Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches (project)

10.7934/p3763 ◽  
2020 ◽  
Author(s):  
W Baker ◽  
V Savolainen ◽  
C Asmussen-Lange ◽  
M Chase ◽  
J Dransfield ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Generic Level

scholarly journals Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches

2009 ◽  
Vol 58 (2) ◽  
pp. 240-256 ◽  
Author(s):  
William J. Baker ◽  
Vincent Savolainen ◽  
Conny B. Asmussen-Lange ◽  
Mark W. Chase ◽  
John Dransfield ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Generic Level

Identification of Photobionts from the lichen family Physciaceae using algal-specific ITS rDNA sequencing

2001 ◽  
Vol 33 (1) ◽  
pp. 73-86 ◽  
Author(s):  
Gert Helms ◽  
Thomas Friedl ◽  
Gerhard Rambold ◽  
Helmut Mayrhofer
Keyword(s):  
Phylogenetic Analyses ◽  
Pcr Primers ◽  
Its Rdna ◽  
Generic Level ◽  
Sequence Comparisons ◽  
Its Phylogeny ◽  
Specific Pcr ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
Geographical Regions

AbstractThe identity of photobionts from 20 species of the Physciaceae from different habitats and geographical regions has been determined by ITS rDNA sequence comparisons in order to estimate the diversity of photobionts within that lichen group, to detect patterns of specificity of mycobionts towards their photobionts and as a part of an ongoing study to investigate possible parallel cladogenesis of both symbionts. Algal-specific PCR primers have been used to determine the ITS rDNA sequences from DNA extractions of dried lichens that were up to 5 years old. Direct comparisons and phylogenetic analyses allowed the assignment of Physciaceae photobionts to four distinct clades in the photobiont ITS rDNA phylogeny. The results indicate a diversity within the genus Trebouxia Puymaly and Physciaceae photobionts that is higher than expected on the basis morphology alone. Physciaceae photobionts belonged to 12 different ITS lineages of which nine could unambiguously be assigned to six morphospecies of Trebouxia. The identity of the remaining three sequences was not clarified; they may represent new species. Specificity at the generic level was low as a whole range of photobiont species were found within a genus of Physciaceae and different ranges were detected. The photobionts of Physcia (Schreb.) Michaux were closely related and represented one morphospecies of Trebouxia, whereas the algal partners of Buellia De Not and Rinodina (Ach.) Gray were in distant lineages of the ITS phylogeny and from several Trebouxia morphospecies. Photobiont variation within a genus of Physciaceae may be due to phylogeny, geographical distance or because photobionts from neighbouring lichens were taken (“algal sharing“). At the species level Physciaceae mycobionts seem to be rather selective and contained photobionts that were very closely related within one morphospecies of Trebouxia.

Species diversity and genetic differentiation of stygofauna (Syncarida:Bathynellacea) across an alluvial aquifer in north-eastern Australia

2012 ◽  
Vol 60 (3) ◽  
pp. 152 ◽  
Author(s):  
B. D. Cook ◽  
K. M. Abrams ◽  
J. Marshall ◽  
C. N. Perna ◽  
S. Choy ◽  
...  
Keyword(s):  
Species Diversity ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Alluvial Aquifer ◽  
Species Level ◽  
Coi Gene ◽  
Generic Level ◽  
Alluvial Aquifers ◽  
Eastern Australia ◽  
North Eastern

Recent research suggests that alluvial aquifers in southern and eastern Australia may contain a diverse subterranean aquatic fauna (i.e. stygofauna). However, to date only a limited number of alluvial aquifers have been studied and little molecular data are available to assess species-level diversity and spatial patterns of genetic variation within stygofaunal species. In this paper, we present the initial results of a stygofaunal survey of the Burdekin River alluvial aquifer in Queensland, extending the northern range of alluvial aquifers along the east coast of Australia that have been investigated. The survey resulted in the collection of bathynellid stygofauna (Syncarida: Bathynellacea) and genetic analyses were conducted to determine species level diversity using the mitochondrial cytochrome oxidase subunit I (COI) gene. We further investigated the phylogenetic relationships of the species with bathynellids from western and southern Australia to assess the generic status of species. Four highly divergent COI lineages within the Parabathynellidae and one lineage within the Bathynellidae were found. These lineages did not group within any described genera, and phylogenetic analyses indicated that both local radiations and the retention of a lineage that was more apical in the genealogy account for the diversity within the Parabathynellidae in the Burdekin River alluvial aquifer. Most COI lineages were sampled from only a single bore, although one taxon within the Parabathynellidae was found to be more widespread in the aquifer. Haplotypes within this taxon were not shared among bores (ΦST = 0.603, P < 0.001). Overall, the high species diversity for bathynellaceans from an alluvial aquifer reported here, and surveys of bathynellaceans in several other alluvial systems in south-eastern Australia, suggests that groundwater ecosystems of eastern Australia may contain high stygofaunal diversity by Australian and world standards, particularly at the generic level for parabathynellids.

