A morphological key for the identification of southern African Synodontis species Cuvier, 1816 (Teleostei: Mochokidae)

The identification of the southern African Synodontis species is hampered by variable and overlapping morphological characteristics such as colour, pigmentation patterns and morphometric ratios. Species are often misidentified due to the complicated nature of the present identification keys. The morphological key proposed in this note uses simplified characters including the shape of the humeral process, size of the outer mandibular barbel, teeth rows, position of the mouth, basal membrane of the maxillary barbel and length of the maxillary barbels, plus the natural distribution range of certain species to facilitate positive identification of southern African Synodontis specimens.     

Phylogenetic relationships among some Ateles species: the use of chromosomic and molecular characters

As with most platyrrhines, the systematics of Ateles is under discussion. In order to help clarify its systematic, we employed chromosomic and molecular characters to analyze the phylogenetic relationship among some species of the genus Ateles. Chromosomic studies were conducted on 14 atelid specimens: eight Ateles from A. paniscus, A. chamek, A. belzebuth and A. geoffroyi, and six Alouatta caraya. Ateles paniscus showed 2N=32, whereas A. chamek, A. belzebuth and A. geoffroyi presented 2N=34, XX/XY (with a submetacentric X and a variable Y) corroborated by male meiosis. Nucleotide sequence variation at the mitochondrial cytochrome c oxidase subunit II gene (COII) was analyzed in ten New World monkey specimens. Parsimony trees showed consistent phylogenetic relationships using both chromosomic forms and mitochondrial COII gene sequences as characters. Particularly, chromosomic phylogenies showed A. hybridus as a divergent taxon from the remaining group, whereas A. chamek, A. belzebuth and A. marginatus form an unresolved clade with A. geoffroyi as sister group.     

Phylogenetic relationships in some diploid species of Triticineae: cytogenetic analysis of interspecific hybrids

Summary Ten diploid species from genera Triticum, Aegilops, Haynaldia and Secale were included in a diallel crossing program. Forty-one different interspecific hybrids were obtained. The number of associations between chromosome arms at metaphase I of meiosis in pollen mother cells from the hybrids was taken as an indication of the degree of homology between parental genomes. Genome relationships were defined and indicated a possible pattern of differentiation from a common ancestor. Breeding strategies based on this information are proposed.     

Phylogenetic relationships amongTetrahymena species determined using the polymerase chain reaction

Summary The species of theTetrahymena pyriformis complex present a conundrum with regard to their highly conservative morphology and widely divergent molecular characteristics. We have investigated the phylogenetic relationships among these species using the nucleotide sequences from the histone H3II/H4II region of the genome. This region includes portions of the two histone coding sequences, as well as the intergenic region. The DNA sequences of these regions were amplified by the polymerase chain reaction (PCR) and the sequence of each was determined. Nucleotide substitutions and insertions/deletions within this set of sequences were compared to determine the phylogenetic relationships among the species of the complex. These data yield phylogenetic trees with identical topologies when different tree-building routines are used, indicating that the data are very robust.Glaucoma chattoni was used as an outgroup to root the trees for this analysis. The genome organization ofG. chattoni and the divergence of its histone H3II/H4II region sequence relative to those of the complex clearly indicate that this species has diverged considerably from the complex. These results show that PCR amplification analysis is feasible over considerable evolutionary distances. However, DNA-DNA hybridization may be more useful than sequence analysis in resolving the relationships among the closely related species in the complex.     

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     

Phylogenetic relationships of someMicrosporum andArthroderma species inferred from mitochondrial DNA analysis

Thirty-eight strains of 12Microsporum and 10Arthroderma (Nannizzia) species were investigated by analysis of mitochondrial DNA with 6 restriction enzymes, and classified into 13 genetic groups. The phylogenetic tree of the 13 groups thus established was constructed. On the tree,M. audouinii, M. langeronii, M. rivalieri, M. distortum, M. equinum, M. ferrugineum andA. otae comprise one genetic group and are suggested to be the same species.A. gypseum, A. fulvum, M. duboisii, M. ripariae, A. incurvatum, A. persicolor andA. obtusum are clustered on one of five boughs of the tree indicating their close relation.A. racemosum andA. cajetani are also closely related.     

