scholarly journals Evolution of Australasian Plantago (Plantaginaceae)

2021 ◽  
Author(s):  
◽  
Mei Lin Tay
Keyword(s):  
New Zealand ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Molecular Dating ◽  
Evolutionary Patterns ◽  
Its Phylogeny ◽  
Suitable Habitats

<p>Phylogenetic analyses using molecular data were used to investigate biogeographic and evolutionary patterns of Australasian Plantago. The Internal Transcribed Spacers (ITS) from nuclear DNA, ndhF-rpl32 from chloroplast DNA and cox1 from mitochondrial DNA were selected from a primer assay of 24 primer pairs for further phylogenetic analyses. Phylogenetic reconstruction and molecular dating of a dataset concatenated from these regions comprising 20 Australasian Plantago species rejected a hypothesis of Gondwanan vicariance for the Australasian group. The phylogeny revealed three independent dispersal events from Australia to New Zealand that match expected direction because of West Wind Drift and ocean currents. Following this study, a dataset with 150 new ITS sequences from Australasian Plantago, combined with 89 Plantago sequences from previous studies, revealed that the New Zealand species appear to have a recent origin from Australia, not long after the formation of suitable habitats formed by the uplift of the Southern Alps (about 5 mya), followed by radiation. The ITS phylogeny also suggests that a single migration event of alpine species to lowland habitats has occurred and that recurrent polyploidy appears to be an important speciation mechanism in the genus. Species boundaries between New Zealand Plantago were unclear using both morphological and molecular data, which was a result of low genetic divergences and plastic morphology. The taxonomy of several New Zealand Plantago species need revision based on the ITS phylogeny.</p>

scholarly journals Evolution of Australasian Plantago (Plantaginaceae)

2021 ◽  
Author(s):  
◽  
Mei Lin Tay
Keyword(s):  
New Zealand ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Molecular Dating ◽  
Evolutionary Patterns ◽  
Its Phylogeny ◽  
Suitable Habitats

<p>Phylogenetic analyses using molecular data were used to investigate biogeographic and evolutionary patterns of Australasian Plantago. The Internal Transcribed Spacers (ITS) from nuclear DNA, ndhF-rpl32 from chloroplast DNA and cox1 from mitochondrial DNA were selected from a primer assay of 24 primer pairs for further phylogenetic analyses. Phylogenetic reconstruction and molecular dating of a dataset concatenated from these regions comprising 20 Australasian Plantago species rejected a hypothesis of Gondwanan vicariance for the Australasian group. The phylogeny revealed three independent dispersal events from Australia to New Zealand that match expected direction because of West Wind Drift and ocean currents. Following this study, a dataset with 150 new ITS sequences from Australasian Plantago, combined with 89 Plantago sequences from previous studies, revealed that the New Zealand species appear to have a recent origin from Australia, not long after the formation of suitable habitats formed by the uplift of the Southern Alps (about 5 mya), followed by radiation. The ITS phylogeny also suggests that a single migration event of alpine species to lowland habitats has occurred and that recurrent polyploidy appears to be an important speciation mechanism in the genus. Species boundaries between New Zealand Plantago were unclear using both morphological and molecular data, which was a result of low genetic divergences and plastic morphology. The taxonomy of several New Zealand Plantago species need revision based on the ITS phylogeny.</p>

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

Gyrothyris williamsi sp. nov. and inter-relationships of some taxa from waters around New Zealand and the southern oceans (Rhynchonelliformea: Terebratelloidea)

2007 ◽  
Vol 98 (3-4) ◽  
pp. 425-435 ◽  
Author(s):  
Maria Aleksandra Bitner ◽  
Bernard L. Cohen ◽  
Sarah. L. Long ◽  
Bertrand Richer de Forges ◽  
Michiko Saito
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Last Common Ancestor ◽  
Rdna Sequences ◽  
Sw Pacific ◽  
Rates Of Evolution ◽  
The Antarctic

