The Karyotype of the Hoatzin (Opisthocomus hoazin) - A Phylogenetic Enigma of the Neornithes

The hoatzin (Opisthocomus hoazin Müller, 1776) is a folivorous bird, endemic to the Amazonian region. It presents some unique characteristics, including wing claws and foregut fermentation, which make its phylogenetic relationship to other birds difficult to determine. There have been various attempts to place it among the Galliformes, Gruiformes, Musophagiformes, Cuculiformes, and Charadriiformes, but phylogenetic analyses always show low supporting values. Nowadays, the hoatzin is included in the monotypic order Opisthocomiformes, but the relationship of this order to other groups of birds is still unclear. Although its karyotype resembles the typical avian model, fissions of the syntenic groups corresponding to chicken chromosomes 1 and 2 and 2 fusions were found. The presence of 18S rDNA clusters in 2 pairs of microchromosomes is another derived character. Hence, different rearrangements were detected in the karyotype of the hoatzin, indicating it has been derived from the putative ancestral karyotype by the occurrence of fissions and fusions. However, as these rearrangements are not exclusive to O. hoazin, they do not clarify the phylogenetic position of this enigmatic species.

Download Full-text

Fungicide Sensitivity and Phylogenetic Relationship of Anthracnose Fungi Isolated from Various Fruit Crops in Japan

Plant Disease ◽

10.1094/pd-90-0506 ◽

2006 ◽

Vol 90 (4) ◽

pp. 506-512 ◽

Cited By ~ 58

Author(s):

Wen-Hsin Chung ◽

Hideo Ishii ◽

Kumiko Nishimura ◽

Masako Fukaya ◽

Kazutaka Yano ◽

...

Keyword(s):

Phylogenetic Relationship ◽

Colletotrichum Gloeosporioides ◽

Phylogenetic Analyses ◽

Interspecific Variation ◽

Fruit Crops ◽

Fungicide Sensitivity ◽

Genetic Groups ◽

Molecular Phylogenetic ◽

Relationship Of ◽

The Relationship

Anthracnose diseases of fruit crops are mainly caused by Colletotrichum gloeosporioides and C. acutatum. In these Colletotrichum species, intra- and interspecific variation in fungicide sensitivity has been reported; however, the relationship between fungicide sensitivity and molecular phylogeny has not been analyzed. Fifty-one isolates from 10 fruit crops, acacia, and tea were tested for their sensitivities to thiophanate-methyl, diethofencarb, and iminoctadine-triacetate, and their internal transcribed spacer (ITS) and 5.8S regions of rDNA were analyzed. C. gloeosporioides isolates were divided into sensitive, less sensitive, intermediate resistant, or resistant to the three fungicides. In contrast, C. acutatum isolates were all less sensitive. In molecular phylogenetic analyses, C. gloeosporioides isolates fell into the same genetic group, whereas C. acutatum isolates were placed into two genetic groups. Although phylogenetic relationship was not closely related to fungicide sensitivity, the isolates of C. gloeosporioides most resistant to iminoctadine-triacetate were found in the same phylogenetic subgroup.

Download Full-text

Morphological and molecular characterization of Megalobatrachonema hainanensis sp. nov. (Nematoda: Ascaridida), with phylogenetic position of Megalobatrachonema in Cosmocercoidea

Journal of Helminthology ◽

10.1017/s0022149x18001086 ◽

2018 ◽

Vol 94 ◽

Author(s):

H.-X. Chen ◽

L.-P. Zhang ◽

L. Li

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Hainan Island ◽

Phylogenetic Position ◽

Phylogenetic Study ◽

Its1 Sequence ◽

Nematode Parasites ◽

Relationship Of ◽

The Relationship

Abstract The genus Megalobatrachonema is a rare group of nematode parasites within Ascaridida. The systematic status of Megalobatrachonema in the superfamily Cosmocercoidea (Ascaridida) has long been controversial. The relationship of Megalobatrachonema and Chabaudgolvania remains unsolved. In the present study, a new species of Megalobatrachonema, M. hainanensis sp. nov., was described based on specimens collected in Amolops hainanensis (Boulenger) and Hylarana spinulosa (Smith) (Amphibia: Anura) from Hainan Island, China. The large ribosomal DNA (28S) and internal transcribed spacer (ITS1-5.8S-ITS2) were also sequenced for molecular identification and phylogenetic study. Phylogenetic analyses using maximum likelihood (ML) inference and Bayesian inference (BI) based on 28S and ITS1 sequence data, respectively, supported that Megalobatrachonema is a member of the family Kathlaniidae. In addition, the genetic comparison and phylogenetic results based on ITS1 sequence data also supported that the genus Chabaudgolvania should be considered as a synonym of Megalobatrachonema.

