Do skin peptide profiles reflect speciation in the Australian treefrog Litoria caerulea (Anura : Hylidae)?

2000 ◽  
Vol 48 (1) ◽  
pp. 33 ◽  
Author(s):  
Stephen C. Donnellan ◽  
Michael J. Tyler ◽  
Paul Monis ◽  
Adam Barclay ◽  
Anna Medlin
Keyword(s):  
Molecular Genetic ◽  
Molecular Data ◽  
Data Sets ◽  
Tree Frog ◽  
Separate Species ◽  
Data Set ◽  
Skin Gland ◽  
Molecular Genetic Data ◽  
Litoria Caerulea ◽  
Peptide Profiles

Profiles of skin gland peptides of the tree frog Litoria caerulea from Australia show substantial divergence among geographic locations. Indeed, two divergent groups of populations, ‘eastern’ and ‘northern’, are apparent from a phenetic analysis of similarities of skin gland peptide profiles among populations of L. caerulea. We analyse variation in nuclear genes (allozyme frequencies) and the mitochondrial genome (haplotype relationships and frequencies) to test the taxonomic significance of differences apparent among profiles of skin gland peptides. Both molecular genetic data sets identified the same two groups apparent in the profiles of skin gland peptides. However, neither molecular data set, under an evolutionary species concept, provides strong enough evidence to support recognition of these groups as separate species. These data imply that the genetic basis of the inheritance and expression of skin gland peptides requires further characterisation.

Molecular data support rejection of the generic concept in the Coccotremataceae (Ascomycota)

2001 ◽  
Vol 33 (4) ◽  
pp. 315-321 ◽  
Author(s):  
Imke Schmitt ◽  
María Ines Messuti ◽  
G. Benno Feige ◽  
H. Thorsten Lumbsch
Keyword(s):  
Morphological Difference ◽  
Its Region ◽  
Molecular Data ◽  
Lsu Rdna ◽  
Data Sets ◽  
Data Set ◽  
Combined Analysis ◽  
Generic Concept ◽  
Parametric Bootstrapping ◽  
Alternative Topology

AbstractThe Coccotremataceae is a small family including two genera: Coccotrema with a crustose, granulate to verrucose thallus and Lepolichen with terete lobes and rhizines. The generic concept based on this morphological difference was re-evaluated using three molecular markers, mt SSU rDNA, nu LSU rDNA, and the nu ITS region. The analysis of the ITS region does not provide sufficient resolution within the Coccotremataceae, while the other two data sets contradict the current generic concept. The mt SSU and nu LSU data sets and the combined analysis of the two data sets all place Lepolichen within Coccotrema. However, an alternative topology with monophyletic Coccotrema cannot be rejected when the ITS data set is included in the combined analyses. This shortcoming of the ITS data set can be overcome by the combined analysis of all three data sets, where monophyletic Coccotrema can be rejected using parametric bootstrapping, as in the mt SSU and nu LSU data sets and combination thereof. It is proposed to reduce Lepolichen into synonymy with Coccotrema. The correct name for the only species previously placed in Lepolichen is Coccotrema coccophontm (Mont.) I. Schmitt, Messuti & Lumbsch.

Phylogenetic analysis of the druid flies (Diptera: Schizophora: Clusiidae) based on morphological and molecular data

2010 ◽  
Vol 41 (3) ◽  
pp. 231-274 ◽  
Author(s):  
Jinzhong Fu ◽  
Owen Lonsdale ◽  
Brian Wiegmann ◽  
Stephen Marshall
Keyword(s):  
Cytochrome Oxidase ◽  
Dna Sequences ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Cytochrome Oxidase Subunit ◽  
Data Set ◽  
Oxidase Subunit ◽  
Morphological And Molecular Data

AbstractIn this paper, the Clusiidae (Diptera: Schizophora) is analyzed phylogenetically using morphological and molecular data sets, and then redefined on the basis of derived morphological characters. The biology and distribution of the Clusiidae are also reviewed, a key is provided to the World genera, the status of the genus Craspedochaeta Czerny is reevaluated and the type of Heterochroa pictipennis Wulp is discussed. Molecular data sets include genomic DNA sequences from the mitochondrial genes COI (cytochrome oxidase subunit I) and COII (cytochrome oxidase subunit II), the large ribosomal nuclear subunit 28S, and the nuclear protein-coding carbomoylphosphate synthase (CPS) domain of CAD (or “rudimentary”). Genes were analyzed separately, in combination with each other, and in combination with a morphological data set. Although individual molecular data sets often provided conflicting phylogenetic signals, the topologies of the cladograms produced from each data set alone or in combination were largely similar. Most genus-level relationships and several basal divergences were unresolved, but Apiochaeta was very strongly and consistently supported as Sobarocephalinae, not Clusiinae. The Clusiinae and Sobarocephalinae are subsequently redefined using an adjusted morphological tree — retaining Apiochaeta in the Sobarocephalinae — that is only slightly longer (8.4%, or seven steps) than the most parsimonious tree. Our results illustrate the benefits of multiple independent data sets for phylogenetic reconstruction in order to verify and refine existing classifications.

