Ultrastructure and Cortical Morphogenesis in the Euplotine Hypotrich Certesia quadrinucleata Fabre-Domergue, 1885 (Ciliophora,Protozoa)1

The cortical development during cell division and the interphase ultrastructure of the marine interstitial hypotrich Certesia quadrinucleata is described using light microscopy and both scanning and transmission electron microscopy. Membranelles are paramembranelles; postciliary microtubules from rightmost membranellar kinetosomes line the buccal cavity and separate parallel arrays of pharyngeal discs that border the cytopharynx. A large paroral membrane is present; an endoral membrane is absent. Alveolar plates lie within alveolar membranes except in regions where organelles and organellar complexes (cirri, the condylopallium, dorsal bristles, membranelles, and the paroral membrane) emerge from the cortex. Muciferous-like bodies attach to the plasma membrane in these regions. Dorsal bristles possess transverse and postciliary microtubules as well as kinetodesmal fiber like those of other hypotrichs. Lasiosomes are present. A unique bulbous structure—the condylopallium—protrudes from the anterior right of the cell. The morphogenetic pattern is euplotine in that cortical development begins in one latitudinal zone, and the oral primordium of the opisthe develops within a subsurface pouch apart from the frontal primordia. Microtubular bundles appear beside (later attached to) developing frontal anlagen; they disappear after cirri are in final interphase locations. Although possessing unique characters, Certesia shares a close phylogenetic relationship with Euplotes.     

A unique euplotid ciliate, Gastrocirrhus (Protozoa, Ciliophora): assessment of its phylogenetic position inferred from the small subunit rRNA gene sequence

ABSTRACT. The morphologically unique genus Gastrocirrhus has been considered a distinct but systematically uncertain euplotid due to the absence of both morphogenetic and molecular information. Based on the small subunit rRNA gene sequence, the phylogenetic position of Gastrocirrhus monilifer Ozaki & Yagui, 1942 was re-addressed using multiple algorithms (neighbor-joining, maximum parsimony, least-squares, and Bayesian inference methods). Results indicate that: (1) all phylogenetic trees using different methods are nearly identical in topology, placing G. monilifer closest to Euplotidium arenarium ; (2) Gastrocirrhus and Euplotidium form a monophyletic group, namely the family Gastrocirrhidae, and appear to be intermediate taxa bridging the evolution of the Diophrys-Uronychia and Euplotes- complexes (i.e. Euplotes, Certesia , and Aspidisca ); (3) the order Euplotida is a paraphyletic group composed of three deeply diverged clades ( Euplotes–Certesia–Aspidisca – Gastrocirrhus–Euplotidium ; Uronychia – Diophrys ; and Prodiscocephalus ); (4) together with Prodiscocephalus , the Diophrys-Uronychia complex forms a group at the suborder level and is placed at the root of the order Euplotida, and (5) results from molecular analyses conspicuously challenge the conclusions deduced from morphological as well as morphogenetical investigations—the characteristics traditionally used to define the euplotid taxa at the generic level and/or above may not be uniformly reliable.     

Distribution of pathogenicity island markers and virulence factors in new phylogenetic groups of uropathogenic <Emphasis Type="Italic">Escherichia coli</Emphasis> isolates

The present study was aimed at investigating the relationship between the new Clermont’s phylogenetic groups, virulence factors, and pathogenicity island markers (PAIs) among uropathogenic Escherichia coli (UPEC) in Iran. This cross-sectional study was carried out on 140 UPEC isolates collected from patients with urinary tract infections in Bushehr, Iran. All isolates were subjected to phylogenetic typing using a new quadruplex-PCR method. The presence of PAI markers and virulence factors in UPEC strains was evaluated by multiplex PCR. The most predominant virulence gene was fimH (85%), followed by iucC (61.4%), papC (38.6%), hlyA (22.1%), cnf-1 (18.6%), afa (10.7%), papG and neuC (each 9.3%), ibeA (3.6%), and sfa/foc (0.7%). The most common phylogenetic group was related to B2 (39.3%), and the least common to A (0.7%). The most prevalent PAI marker was PAI IV536 (77.14%), while markers for PAI III536 (13.57%), PAI IIJ96 (12.86%), and PAI II536 (12.14%) were the least frequent among the UPEC strains. Meanwhile, the PAI IJ96 marker was not detected. There was a significant association between the phylogenetic group B2 and all the studied virulence genes and PAI markers. To our knowledge, this is the first study to compare the relationship between new phylogenetic groups, virulence genes and PAI markers in UPEC strains in Iran. The phylogenetic group B2 was predominantly represented among the studied virulence genes and PAI markers, indicating the preference of particular strains to carry virulence genes.     

