molecular-phylogenetic data

An overview of the literature changes in the systematics of algae in the order Laminariales (Phaeophyta) based on molecular phylogentic data is given. In a recent taxonomic revision by Lane et al., [45], the number and status of the families traditionally included in the order have been revised. One family was transferred to the order Tilopteridales; a new family, the Costariaceae, was described; and the genus Laminaria was split into 2 genera, Laminaria and a newly resurrected genus Saccharina. These innovations have necessitated a systematic revision of the Far Eastern species of the Laminariales. Our genetic studies indicate that 2 species of Laminaria and 12 intraspecific taxa (1 subspecies and 11 forms) from the Russian Pacific coasts should be transferred to the genus Saccharina. The following new nomenclatural combinations are proposed: Saccharina bongardiana, comb. nov. (including 4 forms: f. bifurcata, f. subsessilis, f. subsimplex, f. taeniata) and Saccharina gurjanovae, comb. nov. (including f. lanciformis). In addition, new nomenclature combinations are proposed for intraspecific taxa of the Laminaria species (L. angustata, L. cichorioides, L. japonica) that have already been transferred to the genus Saccharina [45]. These include S. angustata subsp. sibirica, comb. nov., 4 new combinations for the forms of S. cichorioides (f. coriacea, f. sacchalinensis, f. sikotanensis, and f. sinuicola), and 2 new combinations for the forms of S. japonica (f. diabolica, and f. longipes). The taxonomic status of the rest of the members of the Laminariales known from the seas of the Russian Far East is discussed. Laminariaceous algae in this area represent 6 of the 8 known families currently included in the Laminariales (Chordaceae, Pseudochordaceae, Alariaceae, Arthrothamnaceae, Laminariaceae, and Costariaceae).     

Molecular phylogenetics of Uvaria (Annonaceae): relationships with Balonga,Dasoclema and Australian species of Melodorum

An extended molecular phylogenetic analysis of Uvaria (Annonaceae) is presented, using maximum parsimony, maximum likelihood and Bayesian methods, based on sequences of four plastid DNA regions (matK, psbA‐trnH spacer, rbcL and trnL‐F). The additional taxa include the monotypic West African genus Balonga, the monotypic South‐East Asian genus Dasoclema and seven Australian representatives of the genus Melodorum. The results indicate that all of these taxa are nested within a well‐supported clade otherwise consisting of Uvaria species, indicating that their taxonomic treatment needs to be reassessed. The distinguishing morphological characteristics of the taxa are re‐evaluated and interpreted as specialized adaptations of the basic Uvaria structure. The genus Uvaria is accordingly extended following the transfer of these species, necessitating six new nomenclatural combinations and two replacement names. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 33–43.