scholarly journals A Phylogenetic Investigation of the New Zealand  Pteridaceae Ferns

2021 ◽  
Author(s):  
◽  
Whitney L M Bouma
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Native Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxonomic Confusion ◽  
Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

scholarly journals A Phylogenetic Investigation of the New Zealand  Pteridaceae Ferns

2021 ◽  
Author(s):  
◽  
Whitney L M Bouma
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Native Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxonomic Confusion ◽  
Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

2020 ◽  
Vol 84 (4) ◽  
pp. 317-330
Author(s):  
Francisco J. García-Cárdenas ◽  
Mónica Núñez-Flores ◽  
Pablo J. López-González
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences

2009 ◽  
Vol 21 (6) ◽  
pp. 565-570 ◽  
Author(s):  
Kristen L. Kuhn ◽  
Thomas J. Near
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Single Copy ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Phylogenetic Resolution

AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

scholarly journals Phylogenetic Relationship Within Genus Araucaria (Araucariaceae) Assessed by Means of AFLP Fingerprints

2006 ◽  
Vol 55 (1-6) ◽  
pp. 45-52 ◽  
Author(s):  
V. M. Stefenon ◽  
O. Gailing ◽  
R. Finkeldey
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Aflp Markers ◽  
Phylogenetic Study ◽  
The Family ◽  
Chloroplast Dna Sequences

Abstract Highly polymorphic AFLP markers were applied to analyse the phylogenetic relationships of seven species from three sections within genus Araucaria (Araucariaceae) with cladistic and phenetic approaches. The objectives of the study were to compare the intrageneric relationships within Araucaria assessed by AFLP markers with the classification according to chloroplast DNA sequences and morphological characters. The AMOVA revealed 48% of the variation among species. The results of the principal coordinate analysis revealed three distinct groups: (1) A. angustifolia and A. araucana (= section Araucaria), (2) A. bidwillii (= section Bunya) and (3) A. cunninghamii, A. heterophylla, A. rulei and A. scopulorum (= section Eutacta). In the cladistic and phenetic analyses, phylogenetic trees were subdivided into two sister clades, one comprising the samples from section Eutacta, the other one was divided again into two sister clades corresponding to sections Araucaria and Bunya. These results are congruent with a previous phylogenetic study of the family Araucariaceae based on rbcL sequences and with the classification of genus Araucaria based on morphological characters. Both rbcL sequence data and AFLP analyses do not support section Bunya as one of the oldest sections within genus Araucaria, as suggested by the fossil record. The utility of AFLP markers for phylogenetic analyses is discussed.

Monophyly of Verbascum (Scrophularieae : Scrophulariaceae): evidence from nuclear and plastid phylogenetic analyses

2014 ◽  
Vol 62 (8) ◽  
pp. 638 ◽  
Author(s):  
Farrokh Ghahremaninejad ◽  
Mehrshid Riahi ◽  
Melina Babaei ◽  
Faride Attar ◽  
Lütfi Behçet ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nrdna Its ◽  
Starting Point ◽  
High Species Diversity ◽  
Phylogenetic Estimation

Verbascum is one of the main genera of Scrophulariaceae, but delimitation and phylogenetic relationships of this genus are unclear and have not yet been studied using DNA sequences. Here, using four selected molecular markers (nrDNA ITS and the plastid spacers trnS/G, psbA-trnH and trnY/T), we present a phylogeny of Verbascum and test previous infrageneric taxonomic hypotheses as well as its monophyly with respect to Scrophularia. We additionally discuss morphological variation and the utility of morphological characters as predictors of phylogenetic relationships. Our results show that while molecular data unambiguously support the circumscription of Verbascum inferred from morphology, they prove to be of limited utility in resolving infrageneric relationships, suggesting that Verbascum ‘s high species diversity is due to rapid and recent radiation. Our work provides phylogenetic estimation of the genus Verbascum using molecular data and can serve as a starting point for future investigations of Verbascum and relatives.

scholarly journals Two new asexual genera and six new asexual species in the family Microthyriaceae (Dothideomycetes, Ascomycota) from China

MycoKeys ◽  
2021 ◽  
Vol 85 ◽  
pp. 1-30
Author(s):  
Min Qiao ◽  
Hua Zheng ◽  
Ji-Shu Guo ◽  
Rafael F. Castañeda-Ruiz ◽  
Jian-Ping Xu ◽  
...  
Keyword(s):  
New Taxa ◽  
Dna Sequences ◽  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Aquatic Hyphomycetes ◽  
Internal Transcribed Spacers ◽  
The Family

The family Microthyriaceae is represented by relatively few mycelial cultures and DNA sequences; as a result, the taxonomy and classification of this group of organisms remain poorly understood. During the investigation of the diversity of aquatic hyphomycetes from southern China, several isolates were collected. These isolates were cultured and sequenced and a BLAST search of its LSU sequences against data in GenBank revealed that the closest related taxa are in the genus Microthyrium. Phylogenetic analyses, based on the combined sequence data from the internal transcribed spacers (ITS) and the large subunit (LSU), revealed that these isolates represent eight new taxa in Microthyriaceae, including two new genera, Antidactylariagen. nov. and Isthmomycesgen. nov. and six new species, Antidactylaria minifimbriatasp. nov., Isthmomyces oxysporussp. nov., I. dissimilissp. nov., I. macrosporussp. nov., Triscelophorus anisopterioideussp. nov. and T. sinensissp. nov. These new taxa are described, illustrated for their morphologies and compared with similar taxa. In addition, two new combinations are proposed in this family.

