Phylogenetic relationships of New Zealand Asteraceae inferred from ITS sequences

Forty-five sequences from members of all genera of Asteraceae indigenous to New Zealand and 50 published sequences representing the tribal diversity in the family were analyzed to assess the utility of ITS sequences to resolve phylogenetic relationships. Previous studies using chloroplast DNA sequences and morphology provided support for several clades in the Asteraceae, yet the relationships among some of these were uncertain. The results from ITS analysis were largely consistent with these earlier studies. The New Zealand species are included in at least six clades, most of these corresponding to recognized tribes. Our results have also clarified the tribal affinities of a few anomalous genera. Haastia, previously aligned with the Gnaphalieae or the Astereae, is nested in the Senecioneae. Centipeda, previously included in the Astereae or Anthemideae, emerges near the Heliantheae. The relationships of Abrotanella remain unresolved. Received August 8, 2001 Accepted November 6, 2001     

Phylogenetic and phylogeographic relationships in the crayfish genus Austropotamobius inferred from mitochondrial COI gene sequences

The present study explores the utility of mitochondrial COI gene sequences to reveal phylogenetic and phylogeographic relationships for the entire European freshwater crayfish genus Austropotamobius. The two traditional taxa, Austropotamobius pallipes and Austropotamobius torrentium, were monophyletic, showing similar genetic diversity, with 28 and 25 haplotypes, respectively, and an uncorrected average pairwise divergence of 0.059 and 0.041. A third distinct haplotype clade, in sister relation to A. torrentium, was discovered at the Upper Kolpa drainage in the northern Dinaric area. All populations north and west of the Alps are genetically impoverished (nucleotide diversity (pi)=0.000-0.001), while southern populations are more diverse (pi=0.001-0.034). A. pallipes reaches the highest diversity in the region of Istra, probably its primary center of radiation. The genetic diversity center for A. torrentium is the southern Balkan peninsula. Other potential glacial refugia were identified in Southern France, Northwestern Italy, the Apennine Peninsula, and in the northern Dinaric area. The Iberian Peninsula has been stocked artificially from Northern Italy. Three main periods of radiation were tentatively identified: late Miocene/early Pliocene for the divergence of species and main lineages, the Pleistocene for the divergence within populations south from Alps, and a postPleistocene expansion north and west from Alps.     

Phylogenetic relationships ofMicrosphaera andErysiphe sectionErysiphe (powdery mildews) inferred from the rDNA ITS sequences

The genusMicrosphaera has been considered to be derived from sectionErysiphe of the genusErysiphe by a single event. Cleistothecial appendages are the most distinct difference between the two genera and have an important role for overwintering. To understand the phylogenetic relationship betweenErysiphe sectionErysiphe andMicrosphaera more precisely, phylogenetic trees were constructed using the nucleotide sequences of the rDNA ITS region from 11Erysiphe (sectionErysiphe) and 16Microsphaera taxa. The phylogenetic trees indicated the close relationship between the two genera. However, the generaErysiphe (sectionErysiphe) andMicrosphaera did not group into separate monophyletic lineages; instead, they formed several small clusters that were mixed together. This result suggests that the differentiations of the genera occurred two or more times independently. This also supports the idea that appendage morphology does not always accurately reflect the phylogeny of the powdery mildews because the morphology of appendages may evolve convergently under the selection pressure of their particular biotopes (host plants). Contribution No. 144 from the Laboratory of Plant Pathology, Mie University.     

Phylogenetic relationships ofSphaerophoraceae (Ascomycetes) inferred from SSU rDNA sequences

SSU rDNA was sequenced from the lichenized fungiBunodophoron scrobiculatum andLeifidium tenerum (Sphaerophoraceae), andStereocaulon ramulosum andPilophorus acicularis (Stereocaulaceae) and analysed by maximum parsimony with 44 homologous ascomycete sequences in a cladistic study. A small insertion (c. 60 nt.) was found in the sequence ofLeifidium tenerum. Sphaerophoraceae constitutes a strongly supported monophyletic group which groups together withLecanora dispersa and theStereocaulaceae. Together withPorpidia crustulata, this larger group is a sistergroup to thePeltigerineae. This analysis thus supports theLecanorales as monophyletic, includingSphaerophoraceae and thePeltigerineae, but does not provide strong support for this monophyly. The analysis also suggests that the prototunicate ascus in theSphaerophoraceae is a reversion to the plesiomorphic state. Based on morphological, anatomical and chemical reasons,Sphaerophoraceae is proposed to belong to one of the groups presently included in the paraphyletic suborderCladoniineae within theLecanorales.     