New combinations in Campanulorchis (Orchidaceae: Epidendroideae): a reappraisal of the genus

Phytotaxa ◽  
2017 ◽  
Vol 323 (1) ◽  
pp. 93
Author(s):  
JAN PONERT
Keyword(s):  
Type Species ◽  
Morphological Traits ◽  
Dna Analysis ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Morphological Characters ◽  
Generic Level ◽  
Long Time ◽  
Single Genus ◽  
Taxonomic Categories

Tribe Podochileae are a systematically highly challenging orchid group. Although the delimitation of Podochileae is relatively stable and monophyly of this tribe was confirmed by DNA-based phylogenetic analysis (Ng 2002), taxonomic categories within this group have changed frequently. Some groups are well separated morphologically and have been widely accepted as separate genera for a long time, whereas the majority of species was usually placed into a single genus Eria Lindley (1825: 904). Morphological traits have indicated polyphyly of this genus, which led some authors at various times to propose segregate genera. Nevertheless, these concepts were poorly supported by relevant data, and other authors retained these species in Eria s.l. Finally, combined DNA analysis confirmed the polyphyly of Eria (Ng 2002) and resulted in recognition of several previously neglected groups at generic level (Cribb & Ng 2005), including Campanulorchis Brieger (1981: 750).Campanulorchis was originally proposed by Brieger (1981) with the single species C. globifera Brieger (1981: 750). Seidenfaden (1982, 1992) demonstrated that this species was likely to be closely related to other species of Eria and classified it in Eria sect. Strongylaria Pfitzer (1888: 175). Later, Seidenfaden (1992) suggested separation of E. pannea Lindley (1842: 64) from remaining Indochinese species of E. section Strongylaria. Phylogenetic analyses of Ng (2002) confirmed polyphyly of the section Strongylaria. The type species of E. section Strongylaria, E. pannea, was transferred to Mycaranthes Blume (1825: 352; Chen & Wood 2009), and three of the remaining taxa were transferred to a revised concept of Campanulorchis (Ng & Cribb 2005, Cribb & Ng 2005): C. globifera, C. leiophylla (Lindley 1858: 57) Ng & Cribb (2005: 272) and C. pellipes (Riechenbach in Hooker 1890: 802) Ng & Cribb (2005: 272). Four years later Chen & Wood (2009) added C. thao (Gagnepain 1950: 503) Chen & Wood (2009: 346) because it shares many morphological characters with the other Campanulorchis species, especially with C. globifera. Finally, C. pseudoleiophylla (Wood 1981: 209) Wood (2011: 176) was added (Wood et al. 2011) because this species is morphologically similar to C. leiophylla (Wood 1981). Thus, five species were accepted in the most recent orchid classification (Chase et al. 2015, Govaerts 2017). Here I add two more species to Campanulorchis.

scholarly journals Additions to tribe Chromosereae (Basidiomycota, Hygrophoraceae) from China, including Sinohygrocybe gen. nov. and a first report of Gloioxanthomyces nitidus

MycoKeys ◽  
2018 ◽  
Vol 38 ◽  
pp. 59-76 ◽  
Author(s):  
Chao-Qun Wang ◽  
Ming Zhang ◽  
Tai-Hui Li ◽  
Xi-Shen Liang ◽  
Ya-Heng Shen
Keyword(s):  
New Record ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Molecular Evidence ◽  
Generic Level ◽  
First Report ◽  
Thin Walled

