Recombination among multiple mitochondrial pseudogenes from a Passerine genus

PCR products of a fragment of the mitchondrial protein coding subunit 5 of NADH-dehydrogenase (ND5) from eight individuals representing five species of the South American bird genus Conirostrum were cloned. The 130 clones, which were subsequently sequenced, constituted 55 different sequences. Due to the observed differences in substitution patterns 58% of the cloned sequences were identified as pseudogenes. Recombination could be traced in 19% of the inferred nuclear pseudogenes, but this figure probably represents a significant underestimation of the factual recombination events. The nonrecombined pseudogenes consisted of multiple haplotypes found to diverge from 1 to 16% from the mitochondrial gene. The number of mitochondrial nuclear copies and their apparent frequent recombination suggest that pseudogenes constitute a serious potential risk in confounding phylogenetic studies and population genetic analysis.     

The phylogeny of acorn weevils (genus Curculio) from mitochondrial and nuclear DNA sequences: the problem of incomplete data

We considered the contribution of two mitochondrial and two nuclear data sets for the phylogenetic reconstruction of 22 species of seed beetles in the genus Curculio (Coleoptera: Cuculionidae). A phylogenetic tree from representatives found on various hosts was inferred from a combined data set of mitochondrial DNA cytochrome oxidase subunit I, mitochondrial cytochrome b, nuclear elongation factor 1alpha, and nuclear phosphoglycerate mutase, used for the first time as a molecular marker. Separate parsimony analyses of each data set showed that individual gene trees were mainly congruent and often complementary in the support of clades but the analysis was complicated by failure of PCR amplification of nuclear genes for many taxa and hence missing data entries. When the four gene partitions were combined in a simultaneous analysis despite the missing data, this increased the resolution and taxonomic coverage compared to the individual source trees. Alternative approaches of combining the information via supertree methodology produced a comparatively less resolved tree, and hence seem inferior to combining data matrices even in cases where numerous taxa are missing. The molecular data suggest a classification of the European species into two species groups that are in accordance with morphological characteristics but the data do no support any of the previously recognised American species groups.     

Molecular taxonomic position of the elephant schistosome, Bivitellobilharzia nairi, newly discovered in Sri Lanka

Bivitellobilharzia nairi (Mudaliar and Ramanujachar, 1945) Dutt and Srivastava, 1955 was first recorded in India. A number of adult worm specimens of this schistosome species were recovered from a domestic elephant, which died in 1999 in Sri Lanka. This is the first report of this schistosome from Sri Lanka. In the present study, in order to clarify the phylogenetic relationship with other species of schistosomes, sequences from the second internal transcribed spacer (ITS2) of the ribosomal gene repeat, part of the 28S ribosomal RNA gene (28S), and part of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene from B. nairi were analyzed. Two intraspecific variations were seen within 13 individuals in the ITS2 region. In the CO1 region of the mitochondrial DNA, there were four haplotypes in the nucleotide sequences and two haplotypes in the amino acid sequences. Phylogenetic analysis using the nuclear DNA showed that B. nairi was basal to all of species of the genus Schistosoma. The 28S tree also showed that the mammalian lineage was monophyletic. However, phylogenetic analysis using the mitochondrial DNA showed that B. nairi was nested within the genus Schistosoma. The taxonomical position for this species as well as the contradiction between the results from the nuclear and mitochondrial genes were discussed.     