Phylogenetic relationships in Ephedra (Ephedraceae) inferred from chloroplast and nuclear DNA sequences

Sequences of the nuclear ribosomal DNA internal transcribed spacer region 1 and the chloroplast-encoded genes maturase K and ribulose-1,5 biphosphate carboxylase large subunit were obtained from species of Ephedra (Ephedraceae) representing the geographic range and morphological diversity of the genus. Phylogenetic analyses of the DNA data indicate that relationships within the genus are better predicted by geographic region of origin than by ovulate cone characters. The sampled species with dry, winged (versus fleshy) ovulate cone bracts or single-seeded cones do not form monophyletic groups and therefore the previous classification systems of Ephedra based on these aspects of bract morphology appear to be largely unnatural. Three groups were identified among the Old World species studied, one comprising European and Mediterranean species and two including only Asian species. The sequence data suggest a possible early divergence of a New World clade of Ephedra from among the Old World groups. The South American species form a distinct clade apparently related to one of two groups of North American species, which accords with a frequent floristic pattern of close relationships between species groups in western South America and southwestern North America.     

Phylogenetic relationships in the Lejeuneaceae (Hepaticae) inferred using ITS sequences of nuclear ribosomal DNA

Sequences of the ITS1–5.8S–ITS2 region of nuclear ribosomal DNA were generated for 12 species from 9 genera of Lejeuneaceae and a single species of Jubulaceae (outgroup). The taxon sampling of Lejeuneaceae included representatives of the two widely recognized subfamilies, Lejeuneoideae and Ptychanthoideae. The molecular dataset was analysed independently and in combination with a morphological dataset. The nrITS dataset and the combined dataset resulted in identical topologies. The genus Bryopteris, sometimes treated as a separate family Bryopteridaceae, is nested within the Lejeuneaceae subfamily Ptychanthoideae. Lejeuneaceae subfamily Lejeuneoideae proved to be paraphyletic with the tribe Lejeuneeae sister to Ptychanthoideae, albeit without significant bootstrap support. The tribes Brachiolejeuneeae and Cheilolejeuneeae of Lejeuneoideae, established recently based on morphological evidence, are well supported in bootstrap analyses both of the ITS and the combined molecular–morphological datasets. The results support classifications of Lejeuneaceae based on morphological data and demonstrate the usefulness of the ITS region for phylogenetic studies within or among closely related genera of Lejeuneaceae.     

Phylogenetic relationships in family Magnoliaceae inferred from ndhF sequences

The ndhF sequences of 99 taxa, representing all sections in extant Magnoliaceae, were analyzed to address phylogenetic questions in the family. Magnolia macrophylla and M. dealbata, North American species of Magnolia section Rytidospermum, are placed at the base in the subfamily Magnolioideae although its supporting value is low. In the remaining taxa, several distinctive lineages are recognized: (1) Magnolia, the biggest genus in the family, is not monophyletic; (2) Michelia, including section Maingola of Magnolia subgenus Magnolia, is closely related with Elmerrillia and sections Alcimandra and Aromadendron of Magnolia subgenus Magnolia; (3) the associates of Michelia are grouped with Magnolia subgenus Yulania and section Gynopodium of Magnolia subgenus Magnolia; (4) Pachylarnax forms a clade with sections Manglietiastrum and Gynopodium of Magnolia; (5) a well-supported Manglietia clade is recognized; (6) Caribbean species of section Theorhodon of Magnolia subgenus Magnolia, which are section Splendentes sensu Vázquez-Garcia, are closely allied with New World members of Magnolia subgenus Talauma; and (7) section Rytidospermum of Magnolia subgenus Magnolia and subgenus Talauma are polyphyletic. The separated clades in the molecular tree are considerably different from traditional taxonomic dispositions in the family. The molecular data strongly suggest that a taxonomic realignment of infrafamilial delimitations and compositions should be considered.     