Sinohygrocybegen. nov., typified by S.tomentosipessp. nov., is described upon morphological and molecular evidence. The new genus is characterised by its sinuate to subdecurrent or short deccurent, usually furcate and interveined and relatively distant lamellae, dry and whitish tomentose stipe, thin-walled ellipsoid to oviod, non-constricted basidiospores and particularly elongated basidia and a ratio of basidiospore to basidium length of &gt;5 to 8; it is close to genera Chromosera and Gloioxanthomyces of the tribe Chromosereae, but morphologically differs from Chromosera in less umbilicate basidiomata, tomentose stipe and usually longer basidia and differs from Gloioxanthomyces in more robust basidioma and less glutinous pileus and/or stipe surface. Phylogenetic analyses, with ITS-LSU-RPB2 data, also indicate that Sinohygrocybe forms a very distinct and independent clade at the generic level. In addition, a Chinese new record G.nitidus is described here.

scholarly journals Transcriptome-based phylogeny and whole-genome duplication in Theaceae

2021 ◽  
Author(s):  
Qiong Zhang ◽  
Lei Zhao ◽  
Jian-Li Zhao ◽  
Ryan A. Folk ◽  
Nelson Zamora ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Whole Genome ◽  
Land Bridge ◽  
Generic Level ◽  
Interspecific Introgression ◽  
Ecological Importance ◽  
The Relationship

Theaceae, with three tribes and nine genera, is a family of great economic and ecological importance. Recent phylogenetic analyses based on plastid genome resolved the relationship among three tribes and the intergeneric relationships within Gordonieae and Stewartieae. However, generic level relationships within the largest tribe Theeae were not fully resolved and potential hybridization among genera within Theeae revealed previously also remains to be tested further. Here we conducted a comprehensive phylogenomic study of Theaceae based on transcriptomes and low-depth whole-genome sequencing of 57 species as well as additional plastome sequence data from previous work. Phylogenetic analyses suggested that Stewartieae was the first-diverging clade in Theaceae, consistent with previous study using plastomic data. Within Theeae, the highly supported Apterosperma-Laplacea clade grouped with Pyrenaria with maximum support based on the partitioned and unpartitioned concatenation analyses using the 610 low-copy nuclear genes, leaving Camellia and Polyspora as another sister genera in the tribe. PhyloNet analyses suggested one reticulation event within Camellia and Pyrenaria respectively, but no intergeneric reticulations were detected in Theeae. Another introgression was found between Gordonia lasianthus and the common ancestor of Gordonieae during the Late Oligocene. The existing land bridges (e.g. Bering land bridge) might have facilitated this ancient introgression. Further researches need to be conducted to uncover the interspecific introgression pattern within Camellia. Ks distribution analyses supported the tea family shared one whole-genome duplication (WGD) event Ad-β, which was recently mapped to the clade containing core Ericales, Primuloids, Polemonioids and Lecythidaceae.

scholarly journals Molecular phylogeny of the family Vorticellidae (Ciliophora, Peritrichia) using combined datasets with a special emphasis on the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium

2011 ◽  
Vol 61 (4) ◽  
pp. 1001-1010 ◽  
Author(s):  
Ping Sun ◽  
John C. Clamp ◽  
Dapeng Xu ◽  
Yasushi Kusuoka ◽  
Manabu Hori
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Gene ◽  
Evolutionary Divergence ◽  
Ssu Rrna ◽  
Generic Level ◽  
Ssu Rrna Gene ◽  
The Family ◽  
Molecular Phylogenetic

Little is known about the phylogeny of the family Vorticellidae at the generic level because few comprehensive analyses of molecular phylogenetic relationships between members of this group have, so far, been done. As a result, the phylogenetic positions of some genera that were based originally on morphological analyses remain controversial. In the present study, we performed phylogenetic analyses of vorticellids based on the sequence of the small-subunit (SSU) rRNA gene, including one species of the genus Apocarchesium, for which no sequence has previously been reported. Phylogenetic trees were reconstructed with SSU rRNA gene sequences by using four different methods (Bayesian analysis, maximum-likelihood, neighbour-joining and maximum-parsimony) and had a consistent branching pattern. Members of the genera Vorticella (except V. microstoma) and Carchesium formed a clearly defined, well supported clade that was divergent from the clade comprising members of the genera Pseudovorticella and Epicarchesium, suggesting that the differences in the silverline system (transverse vs reticulate) among vorticellids may be the result of genuine evolutionary divergence. Members of the newly established genus Apocarchesium clustered within the family Vorticellidae basal to the clade containing members of the genera Pseudovorticella and Epicarchesium and were distinct from members of the genus Carchesium, supporting the validity of Apocarchesium as a novel genus. Additional phylogenetic analyses of 21 strains representing seven genera from the families Vorticellidae and Zoothamniidae were performed with single datasets (ITS1–5.8S–ITS2, ITS2 alone) and combined datasets (SSU rRNA+ITS1–5.8S–ITS2, SSU rRNA+ITS2) to explore further the phylogenetic relationship between the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium, using characteristics not included in previous analyses. The phylogenetic trees reconstructed with combined datasets were more robust and therefore more reliable than those based on single datasets and supported the results of trees based on SSU rRNA sequences.