Phylogenetic relationships within the genus Tetrahymena inferred from the cytochrome c oxidase subunit 1 and the small subunit ribosomal RNA genes

Details of the phylogenetic relationships among tetrahymenine ciliates remain unresolved despite a rich history of investigation with nuclear gene sequences and other characters. We examined all available species of Tetrahymena and three other tetrahymenine ciliates, and inferred their phylogenetic relationships using nearly complete mitochondrial cytochrome c oxidase subunit 1 (cox1) and small subunit (SSU) rRNA gene sequences. The inferred phylogenies showed the genus Tetrahymena to be monophyletic. The three “classical” morphology-and-ecology-based groupings are paraphyletic. The SSUrRNA phylogeny confirmed the previously established australis and borealis groupings, and nine ribosets. However, these nine ribosets were not well supported. Using cox1 gene, the deduced phylogenies based on this gene revealed 12 well supported groupings, called coxisets, which mostly corresponded to the nine ribosets. This study demonstrated the utility of cox1 for resolving the recent phylogeny of Tetrahymena, whereas the SSU rRNA gene provided resolution of deeper phylogenetic relationships within the genus.     

How do obligate parasites evolve? A multi-gene phylogenetic analysis of downy mildews

Plant parasitism has independently evolved as a nutrition strategy in both true fungi and Oomycetes (stramenopiles). A large number of species within phytopathogenic Oomycetes, the so-called downy mildews, are defined as obligate biotrophs since they have not, to date, been cultured on any artificial medium. Other genera like Phytophthora and Pythium can in general be cultured on standard or non-standard agar media. Within all three groups there are many important plant pathogens responsible for severe economic losses as well as damage to natural ecosystems. Although they are important model systems to elucidate the evolution of obligate parasites, the phylogenetic relationships between these genera have not been clearly resolved. Based on the most comprehensive sampling of downy mildew genera to date and a representative sample of Phytophthora subgroups, we inferred the phylogenetic relationships from a multi-gene dataset containing both coding and non-coding nuclear and mitochondrial loci. Phylogenetic analyses were conducted under several optimality criteria and the results were largely consistent between all the methods applied. Strong support is achieved for monophyly of a clade comprising both the genus Phytophthora and the obligate biotrophic species. The facultatively parasitic genus Phytophthora is shown to be at least partly paraphyletic. Monophyly of a cluster nested within Phytophthora containing all obligate parasites is strongly supported. Within the obligate biotrophic downy mildews, four morphologically or ecologically well-defined subgroups receive statistical support: (1) A cluster containing all species with brownish-violet conidiosporangia, i.e., the genera Peronospora and Pseudoperonospora; (2) a clade comprising the genera with vesicular to pyriform haustoria (Basidiophora, Benua, Bremia, Paraperonospora, Plasmopara, Plasmoverna, Protobremia); (3) a group containing species included in Hyaloperonospora and Perofascia which almost exclusively infect Brassicaceae; (4) a clade including the grass parasites Viennotia oplismeni and Graminivora graminicola. Phylogenetic relationships between these four clades are not clearly resolved, and neither is the position of Sclerospora graminicola within the downy mildews. Character analysis indicates an evolutionary scenario of gradually increasing adaptation to plant parasitism in Peronosporales and that at least the most important of these adaptive steps occurred only once, including major host shifts within downy mildews.     

A phylogeny of members of the family Taeniidae based on the mitochondrial cox1 and nad1 gene data

The cestode family Taeniidae consists of 2 genera, Taenia and Echinococcus, which both have been the focus of intensive taxonomic and epidemiological studies because of their zoonotic importance. However, a comprehensive molecular phylogeny of this family has yet to be reconstructed. In this study, 54 isolates representing 9 Taenia species were characterized using DNA sequences in the mitochondrial cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes. Phylogenetic relationships within the family Taeniidae were inferred by combining cox1 and nad1 sequence data of the present and previous studies. In the phylogenetic analysis, the genus Echinococcus was shown to be monophyletic, but Taenia proved to be paraphyletic due to the position of T. mustelae as a probable sister taxon of Echinococcus. This indicates that T. mustelae should form a genus of its own. Taenia ovis krabbei was placed distant from T. ovis ovis, as a sister taxon of T. multiceps, supporting its recognition as a distinct species, T. krabbei. High intraspecific sequence variation within both T. polyacantha and T. taeniaeformis suggests the existence of cryptic sister species.     

