Phylogeny of the genus Hesperodiaptomus (Copepoda) based on nucleotide sequence data of the nuclear ribosomal gene

The genus Hesperodiaptomus Light, 1938, one of the most diverse groups of freshwater copepods that occur in North and Central America, plays a major role in the food webs of the alpine freshwater communities. Phylogenetic relationships of these taxa remain poorly understood due to difficulties in obtaining reliable morphological characters for phylogenetic analyses. To understand the phylogenetic relationships within this group, we reconstructed a partial phylogeny of the genus Hesperodiaptomus based on nuclear ribosomal gene sequences. Phylogenetic analyses based upon the taxa examined supported the monophyly the genus and revealed two clades. The eiseni clade comprised species that are morphologically similar to Hesperodiaptomus eiseni (Lilljeborg, 1889), and the shoshone clade included species morphologically similar to Hesperodiaptomus shoshone (S.A. Forbes, 1882). The two groups can be distinguished by a modification of the right basis, the arrangement of spinules on the distal pad of the second exopod, and the degree of presence the inner lamellar expansion of the right coxa. Handling editor: P. Spaak     

Phylogeny of the New World medicinal leech family Macrobdellidae (Oligochaeta: Hirudinida: Arhynchobdellida)

Phylogenetic analyses of the leech family Macrobdellidae were accomplished with all nominal species in the family save one. A total of 17 specimens in nine ingroup species were analysed, along with four outgroup taxa. Twenty-two morphological characters based on jaw dentition, sexual anatomy, and external morphology failed to provide a resolution for many of the relationships in the family. DNA sequence data from nuclear 18S rDNA, nuclear 28S rDNA, mitochondrial 12S rDNA, and mitochondrial cytochrome c oxidase subunit I were examined separately and in combination with morphological characters. The resulting combined analysis strongly corroborated the placement of the genus Philobdella within the family Macrobdellidae and as sister to a monophyletic genus Macrobdella , the typical North American medicinal leeches. Furthermore, sequence divergences among these taxa confirmed the existence of two species, Philobdella gracilis and P. floridana , readily distinguishable on the basis of jaw dentition .     

Phylogenetic interrelationships of the barbets (Aves: Capitonidae) and toucans (Aves: Ramphastidae) based on morphology with comparisons to DNA-DNA hybridization

A phylogenetic analysis of the interrelationships of the barbets (Capitonidae) and the toucans (Aves: Ramphastidae, Superfamily Ramphastoidea) is presented. Thirty-two morphological characters from the literature and independent osteological observations were analysed. Character polarity was determined by outgroup comparison to the Picidae, Indicatoridae, Galbulidae, Bucconidae and Coraciiformes. Four alternative phylogenetic hypotheses were compared: (1) the overall most parsimonious morphological phylogeny, (2) the most parsimonious morphological phylogeny in which the capitonids and ramphastids were hypothesized as monophyletic sister groups, and (3) and (4) the most parsimonious hypotheses for the evolution of the morphological characters within two proposed DNA-DNA hybridization phylogenies of the ramphastoids. The analysis focused on the higher level relationships of ramphastids and capitonids and interrelationships among capitonid genera. Two cladistic analyses were performed using 26 phylogenetically informative characters, and the PAUP and CONTREE computer alogorithms. The most parsimonious morphological phylogeny required fewer character changes and had a lower consistency index than any of the alternative hypotheses but congruence between the most parsimonious phylogeny and the second, revised DNA-DNA hybridization hypothesis was very high. Based on these results the monophyly of the Capitonidae is rejected. The ramphastids and the Neotropical capitonids form a well corroborated clade within the pantropical ramphastoid radiation. Neither the African, Asian nor New World capitonids is monophyletic. The genus Trachyphonus is the sister group to all other capitonids and ramphastids. The sister group to the ramphastids is the genus Semnornis. The interrelationships of the Old World capitonids excluding Trachyphonus are not completely resolved by these morphological data but one of the alternative phylogenetic resolutions is presented as a preliminary hypothesis. The clades in this resolved phylogeny are diagnosed and the palaeontology and biogeography of the ramphastoids arc-reviewed in light of this new evidence. A phylogenetic classification is proposed in which the Capitonidae is rejected and the capitonids and ramphastids are placed in seven subfamilies of the Ramphastidae.     