ABSTRACTThis paper describes a terebratelloid articulate brachiopod, Gyrothyris williamsi sp. nov., based on 95 specimens from seamounts on the Lord Howe Rise, Coral Sea, SW Pacific Ocean. The new species is attributed to Gyrothyris on the basis of (a) morphological and growth trajectory similarities; (b) phylogenetic analyses of an alignment of DNA sequence (∼2900-sites) obtained from nuclear-encoded small- and large-subunit ribosomal RNA genes (SSU and LSU); and (c) the presence of a distinctive, two-part deletion in the LSU gene. It is distinguished morphologically from Gyrothyris mawsoni and its subspecies by both internal and external morphology and by its isolated geographical distribution, which extends the patchy, known range of this genus to an area some 2000 km north of its previous northern limit around New Zealand. Phylogenetic analyses of the rDNAs and of mitochondrial cox1 gene sequences (663 sites) confirm previous indications that the New Zealand endemic terebratelloid genera form a clade (Neothyris (Calloria, Gyrothyris, Terebratella), but the position of Terebratella with respect to Calloria and Gyrothyris remains weakly established. These sequences disagree inexplicably about the closeness of the relationship between Neothyris parva and N. lenticularis. Analyses of the first sequences from Calloria variegata, a species restricted to the Hauraki Gulf, New Zealand, are consistent with the possibility that it originated locally, and recently, from C. inconspicua. Magellania venosa from S. America/Falklands joins with Antarctic Magellania fragilis and M. joubini to form an rDNA clade that excludes Terebratalia as the putative sister-group of the New Zealand terebratelloid clade. The cox1 (but not the rDNA) sequences of the New Zealand clade pass a test for clock-like rates of evolution, and maximum likelihood pairwise distances suggest that if genetic isolation between the ancestor of Antarctic Magellania and the last common ancestor of the New Zealand terebratelloid clade was initiated by separation of the Antarctic and New Zealand plates ∼90 Mya, isolation from M. venosa was initiated earlier, perhaps ∼145 Mya. However, in the simple phylogenetic reconstruction presented here from cox1 sequences, S. American and Antarctic Magellania spp. do not yield a well-supported clade, perhaps because of differences in base composition.

scholarly journals Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

2019 ◽  
Vol 42 (1) ◽  
pp. 75-100 ◽  
Author(s):  
C.G. Boluda ◽  
V.J. Rico ◽  
P.K. Divakar ◽  
O. Nadyeina ◽  
L. Myllys ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Delimitation ◽  
Sequence Data ◽  
Species Recognition ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Haplotype Network ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Molecular Sequence Data

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

Gymnosporangium przewalskii sp. nov. (Pucciniales, Basidiomycota) from China and its life cycle

Phytotaxa ◽  
2017 ◽  
Vol 311 (1) ◽  
pp. 67 ◽  
Author(s):  
BIN CAO ◽  
FU-ZHONG HAN ◽  
CHENG-MING TIAN ◽  
YING-MEI LIANG
Keyword(s):  
Life Cycle ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Molecular Data ◽  
Rust Fungi ◽  
Internal Transcribed Spacers ◽  
New Taxon ◽  
The Novel ◽  
Qinghai Province ◽  
Telial Stage

In an investigation of rust fungi in Qinghai Province, northwestern China, the novel rust species Gymnosporangium przewalskii was identified based on morphology and phylogenetic analyses. Phylogenetic analyses using the internal transcribed spacers (ITS) and the large subunit (LSU) rRNA partial gene revealed that G. przewalskii is monophyletic and distinct from other Gymnosporangium species. The life cycle of this new taxon was clarified based on molecular data. Its spermogonial and aecial stages occurred on Sorbus koehneana, and its telial stage was found on Juniperus przewalskii.

