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PubMed2003

Candida albicans clades.

DNA fingerprinting with the complex probe Ca3 has revealed the following five Candida albicans clades: group I, group II, group III, group SA and group E. These groups exhibit geographical specificity. Group SA is relatively specific (i.e., highly enriched) to South Africa, group E is relatively specific to Europe, and group II is absent in the Southwest USA and South America. The maintenance of deep-rooted clades side by side in the same geographical locale and the apparent absence of subclade structure suggest little recombination between clades, but higher rates of recombination within clades. Exclusive 5-fluorocytosine resistance in the majority of group I isolates reinforces the above conclusions on recombination, and demonstrates that clades differ phenotypically. The ramifications of these findings with regard to pathogenesis are discussed. In particular, these findings lay to rest the idea that one strain represents all strains of C. albicans, support the need for a worldwide analysis of population structure and clade-specific phenotypic characteristics, and demonstrate that in the future, pathogenic characteristics must be analyzed in representatives from all five clades.

Candida albicans↗

PubMed1997

Cross-clade immune responses after immunization with a whole-killed gp120-depleted human immunodeficiency virus type-1 immunogen in incomplete Freund's adjuvant (HIV-1 immunogen, REMUNE) in human immunodeficiency virus type-1 seropositive subjects.

Lymphocyte proliferation responses to gp120-depleted HZ321 virus (clade A) antigen were compared to BAL human immunodeficiency virus (HIV) virus antigen (clade B) responses, clade E HIV virus antigen responses, and purified native p24 antigen responses in 15 human immunodeficiency virus type-1 (HIV-1) seropositive subjects immunized with a whole-killed inactivated gp120-depleted HIV-1 antigen in Incomplete Freund's adjuvant (HIV-1 immunogen, REMUNE). A significant increase in lymphocyte proliferation to HZ321 antigen was observed after immunization with the HIV-1 immunogen (p = 0.02). A strong association was demonstrated between the HIV-1 immunizing antigen, HZ321, and native p24 antigen responses (r = 0.80, p < 0.0001). Furthermore, a strong association in terms of proliferative responses was demonstrated between HZ321 virus (clade A) responses and BAL virus (clade B) (r = 0.95, p < 0.0001) and clade E virus antigen (r = 0.92, p < 0.0001). Proliferative responses to HIV antigens also correlated with baseline CD4 counts. Taken together, these results support the specificity of immune responses induced by REMUNE (HIV-1 immunogen). The development of cross-reactive immune responses between clades and to the more conserved epitopes of the virus have implications in the development of therapeutic and prophylactic HIV vaccines.

AIDS Vaccines↗

PubMed2006

Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown Clades.

Inference of evolutionary relationships between nematodes is severely hampered by their conserved morphology, the high frequency of homoplasy, and the scarcity of phylum-wide molecular data. To study the origin of nematode radiation and to unravel the phylogenetic relationships between distantly related species, 339 nearly full-length small-subunit rDNA sequences were analyzed from a diverse range of nematodes. Bayesian inference revealed a backbone comprising 12 consecutive dichotomies that subdivided the phylum Nematoda into 12 clades. The most basal clade is dominated by the subclass Enoplia, and members of the order Triplonchida occupy positions most close to the common ancestor of the nematodes. Crown Clades 8-12, a group formerly indicated as "Secernentea" that includes Caenorhabditis elegans and virtually all major plant and animal parasites, show significantly higher nucleotide substitution rates than the more basal Clades 1-7. Accelerated substitution rates are associated with parasitic lifestyles (Clades 8 and 12) or short generation times (Clades 9-11). The relatively high substitution rates in the distal clades resulted in numerous autapomorphies that allow in most cases DNA barcode-based species identification. Teratocephalus, a genus comprising terrestrial bacterivores, was shown to be most close to the starting point of Secernentean radiation. Notably, fungal feeding nematodes were exclusively found basal to or as sister taxon next to the 3 groups of plant parasitic nematodes, namely, Trichodoridae, Longidoridae, and Tylenchomorpha. The exclusive common presence of fungivorous and plant parasitic nematodes supports a long-standing hypothesis that states that plant parasitic nematodes arose from fungivorous ancestors.