Mitochondrial DNA Phylogeny of the Family Cichlidae: Monophyly and Fast Molecular Evolution of the Neotropical Assemblage

A mitochondrial DNA (mtDNA) phylogeny of cichlid fish is presented for the most taxonomically inclusive data set compiled to date (64 taxa). 16S rDNA data establish with confidence relationships among major lineages of cichlids, with a general pattern congruent with previous morphological studies and less inclusive molecular phylogenies based on nuclear genes. Cichlids from Madagascar and India are the most basal groups of the family Cichlidae and sister to African–Neotropical cichlids. The cichlid phylogeny suggests drift-vicariance events, consistent with the fragmentation of Gondwana, to explain current biogeographic distributions. Important phylogenetic findings include the placement of the controversial genus Heterochromis basal among African cichlids, the South American genus Retroculus as the most basal taxon of the Neotropical cichlid assemblage, and the close relationship of the Neotropical genera Cichla with Astronotus rather than with the crenicichlines. Based on a large number of South American genera, the Neotropical cichlids are defined as a monophyletic assemblage and shown to harbor significantly higher levels of genetic variation than their African counterparts. Relative rate tests suggest that Neotropical cichlids have experienced accelerated rates of molecular evolution. But these high evolutionary rates were significantly higher among geophagine cichlids. Received: 18 September 1998 / Accepted: 16 December 1998     

Phylogeny of Eastern North American Coreopsis (Asteraceae-Coreopsideae): insights from nuclear and plastid sequences, and comments on character evolution

A molecular phylogenetic study of eastern North American Coreopsis and representatives of other genera of tribe Coreopsideae was conducted using combined sequences from nuclear ITS and two plastid regions (matK, rpl16). A total of 25-30 species has been recognized in five sections of Coreopsis in eastern North America. Based on morphological characters, these taxa have generally been considered a monophyletic group. Our well-resolved phylogeny supports the monophyly of sections that have been recognized in Coreopsis, but the sections collectively do not comprise a monophyletic group because species of north temperate Bidens occur within one of the two major Coreopsis clades. The most notable departure of present results from prior views of relationships among sections is the lack of a sister group relationship between sections Calliopsis and Eublepharis; the shared presence of four-lobed disk floret corollas had been used to support a close relationship between these two sections. Relationships within sections show both similarities and differences with the results of previous studies based primarily on morphological characters. Mapping of morphological characters used taxonomically in Coreopsis and related genera onto the phylogeny indicates that the evolution of these characters has been complex, and this compromises their value for defining monophyletic groups. Examples include the annual habit, alternate leaves, winged fruits, red or brown basal spots on the yellow ligules, and four-lobed disk floret corollas.     

A phylogeny of the damselfly genus calopteryx (Odonata) using mitochondrial 16S rDNA markers

We seek to reconstruct the phylogenetic relationships of the damselfly genus Calopteryx, for which extensive behavioral and morphological knowledge already exists. To date, analyses of the evolutionary pathways of different life history traits have been hampered by the absence of a robust phylogeny based on morphological data. In this study, we concentrate on establishing phylogenetic information from parts of the 16S rDNA gene, which we sequenced for nine Calopteryx species and five outgroup species. The mt 16S rDNA data set did not show signs of saturated variation for ingroup taxa, and phylogenetic reconstructions were insensitive to variation of outgroup taxa. Parsimony, neighbor-joining, and maximum-likelihood reconstructions agreed on parts of the tree. A consensus tree summarizes the significant results and indicates problematic nodes. The 16S rDNA sequences support monophyly of the genera Mnais, Matrona, and Calopteryx. However, the genus Calopteryx may not be monophyletic, since Matrona basilaris and Calopteryx atrata are sister taxa under every parameter setting. The North American and European taxa each appear as monophyletic clades, while the Asian Calopteryx atrata and Calopteryx cornelia are not monophyletic. Our data implies a different paleobiogeographic history of the Eurasian and North American species, with extant Eurasian species complexes shaped by glacial periods, in contrast to extant North American species groups.     

Phylogenetic relationships of the genus Hoplia Illiger (Scarabaeidae: Hopliinae)

Results of phylogenetic analysis based on 34 morphological characters of 24 species of 11 genera of Hopliinae from Europe, Japan, South Africa, Madagascar, North and Central America, indicates that the genus Hoplia is a monophyletic group with species distributed in Europe, Japan and America. Based in this analysis the Asiatic genus Ectinohoplia is the closest relative of the genus Hoplia, and the South American genus Barybas (Melolonthinae: Macrodactylini) is the sister group of Hopliinae.     

Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.     