中国黄粉蝶亚科六属间基于COⅡ和EF-1α基因部分序列的系统发育关系（鳞翅目：粉蝶科）

为了探讨中国黄粉蝶亚科属间的系统发育关系,我们对其中6属9种的细胞色素氧化酶Ⅱ（COⅡ）的部分序列和延伸因子基因（EF-1α）部分序列进行了分析。分别采用最大简约法（maximum parsimony, MP）、最大似然法（maximum likelihood, ML）和贝叶斯推论法（bayesian inference, BI）构建黄粉蝶亚科分子系统树。结果表明：在测得的COⅡ基因的648 bp序列和EF-1α基因的504 bp序列中,有261个变异位点,151个简约信息位点,黄粉蝶亚科内各属COⅡ基因A+T含量（77.3%）均明显偏高。系统发育分析显示黄粉蝶属为亚科中较为原始的类群,分化较早,豆粉蝶属和迁粉蝶属亲缘关系较近,但钩粉蝶属与豆粉蝶属、迁粉蝶属之间的亲缘关系还不能确定。本研究结果和传统的基于形态学的黄粉蝶亚科的分类体系有所不同,最显著的分歧是本研究支持内群中分化最早的属应为黄粉蝶属,而不是豆粉蝶属和迁粉蝶属。     

Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches

Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer confidence values by way of nonparametric bootstrapping. Recent developments in phylogenetics suggest the computational burden can be reduced by using Bayesian methods of phylogenetic inference. However, few empirical phylogenetic studies exist that explore the efficiency of Bayesian analysis of large datasets. To this end, we conducted an extensive phylogenetic analysis of the wide-ranging and geographically variable Eastern Fence Lizard (Sceloporus undulatus). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on a combined mitochondrial DNA dataset (12S and 16S rRNA, ND1 protein-coding gene, and associated tRNA; 3,688 bp total) for 56 populations of S. undulatus (78 total terminals including other S. undulatus group species and outgroups). Maximum parsimony analysis resulted in numerous equally parsimonious trees (82,646 from equally weighted parsimony and 335 from weighted parsimony). The majority rule consensus tree derived from the Bayesian analysis was topologically identical to the single best phylogeny inferred from the maximum likelihood analysis, but required approximately 80% less computational time. The mtDNA data provide strong support for the monophyly of the S. undulatus group and the paraphyly of "S. undulatus" with respect to S. belli, S. cautus, and S. woodi. Parallel evolution of ecomorphs within "S. undulatus" has masked the actual number of species within this group. This evidence, along with convincing patterns of phylogeographic differentiation suggests "S. undulatus" represents at least four lineages that should be recognized as evolutionary species.     

Does the Gonostomum-patterned oral apparatus in hypotrichia carry a phylogenetic signal? Evidence from morphological and molecular data based on extended taxon sampling using three nuclear genes (Ciliophora,Spirotrichea)

The classification of hypotrichs based on the gonostomatid oral structure is widely accepted, but the phylogenetic signal of this character is unknown. Here, we infer the species phylogeny of those gonostomatids for which molecular data are available, plus26 new sequences of SSU-rDNA, ITS1-5.8 S-ITS2 and LSU-rDNA genes. The results indicate that:(i) the endoral is more phylogenetically informative than the paroral;(ii) the structure of the endoral and the Gonostomum-pattern adoral zone of membranelles are plesiomorphies for the hypotrichs sensu stricto;(iii) the group of species possessing these features is monophyletic in all our phylogenetic analyses, except that for the SSU-rDNA;(iv) Schmidingerotrichidae is monophyletic in all trees, suggesting that it is a well-defined family;(v) the Gonostomatidae is polyphyletic in the SSU-rDNA and ITS1-5.8 S-ITS2 trees, with Gonostomum, Cladotricha, Cotterillia, Metagonostomum, Paragonostomum and Wallackia distributed among separate clades, but monophyletic in the LSU-rDNA and concatenated trees;(vi) higher hypotrich taxa such as core urostyloids and core sporadotrichids/stichotrichids might have evolved from species that possessed a gonostomatid oral apparatus.     