Amino Acid Substitution↗

PubMed2002

Genetic divergence of human immunodeficiency virus type 1 Ethiopian clade C reverse transcriptase (RT) and rapid development of resistance against nonnucleoside inhibitors of RT.

We sequenced and phylogenetically analyzed the reverse transcriptase (RT) region of five human immunodeficiency virus type 1 isolates from treatment-naive Ethiopian émigrés to Israel. Heteroduplex mobility assays were performed to confirm the clade C status of env genomic regions. The RT sequences showed that the strains clustered phylogenetically with clade C viruses, and a KVEQ-specific motif of silent mutations (amino acids 65, 106, 138, and 161, respectively) at resistance sites was present in the polymerase region of all studied Ethiopian isolates and subtype C reference strains. In addition, many other silent mutations were observed in the clade C viruses at various resistance sites. In general, the Ethiopian isolates were more closely related genotypically to a clade C reference strain from Botswana (southern Africa) than to previously sequenced Ethiopian reference strains. Genotypic analysis showed that two Ethiopian isolates naturally harbored the mutations K70R and G190A associated with resistance to ZDV and nonnucleoside reverse transcriptase inhibitors, respectively. Phenotypic assays revealed that the K70R substitution in this context did not reduce susceptibility to ZDV, whereas the G190A substitution resulted in high-level resistance to nevirapine (NVP). Moreover, variants resistant to NVP, delavirdine (DLV), and efavirenz (EFV) were more rapidly selected at lower drug doses culture with clade C than with clade B wild-type isolates. In the case of subtype C, selection with NVP and/or EFV led to the appearance of several previously unseen mutations in RT, i.e., V106M and S98I, as well as other mutations that have been previously reported (e.g., K103N, V106A, V108I, and Y181C). After selection with DLV, a polymorphism, A62A, initially observed in the Ethiopian isolate 4762, mutated to A62V; the latter is a secondary substitution associated with multidrug resistance against nucleoside RT inhibitors. Phenotypic analysis of clade C mutants selected against NVP, DLV, and EFV revealed broad cross-resistance, particularly in regard to NVP and DLV. These findings suggest that RT genotypic diversity may influence the emergence of drug resistance.

Alkynes↗

PubMed2004

Clade-specific flucytosine resistance is due to a single nucleotide change in the FUR1 gene of Candida albicans.

Population studies have indicated that natural resistance to flucytosine (5FC) in Candida albicans is limited to one of the five major clades, clade I. In addition, while 73% of clade I isolates are less susceptible to 5FC (MIC >/= 0.5 microg/ml), only 2% of non-clade I isolates are less susceptible. In order to determine the genetic basis for this clade-specific resistance, we sequenced two genes involved in the metabolism of 5FC that had previously been linked to resistance (cytosine deaminase and uracil phosphoribosyltransferase), in 48 isolates representative of all clades. Our results demonstrate that a single nucleotide change from cytosine to thymine at position 301 in the uracil phosphoribosyltransferase gene (FUR1) of C. albicans is responsible for 5FC resistance. The mutant allele was found only in group I isolates. The 5FC MICs for strains without copies of the mutant allele were almost exclusively </=0.25 microg/ml, those for strains with one copy of the mutant allele were >/=0.5 microg/ml, and those for strains with two copies of the mutant allele were >/=16 microg/ml. Thus, the two alleles were codominant. The presence of this allele is responsible for clade I-specific resistance to 5FC within the C. albicans population and thus by inference is likely to be the major underlying 5FC resistance mechanism in C. albicans. This represents the first description of the genetic mutation responsible for 5FC resistance.

Amino Acid Sequence↗

PubMed1995

Cross-clade neutralization of primary isolates of human immunodeficiency virus type 1 by human monoclonal antibodies and tetrameric CD4-IgG.