Molecular phylogeny of North American Branchiobdellida (Annelida: Clitellata)

Branchiobdellidans, or crayfish worms, are ectosymbiotic clitellate annelids associated primarily with freshwater crayfishes. The main objectives of our study were to infer a molecular phylogeny for the North American Branchiobdellida, examine its congruence with morphology-based hypotheses of relationships at the subfamily and genus level, and use our dataset to assess consistency of GenBank-archived branchiobdellidan sequences. We used nucleotide sequence data from two mtDNA genes (COI and 16S rDNA) and three nuclear genes (28S rDNA, 18S rDNA, and ITS1) to estimate phylogenetic relationships among 47 described and one undescribed species of Branchiobdellida. We recovered a monophyletic branchiobdellidan clade with generally short branch lengths, suggesting that a large portion of the taxon has likely undergone a recent and rapid radiation in North America. Results from our phylogenetic analyses indicate that current taxonomic groupings are largely unsupported by the molecular data. All four subfamilies are either paraphyletic or polyphyletic, and only three of seven sampled non-monotypic genera were monophyletic. We found a high rate (49%) of inconsistency in GenBank-archived sequences, over 70% of which can be attributed to field- or laboratory-based error.     

Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa)

Partial mitochondrial (mt) cytochrome c oxidase subunit I (COI) and near-complete nuclear (nu) 18S rDNA sequences were obtained from various eimeriid coccidia infecting vertebrates. New and published sequences were used in phylogenetic reconstructions based on nu 18S rDNA, mt COI and concatenated sequence datasets. Bayesian analyses of nu 18S rDNA sequences used secondary structure-based alignments with a doublet nucleotide substitution model; the codon nucleotide substitution model was applied to COI sequences. Although alignment of the mt COI sequences was unambiguous, substitution saturation was evident for comparisons of COI sequences between ingroup (eimeriid) and outgroup (sarcocystid) taxa. Consequently, a combined dataset applying partition-specific analytical and alignment improvements was used to generate a robust molecular phylogeny. Most eimeriid parasites that infect closely related definitive hosts were found in close proximity on the resulting tree, frequently in a single clade. Whether this represents coevolution or co-accommodation or a combination remains an open point. Unlike host associations, basic oocyst configuration (number of sporocysts per oocyst and sporozoites per sporocyst) was not correlated with phylogeny. Neither ‘Eimeria-type’ nor ‘Isospora-type’ oocyst morphotypes formed monophyletic groups. In the combined dataset tree (representing only a tiny fraction of described eimeriid coccidia), at least 10 clades of Eimeria spp. would need to be re-assigned to nine distinct genera to resolve their paraphyly. The apparent lack of congruence between morphotype and genotype will require taxonomists to balance nomenclatural stability and diagnostic ease against the ideal of monophyletic genera. For now, recognition of paraphyletic eimeriid genera defined by basic oocyst configuration may be necessary for reasons of taxonomic stability and diagnostic utility. Future taxonomic revisions to produce monophyletic eimeriid genera will ultimately require the identification of reliable phenotypic characters that agree with the molecular phylogeny of these parasites or, less optimally, acceptance that genotyping may be needed to support monophyletic supraspecific taxonomic groups.     

Molecular resolution of the systematics of a problematic group of fishes (Teleostei: Osmeridae) and evidence for morphological homoplasy

Relationships among the species of Northern Hemisphere smelts (family Osmeridae) have long been debated in the fish systematics literature. Eight independent studies based on morphological characters failed to reach any consensus on osmerid interrelationships. We reconstruct the osmerid phylogeny based on DNA sequence data from three mitochondrial (cytb, 16S, 12S) and three nuclear (ITS2, S71, RAG1) gene regions from multiple individuals of the 14 species in 6 genera, using the Japanese ayu (Plecoglossus altivelis) as the outgroup. Analyses with different combinations of nuclear and mitochondrial datasets yielded a generally well-resolved phylogeny of the genera that conflicts with previous hypotheses of osmerid interrelationships, and Shimodaira–Hasegawa tests suggest our topology with the current molecular dataset is significantly better than earlier reconstructions. In addition, mapping 114 morphological characters used in previous studies onto our phylogeny shows widespread homoplasy, which is likely the source of the systematic disagreement produced in earlier works.     