Phylogenetic relationships between Hapalemur species and subspecies based on mitochondrial DNA sequences

Background  

Phylogenetic relationships of the genus Hapalemur remains controversial, particularly within the Hapalemur griseus species group. In order to obtain more information on the taxonomic status within this genus, and particularly in the cytogenetic distinct subspecies group of Hapalemur griseus, 357 bp sequence of cytochrome b and 438 bp of 12S mitochondrial DNAs were analyzed on a sample of animals captured in areas extending from the north to the south-east of Madagascar. This sample covers all cytogenetically defined types recognized of the genus Hapalemur.     

Phylogenetic relationships amongHomo sapiens and related species based on restriction site variations in rDNA spacers

A rapid method, using 12 restriction enzymes, was employed to analyze variations in ribosomal DNA (rDNA) spacers in a study of phylogenetic relationships betweenHomo sapiens and related species. We mapped restriction sites in the external and internal spacer regions and compared the arrangements of sites. The estimated sequence divergence betweenHomo sapiens andPan troglodytes, Pan paniscus, Gorilla gorilla, Pongo pygmaeus, Hylobates lar, H. agilis, andMacaca fuscata was 2.7, 2.3, 3.8, 7.3, 6.8, 7.8, and 14.1%, respectively. The genetic relationships inferred from these distances generally correspond to those inferred from analyses of other molecular markers in the literature. The divergence betweenH. lar andH. agilis and betweenH. lar andH. syndactylus was 0.34 and 2.4%, respectively.This study was supported in part by Grants-in-Aid for Scientific Research from the Ministry of Education, Science and Culture, Japan, and also by the Cooperative Research Program of the Primate Research Institute, Kyoto University.     

Phylogenetic relationships among cultivated Allium species from restriction enzyme analysis of the chloroplast genome

Summary The genus Allium contains many economically important species, including the bulb onion, chive, garlic, Japanese bunching onion, and leek. Phylogenetic relationships among the cultivated alliums are not well understood, and taxonomic classifications are based on relatively few morphological characters. Chloroplast DNA is highly conserved and useful in determining phylogenetic relationships. The size of the chloroplast genome of Allium cepa was estimated at 140 kb and restriction enzyme sites were mapped for KpnI, PstI, PvuII, SalI, XbaI, and XhoI. Variability at restriction enzyme sites in the chloroplast DNA was studied for at least three accessions of each of six cultivated, old-world Allium species. Of 189 restriction enzyme sites detected with 12 enzymes, 15 mutations were identified and used to estimate phylogenetic relationships. Cladistic analysis based on Wagner and Dollo parsimony resulted in a single, most-parsimonious tree of 16 steps and supported division of the species into sections. Allium species in section Porrum were distinguished from species in sections Cepa and Phyllodolon. Two species in section Rhiziridium, A. schoenoprasum and A. tuberosum, differed by five mutations and were placed in separate lineages. Allium cepa and A. fistulosum shared the loss of a restriction enzyme site and were phylogenetically closer to each other than to A. schoenoprasum. This study demonstrates the usefulness of restriction enzyme site analysis of the chloroplast genome in the elucidation of phylogenetic relationships in Allium.     