We have tested three human monoclonal antibodies (MAbs) IgG1b12, 2G12, and 2F5) to the envelope glycoproteins of human immunodeficiency virus type 1 (HIV-1), and a tetrameric CD4-IgG molecule (CD4-IgG2), for the ability to neutralize primary HIV-1 isolates from the genetic clades A through F and from group O. Each of the reagents broadly and potently neutralized B-clade isolates. The 2F5 MAb and the CD4-IgG2 molecule also neutralized strains from outside the B clade, with the same breadth and potency that they showed against B-clade strains. The other two MAbs were able to neutralize a significant proportion of strains from outside the B clade, although there was a reduction in their efficacy compared with their activity against B-clade isolates. Neutralization of isolates by 2F5 correlated with their possession of the LDKW motif in a segment of gp41 near the membrane-spanning domain. The other two MAbs and CD4-IgG2 recognize discontinuous binding sites on gp120, and so no comparison between genetic sequence and virus neutralization was possible. Our data show that a vaccine based on the induction of humoral immunity that is broadly active across the genetic clades is not impossible if immunogens that express the epitopes for MAbs such as 2F5, 2G12, and IgG1b12 in immunogenic configurations can be created. Furthermore, if the three MAbs and CD4-IgG2 produce clinical benefit in immunotherapeutic trials in the United States or Europe, they may also do so elsewhere in the world.

Acquired Immunodeficiency Syndrome↗

PubMed2002

Human monoclonal antibodies specific for conformation-sensitive epitopes of V3 neutralize human immunodeficiency virus type 1 primary isolates from various clades.

The epitopes of the V3 domain of the human immunodeficiency virus type 1 (HIV-1) gp120 glycoprotein have complex structures consisting of linear and conformational antigenic determinants. Anti-V3 antibodies (Abs) recognize both types of elements, but Abs which preferentially react to the conformational aspect of the epitopes may have more potent neutralizing activity against HIV-1, as recently suggested. To test this hypothesis, human anti-V3 monoclonal Abs (MAbs) were selected using a V3 fusion protein (V3-FP) which retains the conformation of the third variable region. The V3-FP consists of the V3(JR-CSF) sequence inserted into a truncated form of murine leukemia virus gp70. Six human MAbs which recognize epitopes at the crown of the V3 loop were selected with the V3-FP. They were found to react more strongly with molecules displaying conformationally intact V3 than with linear V3 peptides. In a virus capture assay, these MAbs showed cross-clade binding to native, intact virions of clades A, B, C, D, and F. No binding was found to isolates from subtype E. The neutralizing activity of MAbs against primary isolates was determined in three assays: the GHOST cell assay, a phytohemagglutinin-stimulated peripheral blood mononuclear cell assay, and a luciferase assay. While these new MAbs displayed various degrees of activity, the pattern of cross-clade neutralization of clades A, B, and F was most pronounced. The neutralization of clades C and D viruses was weak and sporadic, and neutralization of clade E by these MAbs was not detected. Analysis by linear regression showed a highly significant correlation (P < 0.0001) between the strength of binding of these anti-V3 MAbs to intact virions and the percent neutralization. These studies demonstrate that human MAbs to conformation-sensitive epitopes of V3 display cross-clade reactivity in both binding to native, intact virions and neutralization of primary isolates.

Antibodies, Monoclonal↗

PubMed2002

CCR5 and CXCR4 usage by non-clade B human immunodeficiency virus type 1 primary isolates.

CCR5 and CXCR4 usage has been studied extensively with a variety of clade B human immunodeficiency virus type 1 (HIV-1) isolates. The determinants of CCR5 coreceptor function are remarkably consistent, with a region critical for fusion and entry located in the CCR5 amino-terminal domain (Nt). In particular, negatively charged amino acids and sulfated tyrosines in the Nt are essential for gp120 binding to CCR5. The same types of residues are important for CXCR4-mediated viral fusion and entry, but they are dispersed throughout the extracellular domains of CXCR4, and their usage is isolate dependent. Here, we report on the determinants of CCR5 and CXCR4 coreceptor function for a panel of non-clade B isolates that are responsible for the majority of new HIV-1 infections worldwide. Consistent with clade B isolates, CXCR4 usage remains isolate dependent and is determined by the overall content of negatively charged and tyrosine residues. Residues in the Nt of CCR5 that are important for fusion and entry of clade B isolates are also important for the entry of all non-clade B HIV-1 isolates that we tested. Surprisingly, we found that in contrast to clade B isolates, a cluster of residues in the second extracellular loop of CCR5 significantly affects fusion and entry of all non-clade B isolates tested. This points to a different mechanism of CCR5 usage by these viruses and may have important implications for the development of HIV-1 inhibitors that target CCR5 coreceptor function.