Download Full-text

The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽

10.1093/genetics/146.3.995 ◽

1997 ◽

Vol 146 (3) ◽

pp. 995-1010 ◽

Cited By ~ 1

Author(s):

Rafael Zardoya ◽

Axel Meyer

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Large Data ◽

Molecular Data ◽

Phylogenetic Position ◽

Data Set ◽

Living Fossil ◽

Latimeria Chalumnae ◽

Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

Download Full-text

Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽

10.1515/mammalia-2017-0081 ◽

2019 ◽

Vol 83 (2) ◽

pp. 180-189 ◽

Cited By ~ 2

Author(s):

Adam W. Ferguson ◽

Houssein R. Roble ◽

Molly M. McDonough

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Alternative Hypothesis ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Sister Relationship ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Molecular Phylogenetic ◽

Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

Download Full-text

Anterastes davrazensis sp. n. (Orthoptera, Tettigoniidae): morphology, song and 16S rDNA phylogeny

Zootaxa ◽

10.11646/zootaxa.3401.1.4 ◽

2012 ◽

Vol 3401 (1) ◽

pp. 49 ◽

Cited By ~ 1

Author(s):

SARP KAYA ◽

DRAGAN CHOBANOV ◽

BATTAL ÇIPLAK

Keyword(s):

New Species ◽

16S Rdna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Strong Support ◽

16S Rdna Sequence ◽

Rdna Sequence Data ◽

Male Calling ◽

Relationship Of ◽

The Relationship

The new species Anterastes davrazensis sp. n. (Orthoptera, Tettigoniidae) is described from south-eastern Turkey. Description, diagnosis and relationships of the new species were studied utilizing morphology, male calling songs and 16S rDNA sequence data from all species in the genus. Morphology and song syllable structure indicate A. davrazensis sp. n. is related to A. uludaghensis. Phylogenetic analyses based on representative haplotypes of 16S rDNA, using Sureyaella bella, Parapholidoptera distincta and Bolua turkiyae as outgroups, also suggested strong support to the relationship of these two species. A. davrazensis sp. n. differs from its closest relative A. uludaghensis by the higher number of stridulatory pegs and the song, consisting of irregular syllable groups.

Download Full-text

Phylogenetic Analysis of Mitogenomic Data Sets Resolves the Relationship of Seven Macropostrongyloides Species from Australian Macropodid and Vombatid Marsupials

Pathogens ◽

10.3390/pathogens9121042 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1042 ◽

Cited By ~ 1

Author(s):

Tanapan Sukee ◽

Anson V. Koehler ◽

Ross Hall ◽

Ian Beveridge ◽

Robin B. Gasser ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Mitochondrial Protein ◽

Parasitic Nematodes ◽

Data Sets ◽

Protein Amino Acid ◽

Protein Coding ◽

Relationship Of ◽

The Relationship ◽

Swamp Wallaby

Nematodes of the genus Macropostrongyloides inhabit the large intestines or stomachs of macropodid (kangaroos and wallabies) and vombatid (wombats) marsupials. This study established the relationships of seven species of Macropostrongyloides using mitochondrial (mt) protein amino acid sequence data sets. Phylogenetic analyses revealed that species of Macropostrongyloides (M. lasiorhini, M. baylisi, M. yamagutii, M. spearei, M. mawsonae and M. woodi) from the large intestines of their hosts formed a monophyletic assemblage with strong nodal support to the exclusion of M. dissimilis from the stomach of the swamp wallaby. Furthermore, the mitochondrial protein-coding genes provided greater insights into the diversity and phylogeny of the genus Macropostrongyloides; such data sets could potentially be used to elucidate the relationships among other parasitic nematodes of Australian marsupials.

Download Full-text

A Phylogenomic Approach to Clarifying the Relationship of Mesodinium within the Ciliophora: A Case Study in the Complexity of Mixed-Species Transcriptome Analyses

Genome Biology and Evolution ◽

10.1093/gbe/evz233 ◽

2019 ◽

Vol 11 (11) ◽

pp. 3218-3232

Author(s):

Erica Lasek-Nesselquist ◽

Matthew D Johnson

Keyword(s):

High Throughput Sequencing ◽

Phylogenetic Position ◽

Mixed Species ◽

Data Set ◽

Sequencing Project ◽

Genome Data ◽

Massive Sequencing ◽

Relationship Of ◽

The Relationship

Abstract Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium—M. rubrum, M. major, and M. chamaeleon—being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination—particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate—requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.

Download Full-text

Avirulence gene based RFLP and rep-PCR distinguish the genetic variation of Xanthomonas oryzae pv. oryzae pathotypes in Bangladesh

Plant Science Today ◽

10.14719/pst.1369 ◽

2022 ◽

Vol 9 (1) ◽

pp. 29-40

Author(s):

Mohammad Mahbubul Haque ◽

Md. Mostafa Masud ◽

Samrin Bashar ◽

Mohammad Iqbal Hossain ◽

Md. Zahangir Alam ◽

...