基于rDNA ITS序列探讨部分腐霉种的系统发育与其形态特征

基于对73株计58种腐霉和6种疫霉的核糖体DNA的ITS序列分析,以海生疫霉为外围群,按邻接法构建系统发育树,对腐霉的系统发育关系进行了研究。结果表明:在58种腐霉中,Pythium ostracodes,P.chamaehyphon,P.carbonicum,P.montanum和P.vexans归为同一组,介于其它腐霉和疫霉之间,这5种腐霉的孢子囊均为球形;现已归为疫霉属的P.undulatum 单独为一组,它与腐霉的亲缘关系比疫霉更近;其余52种腐霉聚成一大组,这52种腐霉基本上按孢子囊或菌丝膨大体形态分成Ⅰ、Ⅱ两组:第1组31种腐霉, 其中30种腐霉的孢子囊或菌丝膨大体为球形;第Ⅱ组21种腐霉,其中19种腐霉的孢子囊为丝状、瓣状或裂片状。基于ITS序列分析,腐霉属的其它性状如藏卵器壁是否光滑、卵孢子是否满器、雄器的着生方式和数量、异宗配合等呈多元演化。     

Taxonomic position of Hormaphis similibetulae Qiao & Zhang, 2004 (Hemiptera, Aphididae): molecular and biological evidences

The taxonomic position of Hormaphis similibetulae Qiao & Zhang, 2004 has been reexamined. The phylogenetic position of Hormaphis similibetulae was inferred by maximum parsimony, maximum likelihood and Bayesian analyses on the basis of partial nuclear elongation factor-1α and mitochondrial tRNA leucine/cytochrome oxidase II sequences. The results showed that this species fell into the clade of Hamamelistes species, occupying a basal position, and was clearly distinct from other Hormaphis species. A closer relationship between Hormaphis similibetulae and Hamamelistes species was also revealed by life cycle analysis. Therefore, we conclude that Hormaphis similibetulae should be transferred to the genus Hamamelistes as Hamamelistes similibetulae (Qiao & Zhang), comb. n.     

Characterization of Euplotes lynni nov. spec., E. indica nov. spec. and description of E. aediculatus and E. woodruffi (Ciliophora,Euplotidae) using an integrative approach

Four species belonging to the genus Euplotes have been investigated, namely: E. lynni nov. spec., E. indica nov. spec., E. aediculatus, and E. woodruffi. All populations are from India and were investigated using morphological and molecular markers. The phylogenetic relationships were inferred from small subunit ribosomal rRNA gene (SSU rRNA), internal transcribed spacer (ITS) region, and mitochondrial cytochrome c oxidase subunit I (COI) gene. Predicted secondary structure models for two new species using the hypervariable region of the SSU rRNA gene and ITS2 region support the distinctness of both species. Morphological characters were subjected to principal component analysis (PCA) and genetic variations were studied in-depth to analyze the relatedness of the two new species with their congeners. An integrative approach combining morphological features, molecular analysis, and ecological characteristics was carried out to understand the phylogenetic position of the reported species within the different clades of the genus Euplotes.     

Molecular phylogenetics and the evolution of host plant associations in the nematode genus Fergusobia (Tylenchida: Fergusobiinae)

Fergusobia nematodes (Tylenchida: Fergusobiinae) and Fergusonina flies (Diptera: Fergusoninidae) are putative mutualists that develop together in galls formed in meristematic tissues of many species of the plant family Myrtaceae in Australasia. Fergusobia nematodes were sampled from a variety of myrtaceous hosts and gall types from Australia and one location in New Zealand between 1999 and 2006. Evolutionary relationships of these isolates were inferred from phylogenetic analyses of the DNA sequences of the nuclear ribosomal DNA near-full length small subunit (up to 1689bp for 21 isolates), partial large subunit D2/D3 domain (up to 889bp for 87 isolates), partial mitochondrial cytochrome oxidase subunit I (618 bp for 82 isolates), and combined D2/D3 and mtCOI (up to 1497bp for 66 isolates). The SSU data supported a monophyletic Fergusobia genus within a paraphyletic Howardula. A clade of Drosophila-associated Howardula, including Howardula aoronymphium, was the closest sequenced sister group. Phylogenetic analysis of sequences from D2/D3 and mtCOI, separately and combined, revealed many monophyletic clades within Fergusobia. The relationships inferred by D2/D3 and mtCOI were congruent with some exceptions. Well-supported clades were generally consistent with host plant species and gall type. However, phylogenetic analysis suggested host switching or putative hybridization events in many groups, except the lineage of shoot bud gallers on the broad-leaved Melaleuca species complex.     