Ciliate food vacuole content and bacterial community composition in the warm-monomictic crater Lake Alchichica, México

To evaluate trophic relationships between ciliates and bacterioplankton during the stratification period in a lake, samples from three different layers [the upper part of the metalimnion (UM), the base of the metalimnion (BM) and the hypolimnion] were studied. The autotrophic picoplankton numbers, phylogenetic composition of heterotrophic picoplankton (HPP), and HPP composition in ciliates' food vacuoles were analyzed. Additionally, in situ incubations in dialysis bags were performed at the same selected depths to assess potential changes in picoplankton composition related to ciliates' feeding activity. Among the in situ HPP assemblage, no phylogenetic group dominated in the selected layers within the course of the study. The ciliate assemblage was dominated by scuticociliates, haptorids, and hypotrichs. Comparing ciliates' food vacuole content and in situ HPP composition, a high preference for Alphaproteobacteria was found at all three depths. Planctomycetes, and Delta- and Gammaproteobacteria were selected at BM and hypolimnion, respectively. However, selection of a given phylogenetic group in the time course of this study was observed only for Alphaproteobacteria in the UM. Similar trends were found in the incubations, but no relationship was found between the vacuole content of the ciliates and changes in HPP composition.     

Evolution of discocephalid ciliates: Molecular,morphological and ontogenetic data support a sister group of discocephalids and pseudoamphisiellids (Protozoa,Ciliophora) with establishment of a new suborder Pseudoamphisiellina subord. n.

Discocephalids and pseudoamphisiellids are possibly two of the most confused groups among hypotrichous/euplotid ciliates regarding their systematic position and phylogenetic relationships. The former were often regarded as related to euplotids while the latter, in the absence of molecular data, were mostly assigned to the urostylid-like hypotrichs. In the present work, the small subunit rRNA genes of several rarely observed discocephalid and pseudoamphisiellid genera were analyzed to obtain insights into the phylogenetic relationships of these highly ambiguous Spirotrichea. Four different tree reconstruction algorithms yielded nearly identical topologies, which indicated both groups belong to the same assemblage. This assemblage is clearly isolated as a deep-branching clade and invariably positioned between Euplotida and Hypotricha. The sister group relationship of the Pseudoamphisiellidae and Discocephalidae supports the previous suggestion that they might represent an ordinal taxon, the Discocephalida. Both morphological and morphogenetic features indicate that the pseudoamphisiellids should be placed in the order Discocephalida but as a sister group to other typical discocephalids. Thus we propose establishing a new suborder, Pseudoamphisiellina subord. n. The new taxon is diagnosed by the following characteristics: (i) two distantly separated midventral rows that are morphogenetically formed with an urostylid mode; (ii) absence of the “frontoterminal row”, which is formed from the posterior-most frontoventral-transverse cirral anlage in all other typical urostylids; (iii) numerous caudal cirri that derive from each of the dorsal kinety anlagen; (iv) right marginal row that has a unique de novo origin; and (v) inhabiting periphytic communities. The validity of the suborder Pseudoamphisiellina is firmly supported by molecular data.     