基于16S rDNA和28S rDNA D2基因序列与形态特征联合分析的中国角顶叶蝉亚科系统发育研究（半翅目： 叶蝉科）

首次在国内利用28S rDNA D2区段和16S rDNA基因序列,结合50个形态特征对角顶叶蝉亚科(Deltocephalinae)［半翅目（Hemiptera）: 叶蝉科（Cicadellidae）］19个属进行系统发育分析研究。从无水乙醇浸泡保存的标本中提取基因组DNA并扩增了19个内群和1种外群Typhlocybinae［半翅目(Hemiptera): 叶蝉科(Cicadellidae)］种类的28S rDNA D2基因片段并测序,同时扩增了16S rDNA基因片段并测序11条,采用了GenBank中1个种类的16S rDNA同源序列。采用PAUP*4.0和MrBayes3.0两个分析软件和3种建树方法,利用同源28S D2 rDNA和16S rDNA两个基因序列与形态特征结合进行系统发育分析研究。分析结果表明,二叉叶蝉族Macrostelini是一个单系,并在角顶叶蝉亚科的系统发育中处于基部的位置,是内群中最原始的族;角顶叶蝉族Deltocephalini中除了纹翅叶蝉属Nakaharanus,其余各属构成单系;殃叶蝉族Euscelini内属的归属比较混乱,可能是一个并系群,属间差异有待进一步研究。隆额叶蝉族Paralimnini与顶带叶蝉族Athysanini是姐妹群。带叶蝉属Scaphoideus与纹翅叶蝉属Nakaharanus是姐妹群,二者与木叶蝉属Phlogotettix的关系最近,三者构成一个单系,建议将三者归为带叶蝉族Scaphoideini。研究结果还表明,小眼叶蝉族Xestocephalini和Balcluthini的系统发育位置不明,有待进一步研究。     

Aphis (Hemiptera: Aphididae) species groups found in the Midwestern United States and their contribution to the phylogenetic knowledge of the genus

A phylogeny of the genus Aphis Linnaeus, 1 758 was built primarily from specimens collected in the Midwest of the United States. A data matrix was constructed with 68 species and 41 morphological characters with respective character states of alate and apterous viviparous females. Dendrogram topologies of analyses performed using UPGMA (Unweighted Pair Group Method with Arithmetic Mean), Maximum Parsimony and Bayesian analysis of Cytochrome Oxidase I, Elongation Factor 1‐α and primary endosymbiont Buchnera aphidicola 16S sequences were not congruent. Bayesian analysis strongly supported most terminal nodes of the phylogenetic trees. The phylogeny was strongly supported by EF1‐α, and analysis of COI and EF1‐α molecular data combined with morphological characters. It was not supported by single analysis of COI or Buchnera aphidicola 16S. Results from the Bayesian phylogeny show 4 main species groups: asclepiadis, fabae, gossypii, and middletonii. Results place Aphis and species of the genera Protaphis Börner, 1952, Toxoptera Koch, 1856 and Xerobion Nevsky, 1928 in a monophyletic clade. Morphological characters support this monophyly as well. The phylogeny shows that the monophyletic clade of the North American middletonii species group belong to the genus Protaphis: P. debilicornis (Gillette & Palmer, 1929 ), comb. nov., P. echinaceae (Lagos and Voegtlin, 2009 ), comb. nov., and P. middletonii (Thomas, 1879 ). The genus Toxoptera should be considered a subgenus of Aphis (stat. nov.). The analysis also indicates that the current genus Iowana Frison, 1954 should be considered a subgenus of Aphis (stat. nov.).     

Morphology and phylogeny of Bryophryoides ocellatus n. g., n. sp. (Ciliophora,Colpodea) from in situ soil percolates of Idaho,U.S.A.

We describe the morphology and 18S rDNA phylogeny of Bryophryoides ocellatus n. g., n. sp., a bryophryid ciliate inhabiting in situ soil percolates from Idaho, U.S.A. The new genus is distinguished from other bryophryid genera by a combination of the following features: (1) kreyellid (irregularly meshed) silverline pattern, (2) polymorphic adoral organelles in the preoral suture, (3) absence of vestibular kineties. In phylogenetic analyses, Bryophryoides ocellatus is most closely related to Bryophrya gemmea. The 18S rDNA sequence pairwise distance of 2% between these genera, while similar to that between many colpodidan species, exceeds that between some colpodidan genera (e.g. Mykophagophrys and Pseudoplatyophrya, 1.1%), further supporting establishment of the new genus. Topology hypothesis testing strongly supports the monophyly of the Colpodida including the bryophryids. Despite weak nodal support, tests of topology constraints narrowly reject the non-monophyly of the sequenced Bryophryidae (Bryophrya + Bryophryoides + Notoxoma). Likewise, the monophyletic origin of the sequenced Bryophryidae is indicated in the phylogenetic networks though with low support.     