Phylogenetic relationships between Leymus and related diploid Triticeae species revealed by ISSR markers

To investigate the genetic diversity and phylogenetic relationships between polyploid Leymus and related diploid species of the Triticeae tribe, inter-simple sequence repeats (ISSR) markers was used to analyze 41 Leymus accessions representing 22 species and 2 subspecies, together with Pseudoroegneria stipifolia (St), Psathyrostachys fragilis (Ns), Australopyrum retrofractum (W), Hordeum bogdanii, H. chilense (H) and Lophopyrum elongatum (E^e). A total of 376 clear and reproducible DNA fragments were amplified by 29 ISSR primers, among which 368 (97.87%) fragments were found to be polymorphic. 8–18 polymorphic bands were amplified by each polymorphic primer, with an average of 12.69 bands. The data of 376 ISSR bands were used to generate Nei’s similarity coefficients and to construct a dendrogram by means of UPGMA. The similarity coefficients data suggested great genetic diversity in genus Leymus and related diploid Triticeae species, the genetic diversity among the different species more abundant than that of the different accessions. The dendrogram and principal coordinate analysis showed explicit interspecific relationships and demonstrated close phylogenetic relationships between Leymus species and Psathyrostachys.     

Phylogenetic relationships among Acestrorhynchus species (Ostariophysi: Characiformes: Acestrorhynchidae)

A total of 104 osteological and external morphological features were examined in 13 species of Acestrorhynchus and 15 outgroup taxa to advance a hypothesis of relationships within the genus. Two most parsimonious hypotheses corroborate the monophyly of Acestrorhynchus but differ in the hypothesized relationships of Acestrorhynchus heterolepis . Three proposed supraspecific assemblages are at least partially correlated with groups of species previously diagnosed on the basis of colour pattern: (1) Acestrorhynchus britskii , Acestrorhynchus grandoculis , Acestrorhynchus microlepis , and Acestrorhynchus minimus ; (2) Acestrorhynchus falcirostris , Acestrorhynchus isalineae , and A. Acestrorhynchus nasutus ; and (3) Acestrorhynchus abbreviatus , Acestrorhynchus altus , Acestrorhynchus falcatus , Acestrorhynchus lacustris , and Acestrorhynchus pantaneiro . In one hypothesis A. heterolepis is proposed as the closest relative of the clade formed by A. falcirostris , A. isalineae , and A. nasutus , and in the alternative hypothesis it is proposed as a sister species of the clade formed by A. abbreviatus , A. altus , A. falcatus , A. lacustris , and A. pantaneiro . Relationships among species of the latter clade remain unresolved. Two independent episodes of reduction of body size are hypothesized to have occurred within the genus: one associated with the clade formed by A. grandoculis and A. minimus , and the other with the clade formed by A. isalineae and A. nasutus . © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 691–757.     

Phylogenetic relationships and DNA barcoding of nine endangered medicinal plant species endemic to Saint Katherine protectorate

A high degree of endemism has been recorded for several plant groups collectively in Saint Katherine Protectorate (SKP) in the Sinai Peninsula. Nine endangered endemic plant species in SKP were selected to test the variable abilities of three different DNA barcodes; Riboluse-1,5- Biphosphate Carboxylase/Oxygenase Large subunit (rbcL), Internal Transcribed Spacer (ITS), and the two regions of the plastid gene (ycf1) as well as Start Codon Targeted (SCoT) Polymorphism to find the phylogenetic relationships among them. The three barcodes were generally more capable of finding the genetic relationships among the plant species under study, new barcodes were introduced to the National Centre for Biotechnology Information (NCBI) for the first time through our work. The barcode sequences were efficient in finding the genetic relationships between the nine species. However, SCoT polymorphism could only cluster plant species belonging to the same genus together in one group, but it could not cluster plant species belonging to the same families except for some primers solely. RbcL was the most easily amplified and identified barcode in eight out of the nine species at the species level and the ninth barcode to the genus level. ITS identified all the species to the genus level. Finally, ycf1 identified six out of the eight species, but it could not identify two of the eight species to the genus level.     

Phylogenetic relationships among species of the genus Issatchenkia Kudriavzev

The phylogenetic relatedness of Issatchenkia spp. was estimated from partial rRNA sequences in two regions of the large subunit and one region of the small subunit. I. terricola was the most divergent species of the genus, differing from other members by 18% nucleotide differences in the highly variable 25S-635 region. These data indicate Issatchenkia to be the most divergent ascomycetous yeast genus presently known.     