A comparative fine structural and phylogenetic analysis of resting cysts in oligotrich and hypotrich Spirotrichea (Ciliophora)

So far, neither morphology nor gene sequences have provided a reliable classification of halteriid and hypotrichid spirotrichs. Thus, we performed a comparative study on the fine structure of the resting cysts in some representative species, viz., the oligotrichs Halteria grandinella and Pelagostrombidium fallax and the oxytrichid hypotrichs Laurentiella strenua, Steinia sphagnicola, and Oxytricha granulifera. Main results include: (i) there are three different, very likely non-homologous cyst surface ornamentations, viz., spines (generated by the ectocyst), thorns (generated by the mesocyst), and lepidosomes (produced in the cytoplasm); (ii) Halteria has a perilemma; (iii) Halteria, Meseres and Pelagostrombidium have fibrous lepidosomes, while those of Oxytricha are tubular; (iv) the cyst wall structure of Pelagostrombidium and Strombidium is distinctly different from that of halteriids and oxytrichids, which are rather similar in this respect; (v) cyst ornamentation does not provide a reliable phylogenetic signal in oxytrichid hypotrichs because ectocyst spines occur in both flexible and rigid genera. The new observations and literature data were used to investigate the phylogeny of the core Spirotrichea. The Hennigian argumentation scheme and computer algorithms showed that the spirotrichs are bound together by the macronuclear reorganization band, the subepiplasmic microtubule basket, and the apokinetal stomatogenesis. The Hypotrichida and Oligotrichida are united by a very strong synapomorphy, viz., the perilemma, not found in any other member of the phylum. Halteriid and oligotrichid spirotrichs form a sister group supported by as many as 13 apomorphies. Thus, the molecular data, which classify the halteriids within the core hypotrichs, need to be reconsidered.     

The complete mitochondrial DNA sequence of the Mekong giant catfish (Pangasianodon gigas), and the phylogenetic relationships among Siluriformes

The Mekong giant catfish (Pangasianodon gigas) is the largest scale-less freshwater fish of the world, and a critically endangered species. We determined the complete nucleotide sequence (16,533 bp) of the mitochondrial genome of the Mekong giant catfish, and conducted phylogenetic analyses based on mitochondrial protein (the combined amino acid sequences of all 13 mitochondrial protein coding genes) and rRNA (the combined nucleotide sequences of mitochondrial 12S and 16S rRNA genes) data sets in order to further clarify the relative phylogenetic position of P. gigas, and to recover phylogenetic relationships among 15 out of the 33 families of Siluriformes. Phylogenetic analyses (maximum parsimony, minimum evolution, maximum likelihood, Bayesian inference) of the protein data set were congruent with a basal split of the order into Loricarioidei and Siluroidei, and supported a closer relationship of the Mekong giant catfish (family Pangasiidae) to Siluridae than to Bagridae. The rRNA-based Bayesian phylogeny recovered Callichthyidae as the sister group of all other analyzed non-diplomystid catfish families, rendering Loricarioidei paraphyletic. In addition, Loricariidae were recovered as paraphyletic due to the inclusion of Astroblepidae. However, none of the two relationships received bootstrap support in the maximum parsimony, minimum evolution, and maximum likelihood analyses, and should be interpreted with caution. The derived position of Cetopsidae within Siluroidei, the sister group relationship of Pseudopimelodidae and Pimelodidae, and a close relationship of Doradidae and Auchenipteridae to the exclusion of Mochokidae were strongly supported. Pangasiidae was placed as a single lineage without clear affinities.     

Evolutionary correlation between floral monosymmetry and corolla pigmentation patterns in <Emphasis Type="Italic">Rhododendron</Emphasis>

Floral symmetry and pigmentation are features of flowers that are believed to be associated due to their shared influence on pollinator behaviour. However, the evolution of such associations has so far not been examined. We analysed variation in Rhododendron flowers, in a phylogenetic context, to test whether the evolution of floral symmetry types and pigment patterns are correlated. Variation in floral symmetry due to variation in corolla form, stamen flexion, stamen arrangement, pistil flexion, as well as corolla pigment patterns was documented in 98 species of Rhododendron. Phylogenetic relations among these species were estimated using maximum likelihood (ML) and Bayesian methods, building on a published molecular dataset of sequences of RNA Polymerase II subunit (RPB2-I). Evolution of the floral traits was studied using phylogenetic correlation tests and ancestral state reconstructions (maximum parsimony, MP and ML methods). Significant correlations were found between corolla pigment pattern and type of floral symmetry at the level of corolla form, stamen flexion or arrangement, and pistil flexion. As expected from their similar roles in enhancing attractability to pollinator, monosymmetric corollas and presence of pigment pattern are correlated; in addition, monosymmetry involving other whorls too shows such a relationship with pigment patterns, and with each other. Multiple evolutionary shifts were detected between monosymmetry and polysymmetry of floral traits in Rhododendron. The relationship between floral monosymmetry attributes and presence of corolla pigment patterns, and additionally, frequent evolutionary shifts in these traits suggest pollinator-mediated selective pressures in Rhododendron.     