Amino Acid Sequence↗

PubMed2007

HPA axis activity and neuropathogenesis in HIV-1 clade C infection.

A disturbance in the activity of the hypothalamic-pituitary-adrenal (HPA) axis has been reported among individuals with HIV-1 infection. However, these studies have been carried out in the West where the infecting clade is clade B. HIV-1 infection is rapidly spreading in various parts of South East Asia, including India, where the HIV-1 infecting clade is largely clade C. An investigation of HPA axis activity in this type of infection is warranted since there are many structural differences between clades B and C. This study was carried out to investigate whether HIV-1 infection clade C interferes with the functions of the hippocampus and thereby affects the HPA axis. We tested the hypothesis that when hippocampus activity is disturbed, it leads to the development of neuropathogenesis in HIV-1 C-clade infected individuals. This study included asymptomatic HIV-1 seropositive individuals (n=117) and, age-matched, HIV-1 seronegative controls (n=29). Neuroendocrine function of the HPA axis was evaluated using plasma levels of cortisol, ACTH, and DHEA-S, both in the morning (0800-1000 hr) and evening (2000-2200 hr). A significant elevation of cortisol levels during A.M. and P.M. hours was observed in HIV-1 infected individuals when compared to the controls. Interestingly, no significant change in ACTH level was observed in HIV-1 seropositive subjects, either during A.M or P.M. Elevated levels of cortisol in HIV-1 seropositive subjects appear to be independent of ACTH and may be the result of a defective negative feedback mechanism. On the other hand, a significant decrease in the plasma levels of DHEA-S was observed during A.M. and P.M. hours in HIV-1 infected individuals, leading to an increased cortisol to DHEA-S ratio. Since increased levels of cortisol and decreased levels of DHEA-S are related to the development of neuropathogenesis, it is hypothesized that a study of the development of neurocognitive deficits among HIV-1 seropositive individuals in India is warranted.

Adolescent↗

PubMed2002

Co-receptor usage and HIV-1 intra-clade C polymorphisms in the protease and reverse transcriptase genes of HIV-1 isolates from Ethiopia and Botswana.

Knowledge of baseline amino acid substitutions arising at certain critical positions in the HIV-1 non-clade-B protease (PR) and reverse transcriptase (RT) enzymes may yield important information with regard to anticipation of responses to antiretroviral treatment and development of drug resistance. We have compared RT and PR sequences within HIV-1 clade C strains isolated from 14 treatment-naive patients originating from Ethiopia and Botswana with those of PR and RT consensus subtype B RT and PR sequences. Variations in the frequency of natural polymorphisms were observed in clade C isolates at drug-resistance sites. Intra-clade C divergence among mutations within PR was statistically significant while that within RT was not. Only a M361 substitution in PR was shared among almost all isolates from Ethiopia and Botswana. Analysis of the co-receptor usage of clade C isolates from Ethiopia and Botswana supports the known preferential usage of the CCR5 co-receptor by HIV-1 clade C strains. No Ethiopian or Botswanian isolates exclusively used the CXCR4 co-receptor, which is consistent with most data obtained with HIV-1 clade B isolates.

Amino Acid Substitution↗

PubMed1997

HIV infection and HIV-1 clades among pregnant women in Harare, Zimbabwe.

OBJECTIVE: To determine HIV-1 seropositivity and HIV-1 clades/subtypes among pregnant women attending different clinics in Harare, Zimbabwe. DESIGN: A prospective study. SUBJECTS: 206 pregnant women attending Edith Opperman and Budiriro clinics in Harare. MAIN OUTCOME MEASURES: Frequency distribution of the various HIV-1 clades and rate of HIV-1 seropositivity. RESULTS: Results obtained showed that out of the 206 pregnant women screened, 60 (29.1%) were HIV-1 seropositive. The most predominant clade was HIV-1 clade C (66.6%) whereas HIV-1 clades A and B accounted for 48.3% and 33.3% of HIV-1 clades respectively. Results also revealed dual infections with clades A and C (45%), A and D (10%), B and C (30%) and multiple infections with A, B, C and D (6.6%) whereas two (3.3%) were non-reactive. CONCLUSION: Finally, the data on HIV-1 clades are of immense immunological, molecular and epidemiological importance in Harare, Zimbabwe and should serve as base line data for future investigations in the country.