Phylogenetic relationships among six species of Epistylis inferred from 18S-ITS1 sequences

Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.     

Phylogenetic relationships among isolates of Cryptosporidium: evidence for several new species

Isolates of Cryptosporidium were characterized using nucleotide sequence analysis of the 18S rRNA and dihydrofolate reductase genes and also random-amplified polymorphic DNA analysis. Phylogenetic analysis confirmed the validity of the species of Cryptosporidium examined in this study such as Cryptospordium muris and Cryptosporidium baileyi, and also reinforced evidence from numerous researchers worldwide suggesting that Cryptosporidium parvum is not a single uniform species. The data obtained provided strong support for the validity of Cryptosporidium felis. Evidence suggests that the newly identified marsupial and pig genotypes may also be distinct and valid species, but biological studies are required for confirmation.     

Phylogenetic relationships of annual and perennial wild rice: probing by direct DNA sequencing

Summary The phylogenetic relationships between Asian wild rice strains were analyzed by direct sequencing of PCR-amplified DNA fragments. The sequence of three introns located in the phytochrome gene was determined for eight strains of the Asian wild rice, Oryza rufipogon, and one strain of the related African species, Oryza longistaminata. The number of nucleotide substitutions per site between various strains within a single species, O. rufipogon, ranged between 0.0017 and 0.0050, while those between two related species, O. rufipogon and O. longistaminate, were 0.043–0.049 (23–26 within 532 bp). Taken together with the sequence differences of the 10-kDa prolamin gene, a model is proposed for the phylogenetic relationships and evolutionary history of annuals and perennials within O. rufipogon.     

Nucleolar relationships in some Australian Chironomus species

Members of a group of Australian Chironomus species in the pseudothummi complex show wide variation in number and location of nucleolar organizing regions (NORs). The structure of these regions has been examined by phase contrast microscopy and silver banding of salivary gland polytene chromosomes. Presence of nucleoli was also checked on other types of chromosomes in some species. The contribution of the silver banding technique to nucleolar studies in these chironomid chromosomes is discussed. Nucleoli often seem to emerge from groups of (up to 9) bands. Further studies are necessary to confirm the presence of rRNA cistrons in all of these bands. Banding differences, in particular absence of bands from homologous regions of some species which have smaller nucleoli or lack particular nucleoli, have been found. In the case of Ch. tepperi, however, little banding difference is apparent in the 16B region between the N(IV)⁺ and N(IV)^– chromosomes, although in situ hybridization (Eigenbrod 1978) shows a deletion of rRNA cistrons in the N(IV)^– stock. Differences in heterochromatin amount have also been observed at different NORs. A scheme for the evolution of nucleolar-producing regions in this Chironomus group in terms of these and other known chromosomal changes is presented and discussed.     

Serological relationships among some Pichia species.

Antigenic analyses of five species of the genus Pichia were carried out for taxonomic study by the slide agglutination method using monospecific and absorbed antisera and the agglutinin absorption technique. Comparative studies were also performed with a few strains of each of the same species and their classifications are discussed with respect to the antigenic structures and the patterns of proton magnetic resonance (PMR) spectra of their cell wall polysaccharides. ichia delftensis and Pichia zaruensis possessed thermostable antigens 1,2,5 and 11, and the former had also thermoabile antigen m. Both species were closely related to Candida krusei. Pichia toletana possessed thermostable antigens 1,2,5,11,17 and 49. Pichia bovis contained thermostable antigens 1,2,14,15,16,20 and 21, and it was related to most species of the genus Hansenula, although assimilation of potassium nitrate was negative. Finally, Pichia etchellsii possessed thermostable antigens 1,2,3,4,9 and 14, and was closely related to Pichia vini. Patterns of PMR spectra of mannans of these species also supported their serological relationships. Therfore, P. delftensis, P. zaruensis and P. etchellsii are considered to be the synonyms of Pichia fluxuum, Pichia dispora and P. vini respectively, although P. toletanan and P. bovis are independent species.