Testing the monophyly of the New Zealand and Australian endemic family Conoesucidae Ross based on combined molecular and morphological data (Insecta: Trichoptera: Sericostomatoidea)

Conoesucidae (Trichoptera, Insecta) are restricted to SE Australia, Tasmania and New Zealand. The family includes 42 described species in 12 genera, and each genus is endemic to either New Zealand or Australia. Although monophyly has been previously assumed, no morphological characters have been proposed to represent synapomorphies for the group. We collected molecular data from two mitochondrial genes (16S and cytochrome oxidase I), one nuclear gene (elongation factor 1-α) (2237–2277 bp in total), and 12 morphological characters to produce the first phylogeny of the family. We combined the molecular and morphological characters and performed both a maximum parsimony analysis and a Bayesian analysis to test the monophyly of the family, and to hypothesize the phylogeny among its genera. The parsimony analysis revealed a single most parsimonious tree with Conoesucidae being a monophyletic taxon and sistergroup to the Calocidae. The Bayesian inference produced a distribution of trees, the consensus of which is supported with posterior probabilities of 100% for 15 out of 22 possible ingroup clades including the most basal branch of the family, indicating strong support for a monophyletic Conoesucidae. The most parsimonious tree and the tree from the Bayesian analysis were identical except that the ingroup genus Pycnocentria changed position by jumping to a neighbouring clade. Based on the assumption that the ancestral conoesucid species was present on both New Zealand and Australia, a biogeographical analysis using the dispersal-vicariance criteria demonstrated that one or two (depending on which of the two phylogenetic reconstructions were applied) sympatric speciation events took place on New Zealand prior to a single, late dispersal from New Zealand to Australia.     

基于28S rDNA D2基因片段与形态特征的矛茧蜂亚科系统发育研究（膜翅目：茧蜂科）

本研究选取矛茧蜂亚科Doryctinae（昆虫纲Insecta：膜翅目Hymenoptera：茧蜂科Braconidae）的6族15属18种做内群,茧蜂科其它7亚科11属11种做外群,首次结合同源核糖体28S rDNA D2基因序列片段和100个形态学和解剖学特征对该亚科进行了系统发育学研究。利用“非圆口类"的小腹茧蜂亚科Microgastrinae为根,以PAUP*4.0和MrBayes 3.0B4软件分别应用最大简约法（MP）和贝叶斯法对矛茧蜂亚科的分子数据和分子数据与非分子数据的结合体进行了运算分析;并以PAUP*4.0对矛茧蜂亚科的28S rDNA D2基因序列片段的碱基组成与碱基替代情况进行了分析。结果表明：矛茧蜂亚科的28S rDNA D2基因序列片段的GC含量在39.33%～48.28%之间变动,而对于碱基替代情况来讲,矛茧蜂亚科各成员间序列变异位点上颠换（transversion）大于转换（transition）。不同的分析算法所产生的系统发育树都表明矛茧蜂亚科是一个界限分明的单系群;在矛茧蜂亚科内,除了吉丁茧蜂族Siragrini为单系群外,其他族（矛茧蜂族Doryctini和方头茧蜂族Hecabolini）都是并系群。对于矛茧蜂亚科内各属之间的相互亲缘关系,不同算法所得的系统发育树的拓扑结构不完全一致,表明矛茧蜂亚科内（属及族）的系统发育关系还有待于进一步研究。     

Phylogeny and reclassification of the Caucasigenini radiation from the Caucasus region (Gastropoda,Hygromiidae)

The Caucasigenini is an endemic radiation of hygromiid land snails from the Caucasus region. A phylogenetic analysis of morphological characters of the genitalia and the shell showed that the morphological characters are insufficient for resolving the relationships within the Caucasigenini. Convergences of the few parsimony informative characters in other groups of the Hygromiidae demonstrate that these characters are not reliable indicators of phylogenetic relationships. Phylogenetic analyses of sequences of cox1, 16S rDNA, 5.8S rDNA, ITS2 and 28S rDNA revealed several well‐supported groups. The relationships among these groups could not be resolved. It is likely that these groups originated in a rapid radiation during the uplift of the Caucasus. Based on the molecular phylogeny, we propose a new classification of the species of the Caucasigenini and establish a new genus, Lazicana gen. n.     