scholarly journals Phylogenetic relationships of Chacodelphys (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences

2015 ◽  
Vol 97 (2) ◽  
pp. 394-404 ◽  
Author(s):  
Juan F. Díaz-Nieto ◽  
Sharon A. Jansa ◽  
Robert S. Voss
Keyword(s):  
Soft Tissue ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Morphological Character ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Taxon ◽  
Evolutionary Relationships ◽  
Fresh Material

Abstract Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved. Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.

scholarly journals Nectria-related fungi causing dieback and canker diseases in China, with Neothyronectria citri sp. nov. described

MycoKeys ◽  
2019 ◽  
Vol 56 ◽  
pp. 49-66
Author(s):  
Qin Yang ◽  
Wen-Yan Chen ◽  
Ning Jiang ◽  
Cheng-Ming Tian
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Bright Yellow

To clarify phylogenetic relationships amongst Nectria, Neothyronectria and Thyronectria in Nectriaceae, we examined detailed morphological characters and performed phylogenetic analyses of a concatenated dataset, based on the ITS, LSU, tef1 and tub2 DNA sequences of fungal specimens in China. Four species of nectria-related fungi were identified, i.e. Nectriadematiosa, N.pseudotrichia, Neothyronectriacitri and Thyronectriapinicola. The newly described species, Neothyronectriacitri, is characterised by its ascomatal wall with bright yellow scurf, unitunicate asci, each with 4-spored and ascospores allantoid to short-cylindrical, uniseriate, muriform, hyaline to slightly yellowish-brown. This species has affinities with other one known species of Neothyronectria and can be distinguished by molecular data.

scholarly journals Phylogenetic Relationships in the Genus Rosa Revisited Based on rpl16, trnL-F, and atpB-rbcL Sequences

HortScience ◽  
2015 ◽  
Vol 50 (11) ◽  
pp. 1618-1624 ◽  
Author(s):  
Chengyuan Liu ◽  
Guoliang Wang ◽  
Hui Wang ◽  
Tao Xia ◽  
Shouzhou Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Maternal Inheritance ◽  
Molecular Level ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Morphological Characters ◽  
Seed Parent ◽  
Molecular Analyses ◽  
Rbcl Sequences

Three chloroplast DNA (cpDNA) sequences [the rpl16 intron, the trnL-F, and atpB-rbcL intergenic spacer (IGS)] were employed to study phylogenetic relationships in the genus Rosa. Phylogenetic analyses using these three concatenated sequences were performed using maximum parsimony (MP) and Bayesian inference (BI) methods. Both analyses results suggest that the molecular phylogeny conforms closely to the conventional classification of botanical sections. Morphological similarities between R. sects. Synstylae and Chinenses, and R. sects. Rosa and Carolinae are corroborated on the molecular level in our analyses. Four taxa from R. sect. Pimpinellifoliae are further divided into two small clades, which reflect the morphological characters for these species on a molecular level. Whereas three accessions of R. foetida from R. sect. Pimpinellifoliae form a separate clade. R. ×fortuniana forms a clade with R. laevigata based on its maternal inheritance of cpDNA. R. ×cooperii is hypothesized to be a hybrid with seed parent from R. sects. Synstylae and Chinenses. And R. roxburghii should be classified as a section within the R. subgen. Rosa, rather than being treated as its own subgenus, based on molecular analyses.

A preliminary phylogenetic analysis of the genus Fulvius Stål (Hemiptera:Miridae: Cylapinae) based on molecular data

2008 ◽  
Vol 39 (4) ◽  
pp. 407-417 ◽  
Author(s):  
Izabela Sadowska-Woda ◽  
Tobias Malm ◽  
Frédéric Chérot
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Large Subunit ◽  
Morphological Characters ◽  
Molecular Data ◽  
Dna Sequence Data ◽  
Species Groups ◽  
Coi Sequences ◽  
Preliminary Phylogenetic Analysis

AbstractThe systematics and phylogeny of the genus Fulvius Stål remains unclear. We present herein the first analysis of the phylogenetic relationships within the genus Fulvius based on DNA sequences. The phylogenetic interrelationships in the genus Fulvius are investigated using partial DNA sequence data from two mitochondrial genes, the 16S ribosomal large subunit and the cytochrome oxidase I (COI). DNA sequences for Fulvius species representing three different subgroups distinguished previously on the base of morphological characters alone are compared to sequences from the closely related genera Rhinocylapidius and Cylapus. The data are analyzed using parsimony and Bayesian inference. The results confirm that on the basis of molecular data we can distinguish the same congruent groups of Fulvius species as using morphological characters, however with inclusion of the specimens of the genus Rhinocylapidius in the bifenestratus-group. Additional studies are needed to clarify the phylogenetic relationships within the tribe Fulviini, as well as within the genus Fulvius and its relation to Rhinocylapidius. However, the results of this study suggest that 16S and COI sequences will be very useful as molecular markers for such studies among these species-groups.

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