Molecular phylogeny and divergence time of the water penny genus Eubrianax (Coleoptera: Psephenidae) in Japan

The phylogenetic relationships among the Japanese members of the genus Eubrianax (Coleoptera: Psephenidae) were examined using the mitochondrial cytochrome oxidase subunit I (COI) gene and nuclear 28S rRNA gene sequences. Based on the molecular phylogeny as well as morphological features, the species status of Eubrianax brunneicornis Nakane, 1952 was proposed. The phylogenetic analyses recovered monophyly of the previously proposed pellucidus species group with four Japanese species, whereas a single Japanese species of the granicollis group was included in the lineage of the ramicornis group with five Japanese species. The divergence times of the species were estimated by dating the phylogenetic tree against the fossil record and a molecular clock based on the COI gene. The divergence of the Japanese species was inferred to have occurred during the Pliocene epoch.     

Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae: Teleostei): Inconsistent implications from morphology,nuclear and mitochondrial genomes

In order to infer phylogenetic relationships between tuna species of the genus Thunnus, partial sequences of the mitochondrial cytochrome b and ATPase genes were determined in all eight species. Supplemental restriction analysis on the nuclear rRNA gene was also carried out. Pacific northern bluefin tuna (Thunnus thynnus orientalis) was found to have mtDNA distinct from that of the Atlantic subspecies (T. t. thynnus) but very similar to that from the species albacore (T. alaluga). In contrast, no differentiation in nuclear genome was observed between the Atlantic and Pacific northern bluefin tunas. The Atlantic northern bluefin and southern bluefin tunas possessed mtDNA sequences very similar to species of yellowfin tuna group and not so similar to albacore and bigeye tunas which were morphologically assigned to the bluefin tuna group. The molecular data indicate that (1) mtDNA from albacore has been incorporated into the Pacific population of northern bluefin tuna and has extensively displaced the original mtDNA, and (2) albacore is the earliest offshoot, followed by bigeye tuna in this genus, which is inconsistent with the phylogenetic relationships between these tuna species inferred from morphology. Correspondence to: S. Chow     

Characterization of Phytophthora hybrids from ITS clade 6 associated with riparian ecosystems in South Africa and Australia

Surveys of Australian and South African rivers revealed numerous Phytophthora isolates residing in clade 6 of the genus, with internal transcribed spacer (ITS) gene regions that were either highly polymorphic or unsequenceable. These isolates were suspected to be hybrids. Three nuclear loci, the ITS region, two single copy loci (antisilencing factor (ASF) and G protein alpha subunit (GPA)), and one mitochondrial locus (cytochrome oxidase c subunit I (coxI)) were amplified and sequenced to test this hypothesis. Abundant recombination within the ITS region was observed. This, combined with phylogenetic comparisons of the other three loci, confirmed the presence of four different hybrid types involving the three described parent species Phytophthora amnicola, Phytophthora thermophila, and Phytophthora taxon PgChlamydo. In all cases, only a single coxI allele was detected, suggesting that hybrids arose from sexual recombination. All the hybrid isolates were sterile in culture and all their physiological traits tended to resemble those of the maternal parents. Nothing is known regarding their host range or pathogenicity. Nonetheless, as several isolates from Western Australia were obtained from the rhizosphere soil of dying plants, they should be regarded as potential threats to plant health. The frequent occurrence of the hybrids and their parent species in Australia strongly suggests an Australian origin and a subsequent introduction into South Africa.     