Ixodes philipi (Acari: Ixodidae): phylogenetic status inferred from mitochondrial cytochrome oxidase subunit I gene sequence comparison

Ixodes philipi ticks were collected from the nest burrows of streaked shearwaters, Calonectris luecomelas, on 3 different islands of Japan (Awashima: 38 degrees 45'N, 139 degrees 24'E; Mikurajima: 33 degrees 52'N, 139 degrees 36'E; and Omorijima: 36 degrees 8'N, 133 degrees 10'E). The mitochondrial cytochrome oxidase subunit I (COI) gene sequence was determined for each tick. The COI sequences of 9 other ixodid tick species also were determined, and they were used for taxonomic positioning of I. philipi. A metastriata tick, Amblyomma triguttatum, was used as an outgroup reference for the analysis. Phylogenetic examination indicated that the I. philipi ticks are on the branch with Ixodes turdus and Ixodes acutitarsus weakly, and the bootstrap value of this branching was low. Three different analyses, maximum parsimony, genetic distance, and maximum likelihood, support this conclusion. To further refine this analysis, 2761 base pairs (bp) of sequence, which included the genes for tRNA(Met), NADH dehydrogenase subunit 2 (ND2), tRNA(Trp), tRNA(Cys), tRNA(Tyr), and COI, were determined and compared for 6 I. philipi ticks from the 3 different collection sites. Although a base substitution (T to C in the ND2 gene for an Awashima tick) and 2 transitions (G to A in the COI gene for 1 Omorijima tick) have occurred, the overall sequences were highly conserved. Preserved mitochondrial sequences in the ticks from 3 widely separated locations suggest the possibility of gene flow, which was probably accomplished by migratory seabirds.     

Phylogenetic relationships within parrots (Psittacidae) inferred from mitochondrial cytochrome-b gene sequences

Blood and tissue samples of 40 individuals including 27 parrot species (15 genera; 3 subfamilies) were collected in Indonesia. Their phylogenetic relationships were inferred from 907 bp of the mitochondrial cytochrome-b gene, using the maximum-parsimony method, the maximum-likelihood method and the neighbor-joining method with Kimura two-parameter distance. The phylogenetic analysis revealed that (1) cockatoos (subfamily Cacatuinae) form a monophyletic sister group to other parrot groups; (2) within the genus Cacatua, C. goffini and C. sanguinea form a sister group to a clade containing other congeners; (3) subfamily Psittacinae emerged as paraphyletic, consisting of three clades, with a clade of Psittaculirostris grouping with subfamily Loriinae rather than with other Psittacinae; (4) lories and lorikeets (subfamily Loriinae) emerged as monophyletic, with Charmosyna placentis a basal sister group to other Loriinae, which comprised the subclades Lorius; Trichoglossus+Eos; and Chalcopsitta+ Pseudeos.     

Phylogenetic relationships among Thunnus species inferred from rDNA ITS1 sequence

Intra and interspecific nucleotide sequence variation of rDNA first internal transcribed spacer (ITS1) was analysed using all eight species of the genus Thunnus plus two out‐group species within the same family, skipjack tuna Katsuwonus pelamis and striped bonito Sarda orientalis . Intraspecific nucleotide sequence variation in ITS1, including intra‐genomic variation, was low, ranging from 0·003 to 0·014 [Kimura's two parameter distance (K2P)], whereas variation between species within the genus Thunnus ranged from 0·009 to 0·05. The Atlantic and Pacific northern bluefin tunas Thunnus thynnus thynnus and Thunnus thynnus orientalis , recently proposed to be distinct species, were found to share nearly identical ITS1 sequences (mean K2P = 0·006) well within the range of intraspecific variation. The northern bluefin tuna appeared to be a sister group to albacore Thunnus alalunga , with all other Thunnus species in a distinct clade. The ITS1 phylogeny was consistent with mtDNA phylogeny in clustering the three tropical Thunnus species ( T. albacares , T. atlanticus and T. tonggol ). Southern bluefin Thunnus maccoyii and bigeye Thunnus obesus tunas showed a closer affinity to this tropical tuna group than to the northern bluefin tuna and albacore. The molecular data supported mitochondrial introgression between species and contradicted morphological subdivision of the genus into two subgenera Neothunnus and Thunnus .     