Keyword(s):

Genetic Variation ◽

Bacterial Blight ◽

Phylogenetic Analyses ◽

Control Measures ◽

Avirulence Gene ◽

Effective Control ◽

Repeat Domain ◽

Relationship Of ◽

The Relationship ◽

Pcr Techniques

Bacterial blight (BB) caused by X. oryzae pv. oryzae is one of the devastating diseases of rice mostly in Asia. Genomes of X. oryzae pv. oryzae is highly variable due to rearrangement of the large contents of transposable elements and dynamic changes of X. oryzae pv. oryzae population regulated efficiency of the control measures used for BB management of rice worldwide. In this study, genetic variation of X. oryzae pv. oryzae pathotypes of Bangladesh was studied using aviruelnce gene based RFLP and rep-PCR techniques aimed to formulate pathogen targeted effective control measures against BB of rice. Eight pathotypes of X. oryzae pv. oryzae field isolates were identified based on their reactions against 10 Near Isogenic Lines (NILs). Among eight pathotypes, pathotypes IV and V contained higher number of isolates which were 30.13% and 23.01% respectively while pathotype VIII revealed as minimum containing only 2.51% of total isolates. These eight pathotypes were studied for their genetic variation by RFLP using avrBs3 repeat domain as probe. The results conceded that Bangladeshi X. oryzae pv. oryzae strains seem carrying a minimum of two and maximum of nine avrBs3 family genes homologs. The resistance phenotype on IRBB7 and IRBB10 NILs also indicated presence of two major avrBs3 family genes viz. avrxa7 and avrXa10 in some pathotypes. Relationship of phylogenicity exhibited that X. oryzae pv. oryzae pathotypes assorted into two RFLP haplotypes as well as these haplotypes are largely distributed in Bangladesh. Phylogenetic analyses carried out by (REP, ERIC), rep-PCR and BOX depicted the presence of two main molecular haplotypes of X. oryzae pv. oryzae pathotypes. The relationship between pathotypes and molecular haplotypes of X. oryzae pv. oryzae in Bangladesh indicated that the same lineage possesses different pathotypes and different lineage possesses different pathotypes. The results indicated that eight different pathotypes might have originated from common inherited haplotypes with a wide genetic variation.

Download Full-text

Enhanced genome annotation strategy provides novel insights on the phylogeny of Flaviviridae

10.1101/674333 ◽

2019 ◽

Cited By ~ 3

Author(s):

Adriano de Bernardi Schneider ◽

Denis Jacob Machado ◽

Daniel Janies

Keyword(s):

Phylogenetic Relationship ◽

Soybean Cyst Nematode ◽

Phylogenetic Analyses ◽

Optimality Criteria ◽

Entire Family ◽

Close Phylogenetic Relationship ◽

The Family ◽

Relationship Of ◽

Reference Genomes ◽

Annotation Strategy

The ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and zika, demand a greater understanding of how these viruses evolve, emerge and spread in order to respond. Central to this understanding is an updated phylogeny of the entire family. Unfortunately, most cladograms of Flaviviridae focus on specific lineages, ignore outgroups, and rely on midpoint rooting, hampering their ability to test ingroup monophyly and estimate ingroup relationships. This problem is partly due to the lack of fully annotated genomes of Flaviviridae, which has genera with slightly different gene content, hindering genome analysis without partitioning. To tackle these problems, we developed an annotation pipeline for Flaviviridae that uses a combination of ab initio and homology-based strategies. The pipeline recovered 100% of the genes in reference genomes and annotated over 97% of the expected genes in the remaining non curated sequences. We further demonstrate that the combined analysis of genomes of all genera of Flaviviridae (Flavivirus, Hepacivirus, Pegivirus, and Pestivirus), as made possible by our annotation strategy, enhances the phylogenetic analyses of these viruses for all optimality criteria that we tested (parsimony, maximum likelihood, and posterior probability). The final tree sheds light on the phylogenetic relationship of viruses that are divergent from most Flaviviridae and should be reclassified, especially the soybean cyst nematode virus 5 (SbCNV-5) and the Tamana bat virus. We also corroborate the close phylogenetic relationship of dengue and zika viruses with an unprecedented degree of support.

Download Full-text

Pipunculidae (Diptera) from Australia: the genera Cephalops Fallén and Beckerias Aczél

Invertebrate Systematics ◽

10.1071/it9920143 ◽

1992 ◽

Vol 6 (1) ◽

pp. 143 ◽

Cited By ~ 2

Author(s):

MDe Meyer ◽

P Grootaert

Keyword(s):

Phylogenetic Relationship ◽

Relationship Of ◽

The Relationship

Pipunculid representatives of the genera Cephalops and Beckerias in Australia are revised. Eight species, of which six (Cephalops ariadneae, sp. nov., C. caeruleimontanus, sp. nov., C. cochleatus, sp. nov., C. flaviventris, sp. nov., C. robustus, sp. nov., and C. terraereginensis, sp. nov.) are new to science, are recognised. Three species, formerly placed under Cephalops, are placed in new generic combinations: Microcephalops anthracias (Perkins), M. homoeophanes (Perkins) and M. microdes (Perkins). The relationship of the Australian fauna with other adjacent faunas is discussed, and the phylogenetic relationship of the species is reviewed. A key for the Australian Cephalops and Beckerias species is provided.

Download Full-text