A settled sub-family for the orphan tree: The phylogenetic position of the endemic Colombian genus <Emphasis Type="Italic">Orphanodendron</Emphasis> in the Leguminosae

Orphanodendron is a taxonomically and geographically isolated South American genus of two species. When first described by Barneby and Grimes in 1990, the genus was placed in Leguminosae subfamily Caesalpinioideae, but that placement was doubted and the name Orphanodendron (Gr. orphanos, orphan + dendron, tree) was chosen to reflect the uncertain subfamilial relationship of the genus. In this study, nucleotide sequence data from five Orphanodendron specimens were added to 662 other, previously sampled, Leguminosae taxa representing all three currently recognized subfamilies (Caesalpinioideae, Mimosoideae and Papilionoideae) in a matK maximum parsimony analysis that resolved Orphanodendron as a member of the genistoid s.l. clade of subfamily Papilionoideae. Two additional Bayesian phylogenetic analyses with reduced taxon sampling of plastid (matK combined with trnL-F) and nuclear (ITS) loci strongly support the monophyly of Orphanodendron and unambiguously establish Orphanodendron as a member of the genistoid sensu lato clade. Although our plastid phylogenetic analysis finds relatively low support for a sister-group relationship with the African genus Camoensia, the nuclear-encoded ITS resolves Orphanodendron as sister to the Bowdichia clade with strong support and Camoensia as sister to other core genistoids. The phylogenetic resolution of Orphanodendron as a member of the genistoid s.l. legumes based on nuclear and plastid sequences will undoubtedly advance future evolutionary investigations of this Colombian endemic tropical tree genus.     

The complete mitochondrial genome of <Emphasis Type="Italic">Vanessa indica</Emphasis> and phylogenetic analyses of the family Nymphalidae

Vanessa indica is a small butterfly lacking historical molecular and biological research. Vanessa indica belongs to the family Nymphalidae (Lepidoptera: Papilionoidea), which is the largest group of butterflies and are nearly ubiquitous. However, after more than a century of taxonomic and molecular studies, there is no consensus for family classification, and the phylogenetic relationships within Nymphalidae are controversial. The first objective was to sequence and characterize the complete mitochondrial genome of V. indica. The most important objective was to completely reconstruct the phylogenetic relationships for family members within Nymphalidae. The mitochondrial genomic DNA (mtDNA) of V. indica was extracted and amplified by polymerase chain reaction. The complete mitochondrial sequence was annotated and characterized by analyzing sequences with SeqMan program. The phylogenetic analyses were conducted on thirteen protein coding genes (PCGs) in 95 mtDNA of Nymphalidae downloaded from GenBank for reference using the maximum likelihood method and Bayesian inference to ensure the validity of the results. The complete mitogenome was a circular molecule with 15,191 bp consisting of 13 protein coding genes, two ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA (tRNA) genes, and an A?+?T-rich region (D-loop). The nucleotide composition of the genome was highly biased for A?+?T content, which accounts for 80.0% of the nucleotides. All the tRNAs have putative secondary structures that are characteristic of mitochondrial tRNAs, except tRNA^Ser(AGN). All the PCGs started with ATN codons, except cytochrome c oxidase subunit 1 (COX1), which was found to start with an unusual CGA codon. Four genes were observed to have unusual codons: COX1 terminated with atypical TT and the other three genes terminated with a single T. The A?+?T rich region of 327 bp consisted of repetitive sequences, including a ATAGA motif, a 19-bp poly-T stretch, and two microsatellite-like regions (TA)₈. The phylogenetic analyses consistently placed Biblidinae as a sister cluster to Heliconiinae and Calinaginae as a sister clade to Satyrinae. Moreover, the phylogenetic tree identified Libytheinae as a monophyletic group within Nymphalidae. The complete mitogenome of V. indica was 15,191 bp with mitochondrial characterizations common for lepidopteran species, which enriched the mitochondria data of Nymphalid species. And the phylogenetic analysis revealed different classifications and relationships than those previously described. Our results are significant because they would be useful in further understanding of the evolutionary biology of Nymphalidae.     