Porcelain crabs of the genera Pachycheles Stimpson and Neopisosoma Haig (Decapoda : Anomura : Porcellanidae): new premises based on molecular data and comments on phylogenetic relationships in the family

2016 ◽  
Vol 30 (5) ◽  
pp. 509
Author(s):  
Ivana Miranda ◽  
Fernando L. Mantelatto
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Reconstruction ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Significant Advance ◽  
Body Region ◽  
Isthmus Of Panama ◽  
Porcelain Crabs

Porcellanidae Haworth, 1825 is a family of marine anomuran crabs distributed throughout tropical and temperate regions of all the oceans, typically littoral and sublittoral waters, with a considerable diversity of lifestyles, habitats and colouration. Pachycheles Stimpson, 1858 and Neopisosoma Haig, 1960 share, among other morphological characteristics, the fragmentation of the lateral carapace walls. The morphology of this body region was key to supporting the establishment of Neopisosoma, which increased uncertainty about the taxonomic status of these genera due to the high intraspecific variation of this character. Our study reconstructs the phylogenetic relationship between Pachycheles and Neopisosoma based on mitochondrial and nuclear DNA sequences to evaluate whether these are valid taxa. While Pachycheles seems to be monophyletic, the position of Neopisosoma mexicanum (Streets, 1871) indicates that the group is polyphyletic, and deserves further investigation. Pachycheles is revealed to be older than Neopisosoma, and likely originated in the Indo-Pacific, later spreading to the American continent during the early Tertiary. Neopisosoma may have arisen much later in the Caribbean Province before the closure of the Isthmus of Panama, explaining its distribution, which is restricted mainly to Central America. The inclusion of a considerable number of species from both genera represents a significant advance in the study of this controversial group. The phylogenetic reconstruction of Pachycheles unveiled clades corroborated by morphology, but also revealed unclear relationships, which may indicate the potential existence of cryptic species.

scholarly journals Taxonomic revision and phylogenetic position of the flying squirrel genus Biswamoyopterus (Mammalia, Rodentia, Sciuridae, Pteromyini) on the northern Indo-China peninsula

ZooKeys ◽  
2020 ◽  
Vol 939 ◽  
pp. 65-85
Author(s):  
Guogang Li ◽  
Ye Htet Lwin ◽  
Bin Yang ◽  
Tao Qin ◽  
Phouthong Phothisath ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Molecular Data ◽  
Genetic Distances ◽  
Phylogenetic Position ◽  
Flying Squirrel ◽  
Two Samples

The flying squirrel genus Biswamoyopterus (Rodentia: Sciuridae: Pteromyini) was once considered to contain three species, Biswamoyopterus biswasi from northeastern India, B. laoensis from central Laos and B. gaoligongensis from southwest China, all identified from morphological characteristics of one or two specimens. However, based on similar morphological characteristics of two samples of the genus Biswamoyopterus collected recently from northern Laos and northern Myanmar, and the small genetic distances on mitochondrial DNA and nuclear DNA between them, the results strongly support these two samples as representatives of the same species. The phylogenetic analyses strongly support Biswamoyopterus as an independent genus of Pteromyini, as a sister group to Aeromys. Biswamoyopterus biswasi is distributed in the northern Indo-China peninsula, where it is exposed to a series of threats, such as intense hunting activity, illegal trade, and rapid habitat loss; this should warrant its classification as critically endangered according to the International Union for Conservation of Nature (IUCN) Red List criteria. Here, the molecular data for genus Biswamoyopterus and two new specimen records from northern Laos and northern Myanmar are presented.

Antitropical distribution of Lobelia species (Campanulaceae) between the Ryukyu Archipelago of Japan and Oceania as indicated by molecular data

2012 ◽  
Vol 60 (5) ◽  
pp. 417 ◽  
Author(s):  
Goro Kokubugata ◽  
Koh Nakamura ◽  
Paul I. Forster ◽  
Yumiko Hirayama ◽  
Masatsugu Yokota
Keyword(s):  
New Zealand ◽  
Distribution Pattern ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Sister Species ◽  
Ryukyu Archipelago ◽  
Molecular Phylogenetic

