Phylogeny of the rock-wallabies, Petrogale (Marsupialia : Macropodidae) based on DNA/DNA hybridisation

2001 ◽  
Vol 49 (5) ◽  
pp. 463 ◽  
Author(s):  
Antoine Campeau-Péloquin ◽  
John A. W. Kirsch ◽  
Mark D. B. Eldridge ◽  
François-Joseph Lapointe
Keyword(s):  
Phylogenetic Relationships ◽  
Species Level ◽  
Sister Taxon ◽  
Late Pliocene ◽  
Full Species ◽  
Outgroup Species ◽  
Dna Hybridisation ◽  
Hybridisation Analysis

DNA/DNA hybridisation analysis was undertaken to resolve the phylogenetic relationships within the chromosomally diverse genus Petrogale. Excepting P. concinna, all full species and three subspecies of P. lateralis were examined; all but four of these 16 taxa were labeled, as were four outgroup species. While demonstrating the ability of the technique to resolve relationships at the species level, our study confirmed that divergence of Petrogale species is recent and occurred during the late Pliocene to mid-Pleistocene. Our data placed the first division within Petrogale species between the monophyletic brachyotis group and the paraphyletic xanthopus plus lateralis/penicillata groups, the latter including P. rothschildi; the subspecies P. l. purpureicollisappears to be intermediate between thelateralis and thepenicillata complexes. However, our data could not resolve most relationships amongst the eastern Petrogale radiation, except for a probable grouping of the species P. herberti,P. inornata,P. penicillata, andP. sharmani. Finally, our results support recent suggestions that Dendrolagus rather than Thylogaleis the sister taxon to Petrogale.

scholarly journals Phylogenetic relationships among accessions in Citrus and related genera based on the insertion polymorphism of the CIRE1 retrotransposon

2020 ◽  
Vol 5 (1) ◽  
pp. 243-251
Author(s):  
Akira Horibata ◽  
Tsuneo Kato
Keyword(s):  
Phylogenetic Relationships ◽  
Sweet Orange ◽  
Point Of View ◽  
Insertion Polymorphism ◽  
Navel Orange ◽  
Citrus Germplasm ◽  
Outgroup Species ◽  
Blood Orange

AbstractA total of 145 accessions of the genus Citrus and related genera, maintained in the Conservation Garden for Citrus Germplasm at the Experimental Farm of Kindai University, Yuasa, Wakayama, Japan, were examined for their phylogenetic relationships. The present classification was conducted using an inter-retrotransposon amplified polymorphism (IRAP) method based on the insertion polymorphism of a retrotransposon, CIRE1, identified in C. sinensis. The objective of this study was to evaluate the applicability of the IRAP method for citrus classification. The constructed dendrogram showed that the 145 accessions and two outgroup species were successfully classified into five major clades. A large number of C. sinensis accessions were divided into three traditional groups, navel orange, sweet orange, and blood orange, almost corresponding to the sub-clades in the dendrogram. Several other accessions belonging to the same species, and also many hybrid cultivars from crossbreeding, were localized into the respective sub-clades or near positions in the dendrogram. Several unclassified accessions could also be located in the dendrogram, suggesting novel relationships with other accessions. It was concluded that the IRAP method based on CIRE1 insertion polymorphism was suitable for the classification of citrus from a molecular point of view.

scholarly journals Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bobby Lim-Ho Kong ◽  
Hyun-Seung Park ◽  
Tai-Wai David Lau ◽  
Zhixiu Lin ◽  
Tae-Jin Yang ◽  
...  
Keyword(s):  
Hong Kong ◽  
Comparative Analysis ◽  
Phylogenetic Relationships ◽  
Species Level ◽  
The Other ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Plant Group ◽  
Ilex Rotunda

AbstractIlex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.

scholarly journals High Intraspecific Genetic Diversity ofNocardia brasiliensis, a Pathogen Responsible for Cutaneous Nocardiosis Found in France: Phylogenetic Relationships by Usingsodandhsp65Genes

2018 ◽  
Vol 2018 ◽  
pp. 1-10
Author(s):  
D. Kosova-Maali ◽  
E. Bergeron ◽  
Y. Maali ◽  
T. Durand ◽  
J. Gonzalez ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Characterization ◽  
Haplotype Diversity ◽  
Species Level ◽  
Genotype 1 ◽  
Tropical Regions ◽  
High Bootstrap ◽  
Almost All ◽  
A New Species ◽  
Immunocompetent Patients

