scholarly journals Phylogenetic Relationships of the Red-Bellied Grackle (Icteridae: Hypopyrrhus Pyrohypogaster) Inferred From Mitochondrial DNA Sequence Data

The Condor ◽  
2004 ◽  
Vol 106 (3) ◽  
pp. 664-670 ◽  
Author(s):  
Carlos Daniel Cadena ◽  
Andrés M. Cuervo ◽  
Scott M. Lanyon
Keyword(s):  
New World ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Mitochondrial Genes ◽  
Morphological Data ◽  
South American ◽  
South American Species ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities

Abstract The phylogenetic affinities of the Red-bellied Grackle (Hypopyrrhus pyrohypogaster), a Colombian endemic and the only member of this genus, are enigmatic. Based on phylogenetic analyses of sequences from the cytochrome b and ND2 mitochondrial genes, we present a first hypothesis on the systematic position of Hypopyrrhus. In so doing, we complete the sampling at the genus level for a published phylogeny of New World blackbirds (Johnson and Lanyon 1999). Hypopyrrhus belongs in a clade composed of mostly South American species within the grackles and allies assemblage, one of the five main lineages in the Icteridae. Within this lineage, Hypopyrrhus is consistently placed in a clade with Gymnomystax mexicanus and Lampropsar tanagrinus, but parsimony and maximum-likelihood reconstructions do not agree on which of these species is its sister taxon. Vocal and morphological data suggest that Hypopyrrhus and Gymnomystax are likely sister taxa. The addition of Hypopyrrhus does not cause major topological changes to Johnson and Lanyon's (1999) phylogeny of the grackles and allies; thus, the conclusions of evolutionary studies that used this phylogeny as a baseline remain largely unaltered. Relaciones Filogenéticas de Hypopyrrhus pyrohypogaster (Icteridae) Inferidas a Partir de Secuencias de ADN Mitocondrial Resumen. Las afinidades filogenéticas de Hypopyrrhus pyrohypogaster, el único miembro de este género endémico de Colombia, son enigmáticas. En este estudio establecemos la posición sistemática de Hypopyrrhus con base en análisis filogenéticos de secuencias de los genes mitocondriales citocromo b y ND2. Además, completamos el muestreo a nivel genérico para una filogenia del grupo publicada por Johnson y Lanyon (1999). Hypopyrrhus pertenece a un clado compuesto principalmente por especies suramericanas dentro del grupo de los changos y chamones, uno de los cinco clados principales de los Icteridae. Dentro de este grupo, Hypopyrrhus se ubica consistentemente en un clado junto con Gymnomystax mexicanus y Lampropsar tanagrinus, pero las reconstrucciones de parsimonia y máxima verosimilitud se contradicen en cuanto a cuál de estas especies es su taxón hermano. Datos de vocalizaciones y morfología sugieren que Hypopyrrhus y Gymnomystax son probablemente géneros hermanos. La incorporación de Hypopyrrhus a la filogenia de Johnson y Lanyon (1989) no causó cambios topoló gicos importantes, por lo que las conclusiones de los estudios evolutivos que usaron esta filogenia como base no fueron alteradas.

Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data

Phytotaxa ◽  
2015 ◽  
Vol 219 (3) ◽  
pp. 261 ◽  
Author(s):  
Julian Aguirre-Santoro ◽  
Julio Betancur ◽  
Gregory K. Brown ◽  
Timothy M. Evans ◽  
Fabiano Salgueiro ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Geographic Ranges ◽  
Dna Sequence Data ◽  
Disjunct Genus

A phylogenetic study testing the monophyly of the geographically disjunct genus Ronnbergia (Bromeliaceae, Bromelioideae) is presented. The phylogenetic analyses were based on taxon sampling that included all but one species of Ronnbergia, and representative lineages across the subfamily Bromelioideae. Three chloroplast DNA sequence markers (matK, psbA-trnH, and trnL-trnF) and morphological data were used for the phylogenetic reconstruction. Both the molecular and morphological datasets supported the polyphyly of Ronnbergia, either independently or in combination. These findings suggest that the geographic disjunction of this genus is most likely a product of taxonomic misinterpretation. The results also indicate that the species currently circumscribed in Ronnbergia are closely related to species in the genus Aechmea with similar geographic ranges. The datasets do not have enough resolution power to reconstruct a deep phylogenetic history that involves all the species of Ronnbergia. Nevertheless, this study provides clues for future approaches that should focus on a larger species sampling and the use of multi-locus DNA sequence data.