Amino Acid Sequence↗

PubMed2026

Molecular characterization and biological characteristics of a highly pathogenic recombinant ALV-J strain (HUE2023) with cross-clade gp85 recombination.

Avian leukosis virus subgroup J (ALV-J) has undergone extensive diversification into phylogenetically distinct clades, yet whether recombination between these clades within the gp85 envelope glycoprotein generates variants with altered pathogenicity has received little direct investigation. A field strain (HUE2023) was recovered from breeding roosters displaying vascular tumors. The viral genome was sequenced and subjected to phylogenetic and recombination analyses. The three-dimensional structure of gp85 was predicted with AlphaFold3; electrostatic surface potentials and surface hydrophobicity were computed using the Adaptive Poisson-Boltzmann Solver and the Eisenberg hydrophobicity scale, respectively. Pathogenicity and immunosuppressive effects were assessed in Hy-Line Brown chickens. Recombination analysis revealed that HUE2023 is an inter-clade recombinant derived from Clade 1.1 (major parent: JS14NT01) and Clade 1.2 (minor parent: JS09GY3). A single-residue deletion at position 61 within receptor-binding domain 1 (RBD-1), unique to the recombinant, induced a localized conformational rearrangement that generated a concentrated electronegative surface patch and a contiguous hydrophobic pocket not observed in either parental gp85. Animal challenge showed that HUE2023 is highly pathogenic: female chickens in the high-dose group reached only 61% survival and displayed significant growth retardation (P < 0.05) together with marked immunosuppression. The recombination in the RBD-1 led to local conformational rearrangement, resulting in a concentrated and negatively charged surface area as well as a continuous hydrophobic pocket, which were never present in any of the parental gp85 sequences. These results indicate that gp85 recombination across clades can yield variants with fundamentally altered receptor-binding surfaces and argue for integrating structural surveillance into ALV-J monitoring programmes.

Animals↗

PubMed2006

Strong purifying selection on the Odysseus gene in two clades of sibling species of the Drosophila montium species subgroup.

The Odysseus (OdsH) gene was duplicated from its ancestral neuron-expressed gene, unc-4, and then evolved very rapidly under strong positive Darwinian selection as a speciation gene causing hybrid-male sterility between closely related species of the Drosophila simulans clade. Has OdsH also experienced similar positive selection between Drosophila sibling species other than those of the simulans clade? We cloned and sequenced OdsH and unc-4 from two clades of the Drosophila montium species subgroup, the Drosophila lini and the Drosophila kikkawai clades. The ratios of Ka/Ks for OdsH were remarkably low between sibling species of these two clades, suggesting that OdsH has been subjected to strong purifying selection in these two clades.

Amino Acid Sequence↗

PubMed2026

Saliva versus lesion swabs for PCR diagnosis of acute-phase clade Ib mpox in Uganda: a prospective matched hospital cohort study.

BACKGROUND: As clade Ib mpox expands through HIV-affected populations in east and central Africa, diagnostic specimen selection should balance accuracy, accessibility, and operational feasibility in outbreak settings. Here, we aimed to compare the diagnostic performance of matched plasma, saliva, genital, anal, and skin specimens during the acute rash phase of clade Ib mpox to identify clinically practical and high-yield sampling approaches for outbreak response and clinical care. METHODS: We conducted a prospective cohort study of 155 adults (median age 30 years, IQR 25-36) hospitalised at Uganda's national mpox referral hospital. The specimens were collected between March 3 and April 10, 2025, during the clade Ib outbreak. All participants were admitted with suspected mpox and were subsequently confirmed by MPXV PCR. We collected 836 clinical specimens (acid citrate dextrose plasma, saliva, genital swabs, anal swabs, and skin swabs) during the acute phase (visit 1; 14 days [SD 2] after systemic symptom onset) and at approximately 3 months (visit 2). A matched acute-phase subset (n=80) provided concurrent plasma, saliva, genital, and skin specimens for within-participant comparisons. MPXV DNA was quantified by F3L real-time quantitative PCR, and cycle threshold (Ct) values were compared using paired Wilcoxon signed-rank tests. Whole-genome sequencing of selected acute specimens confirmed clade assignment. FINDINGS: In the matched subset at visit 1, PCR positivity was high in saliva (78 [98%] of 80), skin swabs (78 [98%] of 80), and genital swabs (77 [96%] of 80). Results for the saliva closely mirrored genital and skin swab results, supporting saliva as a high-yield alternative when lesion sampling is painful, operationally difficult, or unacceptable. Plasma had substantially lower sensitivity (34 [43%] of 80) and showed poor agreement with mucocutaneous compartments. At 3 months, persistent MPXV DNA was rare (ten [9%] of 109) and clustered among people with HIV, including the only two participants with persistent plasma positivity. All sequenced genomes clustered within clade Ib. INTERPRETATION: During the established rash phase (14 days [SD 2] after onset), saliva provides diagnostic yield similar to that provided by lesion swabs for clade Ib mpox in this hospitalised cohort. These findings are restricted to this sampling window; further studies are needed to define performance in prodromal, pre-rash, and asymptomatic infection. FUNDING: CEPI through its Centralised Laboratory Network.