Explosive evolution of an ancient group of Cyphophthalmi (Arachnida: Opiliones) in the Balkan Peninsula

Aim  To investigate the phylogeny of the genus Cyphophthalmus in the Balkan Peninsula and to test the current recognition of 'phyletic lines' and phylogenetic groups proposed in previous studies in order to elucidate the biogeographical history of the region.
Location  Europe, Balkan Peninsula, Adria microplate.
Methods  Two mitochondrial (cytochrome c oxidase subunit I and 16S rRNA) and two nuclear (28S rRNA and 18S rRNA) markers were used to infer the phylogenetic history of the group. Molecular dating with relaxed molecular clocks was used to elucidate the relative time of diversification within the genus Cyphophthalmus and its constituent lineages.
Results  Our analyses confirm the monophyly of the genus Cyphophthalmus , and that of the Aegean and gjorgjevici lineages, whereas the 'Dinaric lineage' appears paraphyletic.
Main conclusions  We show that the genus Cyphophthalmus is an old endemic from the Balkan biogeographical region, which gave origin to at least three main lineages. Those lineages have diversified within overlapping ranges. According to our molecular dating, they have also diversified within the same timeframe. The Dinaric Alps, although presenting a large number of species, cannot be inferred as the centre of origin of the group. Instead, the biogeographical evolution of the genus could be related to the palaeogeographic history of the Adria microplate.     

ITS1 Sequences of Nuclear Ribosomal DNA in Wild Rices and Cultivated Rices of China and Their Phylogenetic Implications

he first internal transcribed spacer (ITS1) of nuclear ribosomal DNA of three wild rice species and two subspecies of cultivated rice, which are distributed in China, was amplified using PCR technique and sequenced with automated fluorescent sequencing. The sequences of ITS1 ranged from 193 bp to 218 bp in size and G/C content varied from 69.3%to 72.7%. In pairwise comparison among the five taxa, sequence site divergence ranged from 1.5 % to 10.6%. Phylogenetic analysis of ITS1 sequences using Wagner parsimony generated a single well-resolved tree, which revealed that Oryza rufipogon was much more closely related to cultivated rice species than to the other two wild species. Oryza granulata was less closely related to either cultivated rice species or the other two wild species, and might be a unique and isolated taxon in the genus Oryza. The phylogenetic relationships of the three wild rice species and two cultivated rice subspecies inferred from ITS1 sequences is highly concordant with those based on the molecular evidence from isozyme, chloroplast DNA (cpDNA), mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) of the genus Oryza.     

中国野生稻及栽培稻核糖体DNA第一转录间隔区序列分析及其系统学意义

用 PCR技术从产于我国的 3种野生稻和亚洲栽培稻的 2个亚种中特异地扩增和测序了 r DNA的第一转录间隔区。普通野生稻 (Oryza rufipogon)、药用野生稻 (O.officinalis)、疣粒野生稻 (O.granu-lata)和栽培稻的两个亚种 (O.sativa ssp.indica,O.sativa ssp.japonica)的 ITS1序列为 1 93bp、1 94bp、2 1 8bp、1 94bp和 1 94bp,它们的 G/ C含量为 69.3%～ 72 .7% ,序列中位点趋异率为 1 .5%～ 1 0 .6%。序列的相似性比较和简约性分支分析的结果表明 ,普通野生稻与栽培稻的两个亚种之间的亲缘关系最为密切 ;药用野生稻与普通野生稻和与栽培稻的两个亚种的相似性都为 82 % ,说明它与 AA基因组有一定的亲缘关系 ;疣粒野生稻与普通野生稻、药用野生稻和栽培稻两个亚种的亲缘关系相对较远 ,它在稻属中可能是一个系统地位较独特的类群。以 ITS1序列构建的 3种野生稻和 2个栽培稻亚种的系统发育关系与前人用同工酶、叶绿体 DNA、线粒体 DNA和核 DNA资料重建的稻属的系统发育关系基本一致     