We tested the antitropical distribution of Lobelia loochooensis, endemic to the Ryukyu Archipelago of Japan, and its putative sister species of the same section Hypsela in Oceania (Australia and New Zealand). Molecular phylogenetic analyses based on cpDNA sequences were conducted for 41 Lobelia species of 11 sections including all the species of sect. Hypsela investigated in Asia and Malesia and 32 species of 16 allied genera of family Campanulaceae, because the genus Lobelia is known to be polyphyletic. In the result, L. loochooensis and an Australian endemic L. fluviatilis formed a clade, and this clade was sister to a clade of four New Zealand endemics: L. carens, L. fatiscens, L. fugax and L. ionantha. These two clades were nested in a clade with two other Australian congeners. We conclude that: (1) the lineage of L. loochooensis and the five Lobelia species occurring in Oceania demonstrate an antitropical distribution pattern; and (2) L. loochooensis has likely originated from a dispersal event from Australia to the Ryukyu Archipelago.

A phylogeny and evolutionary natural history of mesoamerican toads (Anura: Bufonidae: Incilius) based on morphology, life history, and molecular data

Zootaxa ◽  
2011 ◽  
Vol 3138 (1) ◽  
pp. 1 ◽  
Author(s):  
JOSEPH R. MENDELSON III ◽  
DANIEL G. MULCAHY ◽  
TYLER S. WILLIAMS ◽  
JACK W. SITES JR.
Keyword(s):  
Natural History ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Dna Sequence Data ◽  
Starting Point ◽  
History Of ◽  
Molecular Relationships ◽  
Significant Support

We combine mitochondrial and nuclear DNA sequence data with non-molecular (morphological and natural history) data to conduct phylogenetic analyses and generate an evolutionary hypothesis for the relationships among nearly every species of Mesoamerican bufonid in the genus Incilius. We collected a total of 5,898 aligned base-pairs (bp) of sequence data from mitochondrial (mtDNA: 12S–16S, cyt b, ND2–CO1, including tRNAsTRP–TYR and the origin of light strand replication; total 4,317 bp) and nuclear (CXCR4 and RAG1; total 1,581 bp) loci from 52 individual toads representing 37 species. For the non-molecular data, we collected 44 characters from 29 species. We also include Crepidophryne, a genus that has not previously been included in molecular analyses. We present results of parsimony and Bayesian analyses for these data separately and combined. Relationships based on the non-molecular data were poorly supported and did not resolve a monophyletic Incilius (Rhinella marina was nested within). Our molecular data provide significant support to most of the relationships. Our combined analyses demonstrate that inclusion of a considerably smaller dataset (44 vs. 5,898 characters) of non-molecular characters can provide significant support where the molecular relationships were lacking support. Our combined results indicate that Crepidophryne is nested within Incilius; therefore, we place the former in the synonymy of the latter taxon. Our study provides the most comprehensive evolutionary framework for Mesoamerican bufonids (Incilius), which we use as a starting point to invoke discussion on the evolution of their unique natural history traits.

Preliminary phylogenetic analysis of the genus Isophya (Orthoptera: Phaneropteridae) based on molecular data

Zootaxa ◽  
2010 ◽  
Vol 2621 (1) ◽  
pp. 27 ◽  
Author(s):  
BEATA GRZYWACZ-GIBAŁA ◽  
DRAGAN P. CHOBANOV ◽  
ELŻBIETA WARCHAŁOWSKA-ŚLIWA
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Mitochondrial Cytochrome ◽  
Mitochondrial Cytochrome B ◽  
High Level ◽  
Mitochondrial Cytochrome Oxidase ◽  
Its1 And Its2 ◽  
Preliminary Phylogenetic Analysis

A preliminary phylogenetic analysis involving 22 taxa of the genus Isophya was conducted using four molecular markers (sequences of mitochondrial cytochrome b (cyt b), fragments of mitochondrial cytochrome oxidase subunit II (COII) and the internal transcribed spacers I and II (ITS1 and ITS2)). Our results indicate that Isophya is a monophyletic group with the exception of one species, I. bivittata. The analysis revealed a high level of polymorphism in the mitochondrial and nuclear genes of all species. MtDNA performs better in the phylogenetic reconstruction of Isophya than the ITS markers. Although the results show some conflict with the systematics of the group known from morphological and bioacoustic data, the study can be the basis for future reconstructions of the phylogeny of Isophya.

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