Adult↗

PubMed2004

Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes.

Many phylogenetic analyses that include numerous terminals but few genes show high resolution and branch support for relatively recently diverged clades, but lack of resolution and/or support for "basal" clades of the tree. The various benefits of increased taxon and character sampling have been widely discussed in the literature, albeit primarily based on simulations rather than empirical data. In this study, we used a well-sampled gene-tree analysis (based on 100 mitochondrial genomes of higher teleost fishes) to test empirically the efficiency of different methods of data sampling and phylogenetic inference to "correctly" resolve the basal clades of a tree (based on congruence with the reference tree constructed using all 100 taxa and 7990 characters). By itself, increased character sampling was an inefficient method by which to decrease the likelihood of "incorrect" resolution (i.e., incongruence with the reference tree) for parsimony analyses. Although increased taxon sampling was a powerful approach to alleviate "incorrect" resolution for parsimony analyses, it had the general effect of increasing the number of, and support for, "incorrectly" resolved clades in the Bayesian analyses. For both the parsimony and Bayesian analyses, increased taxon sampling, by itself, was insufficient to help resolve the basal clades, making this sampling strategy ineffective for that purpose. For this empirical study, the most efficient of the six approaches considered to resolve the basal clades when adding nucleotides to a dataset that consists of a single gene sampled for a small, but representative, number of taxa, is to increase character sampling and analyze the characters using the Bayesian method.

Animals↗

PubMed2026

Cytonuclear conflict and reticulate evolution in the Morelloid clade (Solanum, Solanaceae): Insights from genome skimming and network Phylogenomics.

The Morelloid clade (black nightshades) is one of the most strongly supported clades within the megadiverse Solanum genus. It comprises 76 globally distributed, non-spiny herbaceous and suffrutescent species. While often erroneously considered poisonous weeds, several species are economically important as orphan crops. The clade is closely related to tomato and potato but, due to a lack of focused breeding efforts, remains a putative reservoir of genetic diversity for crop improvement. Despite this potential, we lack fundamental knowledge on the evolution of the Morelloid clade. The group includes polyploid species with unknown parental origins-likely reflecting reticulate processes such as hybridization, introgression, and associated backcrossing events. Prior analyses have been unable to disentangle these processes, leaving the mechanisms underlying reticulate evolution in the Morelloid clade poorly understood. Here, we use genome skimming to produce a well-supported maximum likelihood plastid phylogeny from complete circularized plastomes and a coalescent-based species tree from combined Angiosperms353 and conserved ortholog set nuclear markers. Our dataset, composed of previously published data and deep genome skimming from herbarium samples, spans 26 Morelloid species. To investigate phylogenetic discordance, we used a nuclear phylogenetic network, multispecies coalescent simulations, a fused rooted nuclear chloroplast tree, and quantification of nuclear gene tree concordance. We show that incongruence between nuclear and plastid trees is pervasive and cannot be explained by incomplete lineage sorting alone. Instead, our results demonstrate that events consistent with repeated chloroplast capture have shaped the reticulate evolutionary history of the clade, especially among African polyploid and Pan-American diploid lineages.