scholarly journals Morphology, Morphogenesis, and Molecular Phylogeny of a New Freshwater Ciliate, Quadristicha subtropica n. sp. (Ciliophora, Hypotrichia)

2021 ◽  
Vol 12 ◽  
Author(s):  
Chen Shao ◽  
Qi Gao ◽  
Alan Warren ◽  
Jingyi Wang
Keyword(s):  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Systematic Position ◽  
Phylogenetic Position ◽  
Dna Sequence Data ◽  
Freshwater Pond ◽  
Small Subunit Ribosomal Dna

The morphology and the regulation of cortical pattern associated with the cell size, division, and phylogenetic position of a new hypotrichous ciliate, Quadristicha subtropica n. sp. collected from a freshwater pond in southern China, were investigated. Quadristicha subtropica n. sp. is characterized as follows: size in vivo 60–115 μm × 25–45 μm; 19–21 adoral membranelles; buccal cirrus near anterior end of endoral and paroral; cirrus IV/3 at about level of buccal vertex; right marginal row begins ahead of buccal vertex; 11–16 right and 12–19 left marginal cirri; and dorsal cilia about 5 μm long. The basic morphogenetic process in Q. subtropica n. sp. is consistent with that of the type species, Quadristicha setigera. Phylogenetic analyses based on small subunit ribosomal DNA sequence data reveal that the systematic position of Q. subtropica n. sp. is rather unstable with low support values across the tree and the genus Quadristicha is not monophyletic.

A phylogeny of the enigmatic Madagascan geckos of the genus Uroplatus (Squamata: Gekkonidae)

Zootaxa ◽  
2007 ◽  
Vol 1493 (1) ◽  
pp. 41-51 ◽  
Author(s):  
ELI GREENBAUM ◽  
AARON M. BAUER ◽  
TODD R. JACKMAN ◽  
MIGUEL VENCES ◽  
FRANK GLAW
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Phylogenetic Hypothesis ◽  
Cyt B ◽  
Undescribed Species ◽  
Dna Sequence Data ◽  
Center Of Diversity ◽  
Rag 1 ◽  
High Diversity

Since its discovery in the 17th century, the morphological peculiarities of the gekkonid lizard genus Uroplatus have generated a great deal of attention. A large number of skeletal, integumentary and visceral features are autapomorphic for the genus and some of the more well-known members of the group possess such aberrant characteristics that a separate family was once recognized to accommodate them. Recent phylogenetic analyses confirm that Uroplatus is a typical gekkonid gecko, but the specific affinities of the genus, as well as its intrageneric relationships have remained unresolved. Both nuclear (RAG-1 and PDC) and mitochondrial (ND2 and cyt b) genes (~3.2 Kb) were sequenced for 10 of 13 recognized species of Uroplatus, as well as two Madagascan and mainland African outgroups. The large-bodied forms of Uroplatus (U. fimbriatus, U. giganteus, U. henkeli, and U. sikorae) form a monophyletic group, and the smallbodied, short-tailed species are also monophyletic (U. ebenaui and U. phantasticus). Uroplatus alluaudi + U. pietschmanni comprise another distinct clade, whereas U. lineatus was weakly supported as the sister taxon of the largebodied clade and U. guentheri was sister to all other members of the genus. Our phylogenetic hypothesis based on combined DNA sequence data is mostly congruent with previous hypotheses based on morphological data. Based on a larger, more inclusive dataset, the closest relatives of Uroplatus are mainland African Afrogecko and Madagascan Matoatoa, suggesting that the diverse Malagasy gecko fauna does not comprise a single evolutionary lineage. A high diversity of new taxa (either representing synonyms to resurrect or undescribed species), morphologically similar either to U. ebenaui/phantasticus or to U. henkeli/sikorae, was apparent from our data. Many of these genetically highly divergent lineages originated from localities in northern Madagascar, which indicates this region as the possible center of diversity and endemism for several subgroups of Uroplatus.