This study aims at genetic characterization and phylogenetic relationships ofNocardia brasiliensisfocusing by using housekeepingrrs,hsp65,andsodAgenes.N. brasiliensisis the species responsible for 80% of cases of actinomycetoma, one form of cutaneous nocardiosis which occurs mainly in tropical regions reaching immunocompetent patients in which the disease can lead to amputation. We analyze 36 indigenous cases ofN. brasiliensisthat happened in France. Phylogenetic analysis targetingrrsgene showed no robustness at phylogenetic nodes level. However, the use of a concatenation ofhsp65andsodAgenes showed that the tested strains surprisingly ranked in 3 well-defined genotypes. Genotypes 2 and 3 were phylogenetically closer to each other and both diverged from genotype 1 sustained by a high bootstrap of 81%. This last genotype hosts all the cases of pulmonary forms (3), the sole cerebral form, and almost all the cases of immunocompromised patients (3 out of 4). Moreover, excepting one of them, all the strains belonging to this group present a susceptibility to imipenem which is not the case in the other genotypes that rarely count among them strains being susceptible to this drug. The haplotype diversity (Hd) ofhsp65(0.927) andsodA(0.885) genes was higher than that ofrrs(0.824). For this gene, we obtained 16 polymorphic sites whereas, forhsp65andsodAgenes, up to 27 and 29 were identified, respectively. This study reveals that these two genes have an important genetic discriminatory power for the evaluation of the intraspecies genetic variability ofN. brasiliensisand they may be useful for identification purposes at species level. This study also reveals the possible existence of a new species harbored by genotype 1.

scholarly journals Behaviour of cranes (family Gruidae) mirrors their phylogenetic relationships

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nela Nováková ◽  
Jan Robovský
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Species Level ◽  
Monophyletic Group ◽  
Molecular Tree ◽  
Behavioural Repertoire ◽  
Over Time

Abstract Background The behavioural repertoire of every species evolved over time and its evolution can be traced through the phylogenetic relationships in distinct groups. Cranes (family Gruidae) represent a small, old, monophyletic group with well-corroborated phylogenetic relationships on the species level, and at the same time they exhibit a complex and well-described behavioural repertoire. Methods We therefore investigated the evolution of behavioural traits of cranes in a phylogenetic context using several phylogenetic approaches and two types of trait scoring. The cranes exhibit more than a hundred behavioural displays, almost one third of which may be phylogenetically informative. Results More than half of the analysed traits carry a significant phylogenetic signal. The ancestor of cranes already exhibited a quite complex behavioural repertoire, which remained unchanged in Balearicinae but altered greatly in Gruinae, specifically by the shedding of traits rather than their creation. Trait scoring has an influence on results within the Gruinae, primarily in genera Bugeranus and Anthropoides. Conclusions Albeit the behavioural traits alone cannot be used for resolving species-level relationships within the Gruidae, when optimized on molecular tree, they can help us to detect interesting evolutionary transformations of behaviour repertoire within Gruiformes. The Limpkin (Aramus guarauna) seems to be the most enigmatic species and should be studied in detail for its behavioural repertoire, which may include some precursors of crane behavioural traits.

Phylogenetic relationships among species of Ganoderma (Ganodermataceae, Basidiomycota) from Cameroon

2012 ◽  
Vol 60 (6) ◽  
pp. 526 ◽  
Author(s):  
T. R. Kinge ◽  
A. M. Mih ◽  
M. P. A. Coetzee
Keyword(s):  
Plant Species ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
New Records ◽  
Small Subunit ◽  
Species Level ◽  
Molecular Techniques ◽  
Tropical Species ◽  
The Tropics

Ganoderma is an important genus of the Polyporales in the tropics. Identification of tropical species has mainly been based on morphology, which has led to misidentification. This study aimed to elucidate the diversity and phylogenetic relationships of Ganoderma isolates from different hosts in Cameroon using morphological and molecular techniques. Analyses of basidiocarp morphology and the internal transcribed spacer and mitochondria small subunit were undertaken for 28 isolates from five plant species. The results show that the isolates belong to eight species. Three of the species were identified to species level; of these only G. ryvardense has been previously described from Cameroon while G. cupreum and G. weberianum are new records. The five remaining species did not match with any previously described species and have been designated as Ganoderma with different species affinities.

Reappraisal of arctostylopid mammal Kazachostylops occidentalis from the late Paleocene of Kazakhstan and phylogenetic relationships within Arctostylopida

2019 ◽  
Vol 94 (3) ◽  
pp. 568-579
Author(s):  
Alexander O. Averianov
Keyword(s):  
Phylogenetic Analysis ◽  
North American ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Principal Component ◽  
Sister Taxon ◽  
Phylogenetic Hypothesis ◽  
Lower Eocene ◽  
Principal Component Analyses ◽  
Upper Paleocene

AbstractKazachostylops occidentalis Nesov, 1987b, based on partial maxilla and dentary from the upper Paleocene Zhylga locality in South Kazakhstan, is redescribed. A new phylogenetic hypothesis of Arctostylopida is proposed based on phylogenetic analysis of 26 characters and 17 taxa. Kazachostylops is recovered as a sister taxon to the Arctostylopinae, the advanced clade of Asian and North American arctostylopids characterized by pseudohypocone on upper molars and reduced trigonid of lower molars, with the ectolophid being attached labial on the trigonid. Kazachostylops differs from more basal arctostylopids (Asiostylops, Allostylops, Bothriostylops, and Wanostylops) by higher-crowned molars, M1–3 metaconule absent, m1–3 entoconid connected with ectolophid by entolophid, and m2 wider than m1 and m3. Principal component analyses of the upper and lower dentition of arctostylopids show great distinctness of Kazachostylops from other members of the group. The arctostylopid taxa are reviewed, and the new genus Enantiostylops is erected for ‘Sinostylops’ progressus Tang and Yan, 1976 from the lower Eocene of China, because of uniquely concave parastylar area on upper molars.UUID: http://zoobank.org/a46d8f29-fd73-4e59-88dc-fcc55b12d1d3