Factors influencing the distribution and abundance of diaptomid copepods in high-elevation lakes in the Pacific Northwest, USA

We investigated the impact of abiotic factors and trout density on distribution and abundance of diaptomid copepods in high-elevation lakes in North Cascades National Park Service Complex (NOCA), Washington, USA. The most common large diaptomid, D. kenai (mean length = 1.88 mm), was able to persist over a wide range of abiotic factors, but the small herbivorous diaptomid, D. tyrrelli (mean length = 1.18 mm), was restricted to shallow lakes (maximum depth < ≈ 10 m) with relatively high concentrations of total Kjeldahl nitrogen and total phosphorous. There was a significant negative relationship between the density of D. tyrrelli and the density of large diaptomids ( D. kenai and D. arcticus), which could imply interaction between large and small diaptomids. The abundance of large diaptomids was significantly lower in shallow lakes with high densities of reproducing trout (> 250 fish ha-1) than in fishless lakes, in deep lakes with reproducing trout, or in lakes where trout do not reproduce and are 0periodically stocked with fry at low densities (average 179 fry a-1). In lakes where chemical conditions were suitable for D. tyrrelli, the small diaptomid was often abundant when trout density was high and large diaptomids were either absent or in low abundance. Our research suggests that trout density, nutrient concentration, and lake depth influence the abundance of diaptomid copepods in high lakes in NOCA. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular phylogeny of truffles (Pezizales: Terfeziaceae, Tuberaceae) derived from nuclear rDNA sequence analysis.

Extensive morphological convergence or divergence, a common occurrence in fungi, tends to obscure recognition of phylogenetic relationships among Pezizales, widespread filamentous Ascomycetes with either enclosed underground (hypogeous) or exposed (epigeous) fruit bodies, that often establish mutualistic interactions with arboreous plants. Focusing on hypogeous Pezizales commonly known as truffles, we sequenced the 18S rDNA from nine species belonging to three different families (Tuberaceae, Terfeziaceae, and Balsamiaceae). A data set consisting of 1700 secondary structure-aligned sites, including 24 homologous sequences from the GenBank DNA database and using three reconstruction methods, was employed to infer phylogenies in an interval ranging from the subordinal to the subgeneric level. As revealed by the 18S phylogenetic scheme, Balsamiaceae represent a monophyletic clade, comprising the hypogeous taxa Balsamia and Barssia, nested within Helvellaceae. Similarly, the terfeziacean genera Pachyphloeus and Terfezia constitute together with Cazia a distinct hypogeous clade nested within Pezizaceae. The lack of clustering between Terfezia arenaria and Terfezia terfezioides strongly supports the reassignment of the latter taxon to the original monotypic genus Mattirolomyces. Within Tuberaceae, which are sister to the highly evolved Helvellaceae, the genus Tuber cannot be considered monophyletic if Choiromyces is recognized. The paraphyly of Tuber and other relationships that were not supported by high bootstrap values, nor corroborated by morphological evidence, were supported by a parallel analysis of the faster evolving internal transcribed spacer (ITS) rDNA. Distinct episodes of fruit body morphology shifts are discernable in the 18S rDNA phylogenetic tree. In all cases, the shift from an epigeous to a hypogeous form is the most parsimonious interpretation of character transformation, without any instance of character reversal.     

Phylogeny of Nerillidae (Polychaeta, Annelida) as inferred from combined 18S rDNA and morphological data

A phylogeny of the meiofaunal polychaete family Nerillidae based on morphological, molecular and combined data is presented here. The data sets comprise nearly complete sequences of 18S rDNA and 40 morphological characters of 17 taxa. Sequences were analyzed simultaneously with the morphological data by direct optimization in the program POY, with a variety of parameter sets (costs of gaps: transversions: transitions). Three outgroups were selected from the major polychaete group Aciculata and one from Scolecida. The 13 nerillid species from 11 genera were monophyletic in all analyses with very high support, and three new apomorphies for Nerillidae are identified. The topology of the ingroup varied according to the various parameter settings. Reducing the number of outgroups to one decreased the variance among the phylogenetic hypotheses. The congruence among these was tested and a parameter set, with equal weights (222) and extension gap weighted 1, yielded minimum incongruence (ILD). Several terminal clades of the combined analysis were highly supported, as well as the position of Leptonerilla prospera as sister terminal to the other nerillids. The evolution of morphological characters such as segment numbers, chaetae, appendages and ciliation are traced and discussed. A regressive pathway within Nerillidae is indicated for several characters, however, generally implying several convergent losses. Numerous genera are shown to require revision. © The Willi Hennig Society 2005.