The phylogeny, biogeography and morphological evolution of Gaultheria (Ericaceae) from Australia and New Zealand

2009 ◽  
Vol 22 (4) ◽  
pp. 229 ◽  
Author(s):  
Catherine M. Bush ◽  
Steven J. Wagstaff ◽  
Peter W. Fritsch ◽  
Kathleen A. Kron
Keyword(s):  
New Zealand ◽  
Sequence Data ◽  
Morphological Evolution ◽  
Morphological Characters ◽  
South American ◽  
South American Species ◽  
Dna Sequence Data ◽  
Biogeographical Analysis ◽  
Dispersal Events ◽  
South American Origin

Phylogenetic relationships within Gaultheria L. from Australia and New Zealand were examined by using DNA sequence data from matK, ndhF, nrITS, waxy and lfy. In the combined parsimony and maximum likelihood analyses, all Australia/New Zealand species form a clade that is sister to a clade of temperate South American species. Optimisation of morphological characters that have been emphasised in classifications of Gaultheria onto the molecular phylogeny revealed that, within the Australia/New Zealand clade, non-fleshy fruiting calyces, berries and solitary-flowered inflorescences each evolved twice, from fleshy fruiting calyces, capsules and multiple-flowered inflorescences, respectively. A historical biogeographical analysis that included the temperate southern hemisphere element in Gaultheria supports a South American origin of the Australia/New Zealand clade, followed by three dispersal events from New Zealand to Australia. Whether the origin is from temperate or tropical South America is ambiguous in our analysis.

Molecular evolution and diversification of the vestimentiferan tube worms

1993 ◽  
Vol 73 (2) ◽  
pp. 437-452 ◽  
Author(s):  
Nic A. Williams ◽  
David R. Dixon ◽  
Eve C. Southward ◽  
Peter W. H. Holland
Keyword(s):  
Dna Sequences ◽  
Deep Sea ◽  
Marine Invertebrates ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Sequence Data ◽  
Evolutionary Diversification ◽  
Tube Worms ◽  
Eastern Atlantic Ocean ◽  
Phylogenetic Affinities

The Vestimentifera, or deep-sea tube worms, comprise an ecologically and anatomically unusual group of marine invertebrates, with poorly understood biogeography, ecology, phylogenetic affinities and evolutionary radiation. To gain insight into evolutionary diversification within the group, we have used a molecular biological approach. We report the cloning of a region of 28S ribosomal DNA from representatives of five vestimentiferan genera plus, for comparison, a polychaete and a perviate pogonophore. Phylogenetic analyses using these DNA sequences confirm thatRidgeiaandTevniaare closely related genera. The analyses also lead us to propose the hypothesis that the earliest vestimentiferan lineage to diverge gave rise to the genusLamellibrachiaonly. In addition, our comparative DNA sequence data now provide a means to use molecular methods for identification of deep-sea tube worms; we employed this approach to demonstrate that the first vestimentiferan specimen from the eastern Atlantic Ocean belongs to the genusLamellibrachia. DNA-based identification should have wide applications in the study of vestimentiferan biogeography and ecology.

Phylogenetic relationships among southern South American species of Camptosema, Galactia and Collaea (Diocleinae: Papilionoideae: Leguminosae) on the basis of molecular and morphological data

2009 ◽  
Vol 57 (1) ◽  
pp. 76 ◽  
Author(s):  
Silvana M. Sede ◽  
Daniela Tosto ◽  
Paola Talia ◽  
Melissa Luckow ◽  
Lidia Poggio ◽  
...  
Keyword(s):  
South America ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Morphological Data ◽  
South American ◽  
South American Species ◽  
Aflp Data ◽  
Southern South America ◽  
Good Support

The neotropical genus Camptosema in its southern distribution is represented by the following four species: Ca. paraguariense, Ca. praeandinum, Ca. rubicundum and Ca. scarlatinum. Ca. rubicundum is the only species with all the diagnostic characters of the genus, i.e. tubular calyx. The other three taxa are related morphologically and cytologically to Galactia and Collaea, two closely allied genera in the subtribe Diocleinae. Individual and combined phylogenetic analyses of morphology, ITS and trnL-F were conducted to examine the position of these species as well as to explore their relationship with Galactia and Collaea species in southern South America. In none of the analyses does Camptosema species form a monophyletic group. Instead, they are scattered in different groups. These results together with cytological, morphological and AFLP data provide good support for re-evaluating the taxonomic position of these species within Camptosema.

scholarly journals Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8999
Author(s):  
Sigrid Liede-Schumann ◽  
Guido W. Grimm ◽  
Nicolai M. Nürk ◽  
Alastair J. Potts ◽  
Ulrich Meve ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Cape Floristic Region ◽  
Rapid Radiation ◽  
Widespread Species ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities ◽  
African Genus

Background Drosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum, together with the highly succulent and species-rich tribe Ruschieae, constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution. Methods Using chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence dataset comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole. Results Phylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.

scholarly journals A Phylogenetic Assessment of Endocalyx (Cainiaceae, Xylariales) With E. Grossus Comb. et Stat. Nov.