Phylogenetic relationships of captorhinomorph reptiles

1986 ◽  
Vol 23 (3) ◽  
pp. 402-418 ◽  
Author(s):  
M. J. Heaton ◽  
R. R. Reisz
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Character ◽  
Sister Taxon ◽  
Morphological Pattern ◽  
Natural Group

The Captorhinomorpha consists of two families, the Captorhinidae and the Protorothyrididae. The distribution of morphological character states of the skeleton permits reevaluation of currently accepted theories of the relationships of captorhinomorph reptiles. Identification of characters states that are primitive for reptiles (amniotes) has been made through outgroup comparison. The Captorhinidae, Protorothyrididae, and Diapsida form a natural group that share such derived characters as reduced supratemporal, reduced tabular, narrow supraoccipital with anteriorly directed crista alaris, loss of supratemporal–postorbital contact, loss of opisthotic–tabular contact, and loss of the medial centralia pedis. These shared derived character states indicate that captorhinomorphs are not the sister taxon of all other reptiles but are advanced relative to pelycosaurs, pareiasaurs, and procolophonids. Protorothyridids share with diapsids such derived characters as short postorbital region of the skull, keeled anterior presacral pleurocentra, slender limbs, and long, slender feet. This distribution of character states indicates that protorothyridids are more closely related to diapsids than either of these taxa is to captorhinids.The morphological pattern of small, lightly built, agile insectivores, represented by protorothyridids and early diapsids, is no longer considered to be the primitive amniote condition. Available evidence indicates that the most primitive amniote adaptation was, instead, that of a small, relatively slow carnivore that probably fed on primitive, terrestrial annelids and arthropods.

Evidence of full species status of the neotropical leaf-frog Phyllomedusa burmeisteri bahiana (A. Lutz, 1925) (Amphibia, Anura, Hylidae)

Zootaxa ◽  
2006 ◽  
Vol 1113 (1) ◽  
pp. 51 ◽  
Author(s):  
IVAN S.N. SILVA-FILHO ◽  
FLORA A. JUNCÁ
Keyword(s):  
Color Pattern ◽  
Species Level ◽  
Advertisement Call ◽  
Species Status ◽  
Oral Disc ◽  
Temporal Characteristics ◽  
Dorsal Fin ◽  
Full Species

The full species status of Phyllomedusa burmeisteri bahiana was investigated based on tadpoles and vocalizations characteristics. We found distinct characteristics between the tadpoles and advertisement and territorial calls of the former and that of Phyllomedusa burmeisteri burmeisteri. The main tadpole differences are related with a skin projection protecting the spiracle, origin of dorsal fin, morphology of ventral fin and distribution of papillae on the oral disc. The advertisement call and territorial call of Phyllomedusa b. bahiana were different from the P. b. burmeisteri calls especially for the structure and temporal characteristics (pulses/second principally). The color of newly metamorphosed Phyllomedusa b. bahiana suggests that the color pattern of the internal sides of the thigh of P. b. burmeisteri can be related to a neotenic pattern of development. We elevate Phyllomedusa b. bahiana to species level based on morphological and acoustical traits decribed here.

scholarly journals Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes

2004 ◽  
Vol 54 (5) ◽  
pp. 1511-1519 ◽  
Author(s):  
L. Soler ◽  
M. A. Yáñez ◽  
M. R. Chacon ◽  
M. G. Aguilera-Arreola ◽  
V. Catalán ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Housekeeping Genes ◽  
Nucleotide Sequences ◽  
Aeromonas Salmonicida ◽  
Species Level ◽  
Substitution Rates ◽  
Aeromonas Veronii ◽  
Taxonomic Organization ◽  
Phylogenetic Divergence

The phylogenetic relationships of all known species of the genus Aeromonas, and especially Aeromonas bestiarum and Aeromonas salmonicida, were investigated on 70 strains using the rpoD sequence, which encodes the σ 70 factor. This analysis was complemented with the sequence of gyrB, which has already proven useful for determining the phylogenetic relationships in the genus. Nucleotide sequences of rpoD and gyrB showed that both genes had similar substitution rates (<2 %) and a similar number of variable positions (34 % for rpoD versus 32 % for gyrB). Strain groupings by analysis of rpoD, gyrB and a combination of both genes were consistent with the taxonomic organization of all Aeromonas species described to date. However, the simultaneous analysis of both clocks improved the reliability and the power to differentiate, in particular, closely related taxa. At the inter-species level, gyrB showed a better resolution for differentiating Aeromonas sp. HG11/Aeromonas encheleia and Aeromonas veronii/Aeromonas culicicola/Aeromonas allosaccharophila, while rpoD more clearly differentiated A. salmonicida from A. bestiarum. The analysis of rpoD provided initial evidence for clear phylogenetic divergence between the latter two species.

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