Phylogenetic relationships betweenVicia faba (Fabaceae) and related species inferred from chloroplasttrnL sequences

The chloroplasttrnL intron from 46 differentVicia accessions, representing five of the nine sections of the genusVicia subg.Vicia sensuMaxted (1991a) were amplified by the Polymerase Chain Reaction (PCR) using oligonucleotide primers homologous to conserved regions intrnL. The products fell into two distinct groups; those of approximately 250 nt and those of around 450 nt in length. Of these, products from 17 differentVicia species were cloned and their nucleotide sequences determined. Multiple alignments were assembled and phylogenetic trees constructed by the weighted least-squares distance method. ALathyrus latifolius trnL intron sequence was used as an outgroup. The resulting trees clearly group and separate the sectt.Narbonensis, Bithynica andFaba species but were less able to distinguish species from sectt.Hypechusa andPeregrinae. Based on these sequence data,V. faba appears to be more distant from sect.Narbonensis than sectt.Hypechusa andPeregrinae. The results are in general agreement with a recent treatment ofVicia subg.Vicia (Maxted 1993) and lend further support to placingV. faba in the monospecific sect.Faba.     

Molecular phylogenetic relationships inAveneae (Poaceae) species and other grasses as inferred from ITS1 and ITS2 rDNA sequences

A phylogenetic analysis was conducted on sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA in 23 species ofAveneae (Poaceae subfam.Pooideaae). These sequences ofHelictotrichon spp.,Arrhenatherum elatius, Avena spp.,Trisetum spp.,Koeleria spp.,Holcus lanatus, Alopecurus vaginatus together with published ITS sequences of furtherAveneae, Poeae, Triticeae, andBromeae were analysed by the neighbor-joining distance method to assess the molecular phylogenetic relationship in perennial and annualAveneae. The results suggest unexpectedly close affinities of the agronomically important genusAvena to comparatively small-flowered taxa ofAveneae. GenusArrhenatherum and small-flowered subgenera ofHelictotrichon are close extant relatives. The large genusHelictotrichon is para- if not polyphyletic, only its subgenera are monophyletic.Trisetum is clearly separated fromHelictotrichon and forms together withKoeleria and perhaps others a monophyletic lineage which is characterised by a conspicuous 9-bp deletion in ITS1. The impact of the ITS data on the delineation of some genera and subtribes ofAveneae and on the recognition of their biogeographical and ecological patterns is outlined.     

Phylogenetic relationships among Bactrocera species (Diptera: Tephritidae) inferred from mitochondrial DNA sequences

Several members of the dipteran family Tephritdae are serious pests because females lay eggs in ripening fruit. The genus Bactrocera is one of the largest within the family with over 500 described species arranged in 28 subgenera. The phylogenetic relationships among the various species and subgenera, and the monophyly of specific groups have not been examined using a rigorous phylogenetic analysis. Therefore, phylogenetic relationships among 24 Bactrocera species belonging to 9 subgenera were inferred from DNA sequence of portions of the mitochondrial 16S rRNA, cytochrome oxidase II, tRNA(Lys), and tRNA(Asp) genes. Two morphological characters that traditionally have been used to define the four groups within the subgenus Bactrocera were evaluated in a phylogenetic context by mapping the character states onto the parsimony tree. In addition, the evolutionary trend in male-lure response was evaluated in a phylogenetic context. Maximum parsimony analyses suggested the following relationships: (1) the genus Bactrocera is monophyletic, (2) the subgenus B. (Zeugodacus) is paraphyletic, (3) the subgenus B. (Daculus) is a sister group to subgenus B. (Bactrocera), and (4) the subgenus B. (Bactrocera) is monophyletic. The mapping analyses suggested that the morphological characters exhibit a simple evolutionary transition from one character state to another. Male-lure response was identified as being a labile behavior that has been lost on multiple occasions. Cue-lure response was plesiomorphic to methyl-eugenol response, and the latter has evolved independently within the Bactrocera and Zeugodacus groups of subgenera. The implications of our results for devising a coherent, consolidated classification for Bactrocera is discussed.     

Phylogenetic relationships of the Far Eastern Araliaceae inferred from ITS sequences of nuclear rDNA

In eight species of the family Araliaceae, inhabiting the territory of the Russian Far East, the sequences of ITS regions of nuclear rDNA were determined. A comparison of these sequences enabled establishment of phylogenetic relationships between the Far Eastern and other members of the family. It was demonstrated that Aralia sensu populations from Primorye and Sakhalin were genetically different and, hereby, could be classified as interspecific taxa. Aralia continentalis along with A. cordata were attributed to the section Aralia sensu. Oplopanax elaus and O. horridus were found to be very close to each other, possibly being the subspecies of one species or relatively young species. Legitimacy of the isolation of two sections within the genus Eleutherococcus was confirmed.     