MITOCHONDRIAL DNA PHYLOGENY OF THE SYMBIOTIC DINOFLAGELLATES (SYMBIODINIUM,DINOPHYTA)1

Symbiotic dinoflagellates belonging to the genus Symbiodinium (Freudenthal) are found worldwide in association with shallow‐water tropical and subtropical marine invertebrates. Most phylogenetic studies of Symbiodinium have used nuclear rRNA (nrDNA) genes to infer relationships among members of the genus. In this report, we present the first phylogeny of Symbiodinium based on DNA sequences from a mitochondrial protein‐coding gene (cytochrome oxidase subunit I [cox1]). Two principal groups, one comprised of Symbiodinium clade A and the second encompassing Symbiodinium clades B/C/D/E/F, are strongly supported in the cox1 phylogeny. Relationships within Symbiodinium clades B/C/D/E/F, however, are less well resolved compared with phylogenies inferred from nrDNA and chloroplast large subunit (cp23S)‐rDNA genes. Statistical tests between alternative tree topologies verified, with an exception being the position of one controversial member of Symbiodinium clade D, that relationships inferred from cox1 are congruent with those inferred from nrDNA and cp23S‐rDNA. Taken together, the relationships between the major Symbiodinium clades are robust, and there appears to be no evidence of hybridization or differential introgression of nuclear and plastid genomes between clades.     

THE INTERFACE BETWEEN PHYLOGENETICS AND POPULATION GENETICS: INVESTIGATING GENE TREES,SPECIES TREES,AND POPULATION DYNAMICS IN THE PHYLLOPHAGA FRATERNA SPECIES GROUP

This study uses traditional and contemporary phylogenetic and population genetic analyses to assess the causes of discordance (i.e., lineage sorting and introgression) among mitochondrial and nuclear gene trees for a clade of eastern North American scarab beetles (fraterna species group, genus Phyllophaga). I estimated gene trees using individual and combined analysis of one mitochondrial and two nuclear loci in MrBayes , and inferred a species tree using a hierarchical coalescent approach based on all loci in the program Best . Because hybridization violates the assumptions of Best , I tested for introgression by comparing species monophyly between the mitochondrial and nuclear gene trees based on the prediction that cytoplasmic genomes introgress more readily than nuclear genomes. Haplotype exclusivity was identified using Bayesian tests of monophyly and the genealogical sorting index. I used the results of the phylogenetic analyses and monophyly tests to develop an explicit hypothesis of introgression that could be tested in the program IMa. Results from these analyses provided evidence for introgression across clades within the fraterna group. The tiered analytical approach used in this study demonstrated how the use of multiple methods can identify when assumptions are violated and methods are prone to yield misleading results.     

A molecular perspective on the genera Paragonimus Braun, Euparagonimus Chen and Pagumogonimus Chen

The status of the genera Euparagonimus Chen, 1963 and Pagumogonimus Chen, 1963 relative to Paragonimus Braun, 1899 was investigated using DNA sequences from the mitochondrial cytochrome c oxidase subunit I (CO1) gene (partial) and the nuclear ribosomal DNA second internal transcribed spacer (ITS2). In the phylogenetic trees constructed, the genus Pagumogonimus is clearly not monophyletic and therefore not a natural taxon. Indeed, the type species of Pagumogonimus, P. skrjabini from China, is very closely related to Paragonimus miyazakii from Japan. The status of Euparagonimus is less obvious. Euparagonimus cenocopiosus lies distant from other lungflukes included in the analysis. It can be placed as sister to Paragonimus in some analyses and falls within the genus in others. A recently published morphological study placed E. cenocopiosus within the genus Paragonimus and probably this is where it should remain.