Phylogenetic Relationships within <Emphasis Type="Italic">Phyllophaga</Emphasis> Harris (sensu <Emphasis Type="Italic">lato</Emphasis>) (Coleoptera: Melolonthidae,Melolonthinae) with Emphasis on <Emphasis Type="Italic">Listrochelus</Emphasis> Blanchard

As partial results of a long-term project for the revision of the supraspecific classification of the American Melolonthini, using phylogenetic methods, interesting information on the relationships between the subgeneric groups of Phyllophaga Harris proposed by Saylor were obtained. The genus Listrochelus was described by Blanchard in 1851. However, in 1940, Saylor reduced it as a subgenus of Phyllophaga. The objective of the present study is to confirm the monophyly of Listrochelus by means of a phylogenetic analysis. A total of 132 species were analyzed; 31 species of them belong to Listrochelus, 76 are from other groups of Phyllophaga, and 25 species are from the outgroup. A morphological matrix with 281 characters was codified. A traditional search with 1000 iterations was performed in TNT. Branch support was investigated using the bootstrap method. Parsimony analysis resulted in ten equally parsimonious trees. The topology obtained in the strict consensus tree shows that the limits of Listrochelus are very clear (bootstrap 99%), supported by five synapomorphies and a combination of eight character states that are not exclusive to the group. Based on the hypothesis obtained, the restitution of the genus Listrochelus is proposed.     

<Emphasis Type="Italic">Lactobacillus futsaii</Emphasis> CS3, a New GABA-Producing Strain Isolated from Thai Fermented Shrimp (<Emphasis Type="Italic">Kung</Emphasis>-<Emphasis Type="Italic">Som</Emphasis>)

Kung-Som is a popular traditional Thai fermented shrimp product. It is rich in glutamic acid, which is the major substrate for the biosynthesis of gamma-aminobutyric acid (GABA) by lactic acid bacteria (LAB). In the present study, LAB from Kung-Som were isolated, screened for GABA formation, and the two isolates that transform glutamic acid most efficiently into GABA were identified. Based on the API-CHL50 fermentation profile and a phylogenetic tree of 16S rDNA sequences, strain CS3 and CS5 were identified as Lactobacillus futsaii, which was for the first time shown to be a promising GABA producer. L. futsaii CS3 was the most efficient microorganism for the conversion of 25 mg/mL monosodium glutamate (MSG) to GABA, with a maximum yield of more than 99% conversion rate within 72 h. The open reading frame (ORF) of the glutamate decarboxylase (gad) gene was identified by PCR. It consists of 1410 bp encoding a polypeptide of 469 amino acids with a predicted molecular weight of 53.64 kDa and an isoelectric point (pI) of 5.56. Moreover, a good quality of the constructed model of L. futsaii CS3 was also estimated. Our results indicate that L. futsaii CS3 could be of interest for the production of GABA-enriched foods by fermentation and for other value-added products.     

广义青篱竹属(Arundinaria)核糖体DNA ITS序列及亲缘关系研究

利用PCR扩增产物直接测序的方法分析广义青篱竹属(Arundinaria)中有关争议类群的代表种或模式种(毛竹为外类群)等18种竹种的核糖体DNA内转录间隔区(Internal Transcribed Spacers,ITS)序列。通过最简约性分析产生的ITS系统发育树表明,供试竹种形成一个自然的单系类群,这说明广义青篱竹属中这些不同的类群归属青篱竹属是合理的。17种竹种可聚为2大分支：其中斑苦竹(A,oleosa)、仙居苦竹(A．hsienchuensis)、茶秆竹(A．amabilis)、长叶苦竹(A．chino)、苦竹(A．amara)、宜兴苦竹(A．yixingensis)、菲白竹(A．fortunei)、翠竹(A．pygmaea)为一个分支;而大明竹(A．graminea)、巴山木竹(A．fargesii)、冷箭竹(A．faberi)、凤竹(A．hupehense)、鼓节矢竹(Pseudosasa japonica cv．Tsutsumiana)、矢竹(Pseudosasa japonica)、短穗竹(Brachystachyum densiflorum)、肿节竹(A．oedogonata)、少穗竹(A．sulcata)组合在另一分支。ITS系统发育树还表明,大明竹与巴山木竹、鼓节矢竹与矢竹、少穗竹与短穗竹和肿节竹关系极为密切,均得到较高的Bootstrap(分别为99％、100％和87％)的支持;茶秆竹与仙居苦竹关系非常密切,茶秆竹可归隶到青篱竹属中;翠竹和菲白竹关系密切,且与苦竹类竹种分为两个分支。     