Evolution, characterization and phylogenetic utility of ITS2 gene in Orthoptera and some Polyneoptera: Highly variable at the order level and highly conserved at the species level

Zootaxa ◽  
2020 ◽  
Vol 4780 (1) ◽  
pp. 54-76
Author(s):  
ONUR ULUAR ◽  
BATTAL ÇIPLAK
Keyword(s):  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Species Level ◽  
Phylogenetic Information ◽  
Generic Level ◽  
Variable Pattern ◽  
Potential Marker ◽  
Evolutionary Studies

ITS2 is often suggested as a potential marker for evolutionary studies and species barcoding. However, there are many lineages have not been studied. This study focuses on ITS2 in Polyneoptera at the order and species levels. ITS2 sequences representing six polyneopteran orders and 15 species in the genus Anterastes are studied. We arrived at the following conclusions: (i) ITS2 is highly variable and contains little phylogenetic information in Polyneoptera, (ii) the shortest length and the highest GC content of ITS2 is found in Orthoptera among insects, (iii) the secondary structure exhibits general characteristics of eukaryotes especially in helices II and III, and with no order-specific architecture, (iv) ITS2 is highly conserved at the species level, both in linear sequences and secondary structures, (v) helices I, IA, II, IIA and III almost invariable in nucleotide sequence shared by all species in the genus. At the generic level, the most conspicuous result is the variable pattern in ITS2. It is highly conserved in helical sequences, but highly variable in non/peri-helical regions which we considered to be mutation islands. These frequently mutated regions contain a significant amount of molecular homoplasy, thus, the utility of ITS2 in phylogenetic analyses and species barcoding is low, at least in Polyneoptera. 

Exploring species diversity of lissorchiid trematodes (Digenea: Lissorchiidae) associated with the gravel snail, Lithoglyphus naticoides, in European freshwaters

2020 ◽  
Vol 94 ◽  
Author(s):  
R. Petkevičiūtė ◽  
G. Stanevičiūtė ◽  
V. Stunžėnas
Keyword(s):  
Developmental Stages ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Rutilus Rutilus ◽  
Life Cycles ◽  
Species Identity ◽  
Generic Level ◽  
Rdna Sequences ◽  
28S Rdna Sequence ◽  
Lithoglyphus Naticoides

Abstract Comparative analysis using complete ITS2 and partial 28S rDNA sequence data revealed that cercariaeum developing in rediae in Lithoglyphus naticoides represent two different lissorchiid species. One morphotype of cercariaeum is conspecific with adult Palaeorchis incognitus from European roach, Rutilus rutilus. The other cercariaeum is attributable to the genus Asymphylodora, but the species identity is not yet determined. We also generate the first rDNA sequences for Asymphylodora progenetica based on new collections from Bithynia tentaculata from Lithuania. Phylogenetic analyses of the newly generated sequences, together with information for other lissorchiids available on GenBank, showed that all representatives of Lissorchiidae form a strongly supported clade. Three monophyletic lineages, Asymphylodora, Palaeorchis and Lissorchis, were recognized at the generic level. Karyological analysis of the chromosome set of larval P. incognitus revealed a diploid number of 2n = 20. Its karyotype with subtelocentric chromosomes prevailing can be regarded as comparatively ‘primitive’, which is consistent with the basal position of P. incognitus in the 28S tree relative to the representatives of the genus Asymphylodora. The present study adds significant new information for establishing species-specific markers for the confident characterization of different developmental stages of lissorchiid species and clarification of their life cycles.

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