2021 ◽  
Author(s):  
Gregorio Delgado ◽  
Andrew N Miller ◽  
Akira Hashimoto ◽  
Toshiya Iida ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Ribosomal Dna ◽  
Species Status ◽  
Characteristic Mode ◽  
Dna Sequence Data ◽  
Monophyletic Lineage ◽  
The Family ◽  
Phylogenetic Affinities ◽  
Lsu Nrdna

Abstract The phylogenetic affinities of four representative Endocalyx taxa, including three species and two varieties, are studied based on materials collected on different palm hosts in Japan and the states of Hawaii and Texas, USA. They include specimens and their isolates belonging to E. cinctus, E. indumentum, E. melanoxanthus var. grossus and E. melanoxanthus var. melanoxanthus. Phylogenetic analyses of nuclear ribosomal DNA sequence data (ITS-LSU nrDNA) confirmed that Endocalyx belongs to the order Xylariales (Sordariomycetes) where all species and varieties treated form a strongly supported monophyletic lineage within the family Cainiaceae. They were also phylogenetically well resolved and consistent with their morphological and ecological circumscription. Species status is proposed for E. melanoxanthus var. grossus under the name E. grossus comb. et stat. nov. on the basis of its distinct morphological, molecular, cultural and ecological characteristics. The putative placement of Endocalyx within the family Apiosporaceae (Amphisphaeriales) based on the presence of basauxic conidiophores is rejected considering that all species treated clustered within the distant Cainiaceae (Xylariales). This characteristic mode of conidiophore elongation is determined to have evolved independently within unrelated or distant ascomycetous lineages. Novel morphological and cultural features of Endocalyx taxa based on new isolates are commented. The recently described E. metroxyli is reduced to synonym with E. melanoxanthus.

scholarly journals Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

2019 ◽  
Author(s):  
Sigrid Liede-Schumann ◽  
Guido W. Grimm ◽  
Nicolai M. Nürk ◽  
Alastair J. Potts ◽  
Ulrich Meve ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Cape Floristic Region ◽  
Rapid Radiation ◽  
Data Set ◽  
Widespread Species ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities

AbstractBackgroundDrosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum together with the highly succulent and species-rich tribe Ruschieae constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.MethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species represented by multiple accessions of Drosanthemum. A well-curated, geo-referenced occurrence data set comprising the phylogenetically studied and 867 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.ResultsPhylogenetic inference supports nine clades within Drosanthemum, seven of them group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region revealed phylogenetic affinities not obvious in the phylogenetic tree. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are molecular and morphologically diverse. In contrast, less species-rich, molecularly less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest initial rapid radiation generating the main lineages, with some clades showing subsequent diversification.

Saprobic Lophiostomataceae (Dothideomycetes): Pseudolophiostoma mangiferae sp. nov. and Neovaginatispora fuckelii, a new record from Mangifera indica

Phytotaxa ◽  
2018 ◽  
Vol 364 (2) ◽  
pp. 157 ◽  
Author(s):  
DANUSHKA SANDARUWAN TENNAKOON ◽  
CHANG-HSIN KUO ◽  
RAJESH JEEWON ◽  
KASUN MADHUSANKA THAMBUGALA ◽  
KEVIN DAVID HYDE
Keyword(s):  
Dna Sequence ◽  
New Record ◽  
Sequence Data ◽  
Mangifera Indica ◽  
Morphological Data ◽  
Similar Species ◽  
Bayesian Analyses ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities ◽  
A New Species

Pseudolophiostoma mangiferae, isolated from a dead stem of Mangifera indica, collected in Fanlu Township area, Dahu village in Chiayi, Taiwan (Elevation 634 m) and is introduced as a new species based on morphological data and DNA sequence analyses. Maximum parsimony, Maximum likelihood and Bayesian analyses of combined ITS, LSU, SSU and tef1-α sequence data were performed to clarify the phylogenetic affinities of the species. Pseudolophiostoma mangiferae is distinguished from the other Pseudolophiostoma species based on distinct size differences in ascomata, asci, ascospores and DNA sequence data. In addition, Neovaginatispora fuckelii is described as a new record from Taiwan. Both species are compared with other similar species and comprehensive descriptions and micrographs are provided.

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