Questing behaviour of Ixodes ricinus ticks (Acari: Ixodidae)

The vertical distribution in the vegetation of questing Ixodes ricinus ticks was investigated in two different vegetation types (high and low vegetation) at two localities in south-central Sweden during 1992-1993 (Toro) and 1995 (Bogesund). Significant correlations were found between the vertical distribution of immature ticks and the height of the vegetation. The greatest mean availabilities of the larvae and nymphs in low vegetation were in the intervals 0-9 and 30-39 cm, respectively. The larval numbers were greatest close to the ground (0-29 cm) in both high and low vegetation. The larval : nymphal ratio, at ground level at localities free of ground vegetation, varied between 8 : 1 and 32 : 1. In high vegetation, the greatest mean numbers of nymphal and adult ticks were at height intervals of 50-59 and 60-79 cm, respectively. These ranges are within the estimated height interval (40-100 cm) of the main part of the body surface of their preferred host, the roe deer (Capreolus capreolus). The presence of most questing I. ricinus larvae at ground level would favour the transmission of Borrelia burgdorferi s.l., since this is where the highly reservoir-competent rodents and shrews usually occur.     

The midgut hemolysin of Ixodes dammini (Acari:Ixodidae)

Midgut homogenates of the hard tick, Ixodes dammini, lyse erythrocytes from rabbits, rats, hamsters, and guinea pigs. The activity displays sigmoidal kinetics, has an alkaline pH optimum, and is activated by temperature. Hemolytic activity is lost when homogenates are incubated with trypsin or heated for 1 hr at 60 C. Activity is not detectable in nonfed ticks as well as ticks attached for up to 2 days to a host, but increases during the growth phase of feeding. Such activity is postulated to help the initial process of the blood meal digestion by releasing the contents of erythrocytes for further enzymatic hydrolysis.     

Phylogenetic relationships of Palaeacanthocephala (Acanthocephala) inferred from SSU and LSU rDNA gene sequences

The Palaeacanthocephala is traditionally represented by 2 orders, Echinorhynchida and Polymorphida, with 10 and 3 families, respectively. To test the monophyly of the class, these 2 orders, and certain families, phylogenies were inferred using nuclear small-subunit (SSU) and large-subunit (LSU) ribosomal DNA sequences obtained for 29 species representing 10 families, 2 other classes of acanthocephalans, and 3 rotifer outgroups. Phylogenetic relationships were inferred by analyzing combined SSU and LSU sequences using maximum parsimony (MP) and maximum likelihood (ML) methods. Parsimony and ML trees inferred from combined analysis of these rDNA data strongly supported monophyly of Palaeacanthocephala and provided good resolution among species. Neither Polymorphida nor Echinorhynchida was monophyletic. Gorgorhynchoides bullocki (Echinorhynchida) was nested within the 6 species representing Polymorphida, and this clade was nested within species representing Echinorhynchida. Three of 4 palaeacanthocephalan families that could be evaluated were not monophyletic, and this finding was strongly supported. These results indicate that the family level classification of palaeacanthocephalans, which is mainly based on combinations of shared characters (not shared derived characters), needs to be reevaluated with respect to comprehensively sampled phylogenetic hypotheses.     

Phylogenetic relationships of sect.Nummularia (Lysimachia):evidence from ITS sequences

测定了紫脉过路黄、临时救和过路黄的nrDNA ITS序列,并分析了珍珠菜属过路黄组17个物种的遗传距离及亲缘关系.结果表明,过路黄组植物的ITS序列长度在620～628间,一致性高达90.59%,种间遗传距离为0.002～0.199.系统发育树表明:(1)紫脉过路黄、临时救和小茄亲缘关系较近;(2)大叶过路黄、落地梅和过路黄亲缘关系较近;(3)山萝过路黄、贯叶过路黄、管茎过路黄、叶头过路黄、峨眉过路黄及三角叶过路黄亲缘关系较近.ITS序列分析结果为组内植物的鉴定、分类及系统进化提供了新的参考.