Phylogeny↗

PubMed1999

Evidence for host-specific clades of tetraphyllidean tapeworms (Platyhelminthes: Eucestoda) revealed by analysis of 18S ssrDNA.

Sequence data from the V4 and V7-V9 variable regions of the 18S small subunit ribosomal DNA (ssrDNA) gene were used to examine relationships among 26 tetraphyllidean and two lecanicephalidean taxa. Newly collected specimens of 21 of the tetraphyllidean species were used to generate ssrDNA sequences that were combined with sequences previously available, including those of two diphyllidean taxa used for outgroup rooting. The sequences were aligned by eye according to secondary structural motifs of the conserved core of the molecule. Of the 1520 sites in the alignment, 874 (58%) were excluded from analysis due to alignment gaps and lack of positional homology as inferred by manual inspection. Genetic variability of the ssrDNA gene regions compared was greater than would be expected, based on the present taxonomy of the ingroup species, and the genetic divergences among tetraphyllidean 'families' and genera were comparable to that among tapeworm orders. Phylogenetic hypotheses were generated by the methods of maximum parsimony and maximum likelihood (GTR + I + Gamma nucleotide substitution model). Four most parsimonious trees resulted from analysis by maximum parsimony. Strict consensus of the four trees supported the monophyly of the Tetraphyllidea, with the lecanicephalidean taxa forming a sister lineage. Among the tetraphyllidean taxa included in the analysis were three major clades: a basal clade including species of the phyllobothriid genera Anthocephalum, Echeneibothrium, Rhinebothrium, Rhodobothrium and Spongiobothrium; a clade uniting the phyllobothriids of the genus Duplicibothrium with the dioecotaeniid genus Dioecotaenia; and a larger sister clade to the Duplicibothrium + Dioecotaenia clade that included the phyllobothriid genera Caulohothrium, Ceratobothrium, Clistobothrium, Paraoryigmatobothrium and Prosobothrium, the litobothriid genus Litobothrium and the onchobothriid genera Acanthobothrium, Calliobothrium, Phoreiobothrium and Platybothrium. Maximum likelihood analysis resulted in a topology that was congruent where nodes were strongly supported by parsimony analysis, but differed in the relative positions of the well-supported clades. In addition,maximum likelihood analysis grouped the lecanicephalidean taxa among the tetraphyllidean taxa, indicating paraphyly of the order Tetraphyllidea as currently defined. Relationships suggested by both methods of analysis reflected common host associations of the taxa better than their current classification, suggesting that coevolution has had a significant role in the evolution of the group.

Animals↗

PubMed2002

One hundred and seventeen clades of euagarics.

This study provides a first broad systematic treatment of the euagarics as they have recently emerged in phylogenetic systematics. The sample consists of 877 homobasidiomycete taxa and includes approximately one tenth (ca. 700 species) of the known number of species of gilled mushrooms that were traditionally classified in the order Agaricales. About 1000 nucleotide sequences at the 5(') end of the nuclear large ribosomal subunit gene (nLSU) were produced for each taxon. Phylogenetic analyses of nucleotide sequence data employed unequally weighted parsimony and bootstrap methods. Clades revealed by the analyses support the recognition of eight major groups of homobasidiomycetes that cut across traditional lines of classification, in agreement with other recent phylogenetic studies. Gilled fungi comprise the majority of species in the euagarics clade. However, the recognition of a monophyletic euagarics results in the exclusion from the clade of several groups of gilled fungi that have been traditionally classified in the Agaricales and necessitates the inclusion of several clavaroid, poroid, secotioid, gasteroid, and reduced forms that were traditionally classified in other basidiomycete orders. A total of 117 monophyletic groups (clades) of euagarics can be recognized on the basis on nLSU phylogeny. Though many clades correspond to traditional taxonomic groups, many do not. Newly discovered phylogenetic affinities include for instance relationships of the true puffballs (Lycoperdales) with Agaricaceae, of Panellus and the poroid fungi Dictyopanus and Favolaschia with Mycena, and of the reduced fungus Caripia with Gymnopus. Several clades are best supported by ecological, biochemical, or trophic habits rather than by morphological similarities.

Basidiomycota↗