The phylogenetic position of the Talpidae within eutheria based on analysis of complete mitochondrial sequences

The complete mitochondrial (mt) genome of the mole Talpa europaea was sequenced and included in phylogenetic analyses together with another lipotyphlan (insectivore) species, the hedgehog Erinaceus europaeus, and 22 other eutherian species plus three outgroup taxa (two marsupials and a monotreme). The phylogenetic analyses reconstructed a sister group relationship between the mole and fruit bat Artibeus jamaicensis (order Chiroptera). The Talpa/Artibeus clade constitutes a sister clade of the cetferungulates, a clade including Cetacea, Artiodactyla, Perissodactyla, and Carnivora. A monophyletic relationship between the hedgehog and the mole was significantly rejected by maximum parsimony and maximum likelihood. Consistent with current systematic schemes, analyses of complete cytochrome b genes including the shrew Sorex araneus (family Soricidae) revealed a close relationship between Talpidae and Soricidae. The analyses of complete mtDNAs, along with the findings of other insectivore studies, challenge the maintenance of the order Lipotyphla as a taxonomic unit and support the elevation of the Soricomorpha (with the families Talpidae and Soricidae and possibly also the Solenodontidae and Tenrecidae) to the level of an order, as previously proposed in some morphological studies.     

基于28S rDNA D2基因片段与形态特征的优茧蜂亚科系统发育研究

本研究选取优茧蜂亚科Euphorinae(膜翅目Hymenoptera:茧蜂科Braconidae)的8族19属23种作为内群,茧蜂其它6个亚科的8属8种作外群,首次结合同源核糖体28S rDNA D2基因序列片段和41个形态学特征对该亚科进行了系统发育学研究。利用"圆口类"的内茧蜂亚科Rogadinae、茧蜂亚科Braconinae、矛茧蜂亚科Doryctinae的3个亚科为根,以PAUP*4.0和MrBayes3.0B4软件分别应用最大简约法(MP)和贝叶斯法对优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分析;并以PAUP*4.0对优茧蜂亚科的28S rDNA D2基因序列的片段的碱基组成与碱基替代情况进行了分析。结果表明:优茧蜂亚科的28S rDNA D2基因序列片段的GC%含量在40.00%~49.25%之间变动,而对于碱基替代情况来讲,优茧蜂亚科各个成员间序列变异位点上颠换(transversion)大于转换(transition);不同的分析和算法所产生的系统发育树都表明目前根据形态定义出的优茧蜂亚科Euphorinae不是一个单系群,而是一个与蚁茧蜂亚科Neoneurinae和高腹茧蜂亚科Cenocoelinae混杂在一起的并系群;在优茧蜂亚科内部,悬茧蜂族Meterorini和食甲茧蜂族Microctonini(排除猎户茧蜂属Orionis)为单系群,而宽鞘茧蜂族Centistini、大颚茧蜂族Cosmophorini、优茧蜂族Euphorini、瓢虫茧蜂族Dinocampini为并系群;悬茧蜂族Meterorini在优茧蜂亚科Euphorinae内位于基部位置的观点得到部分的支持,同时食甲茧蜂族Microctonini被判定为相对进化的类群。此外对于优茧蜂亚科内各属之间的相互亲缘关系,不同算法所得到的系统发育属的结果不完全一致,这表明优茧蜂亚科内(属及族)的系统发育关系还有待于进一步研究。