scholarly journals Characterizing and Comparing Phylogenetic Trait Data from Their Normalized Laplacian Spectrum

2019 ◽  
Vol 69 (2) ◽  
pp. 234-248
Author(s):  
Eric Lewitus ◽  
Leandro Aristide ◽  
Hélène Morlon
Keyword(s):  
Resource Use ◽  
Simulated Data ◽  
Graph Laplacian ◽  
Molecular Data ◽  
Nonparametric Analysis ◽  
Data Sets ◽  
New World Monkeys ◽  
Phenotypic Evolution ◽  
Laplacian Spectrum ◽  
Data Set

Abstract The dissection of the mode and tempo of phenotypic evolution is integral to our understanding of global biodiversity. Our ability to infer patterns of phenotypes across phylogenetic clades is essential to how we infer the macroevolutionary processes governing those patterns. Many methods are already available for fitting models of phenotypic evolution to data. However, there is currently no comprehensive nonparametric framework for characterizing and comparing patterns of phenotypic evolution. Here, we build on a recently introduced approach for using the phylogenetic spectral density profile (SDP) to compare and characterize patterns of phylogenetic diversification, in order to provide a framework for nonparametric analysis of phylogenetic trait data. We show how to construct the SDP of trait data on a phylogenetic tree from the normalized graph Laplacian. We demonstrate on simulated data the utility of the SDP to successfully cluster phylogenetic trait data into meaningful groups and to characterize the phenotypic patterning within those groups. We furthermore demonstrate how the SDP is a powerful tool for visualizing phenotypic space across traits and for assessing whether distinct trait evolution models are distinguishable on a given empirical phylogeny. We illustrate the approach in two empirical data sets: a comprehensive data set of traits involved in song, plumage, and resource-use in tanagers, and a high-dimensional data set of endocranial landmarks in New World monkeys. Considering the proliferation of morphometric and molecular data collected across the tree of life, we expect this approach will benefit big data analyses requiring a comprehensive and intuitive framework.

scholarly journals Analysis of Genetic Diversity in Chrysopogon aciculatus Using Intersimple Sequence Repeat and Sequence-related Amplified Polymorphism Markers

HortScience ◽  
2016 ◽  
Vol 51 (8) ◽  
pp. 972-979 ◽  
Author(s):  
Xinyi Zhang ◽  
Li Liao ◽  
Zhiyong Wang ◽  
Changjun Bai ◽  
Jianxiu Liu
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Genetic ◽  
Issr Markers ◽  
Data Sets ◽  
Sequence Repeat ◽  
Data Set ◽  
Srap Markers ◽  
Molecular Genetic Diversity ◽  
High Level

Molecular genetic diversity and relationships among 86 Chrysopogon aciculatus (Retz.) Trin. accessions were assessed using intersimple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Twenty-five ISSR markers generated 283 amplification bands, of which 266 were polymorphic. In addition, 576 polymorphic bands were detected from 627 bands amplified using 30 SRAP primers. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher proportion of polymorphic loci (PPL; 94%) than SRAP markers (91.87%). The ISSR and SRAP data were significantly correlated (r = 0.8023). Cluster analysis of the separate ISSR and SRAP data sets clustered the accessions into three groups, which generally were consistent with geographic provenance. Cluster analysis of the combined ISSR and SRAP data set revealed four major groups similar to those based solely on ISSR or SRAP markers. The findings demonstrate that ISSR and SRAP markers are reliable and effective tools for analysis of genetic diversity in C. aciculatus.

Integration of morphological and molecular data sets in estimating fungal phytogenies

1995 ◽  
Vol 73 (S1) ◽  
pp. 649-659 ◽  
Author(s):  
François Lutzoni ◽  
Rytas Vilgalys
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Molecular Data ◽  
Morphological Data ◽  
Homogeneity Test ◽  
Data Sets ◽  
Data Set ◽  
Sampling Statistics ◽  
Combined Data

To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history. Key words: data sets heterogeneity, homogeneity test, lichen phylogeny, Omphalina, ribosomal DNA.

scholarly journals Morphological and Molecular Variation Between Fusarium avenaceum, Fusarium arthrosporioides and Fusarium anguioides Strains

Pathogens ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 94
Author(s):  
Tapani Yli-Mattila ◽  
Taha Hussien ◽  
Olga Gavrilova ◽  
Tatiana Gagkaeva
Keyword(s):  
Species Complex ◽  
Phylogenetic Analyses ◽  
Molecular Genetic ◽  
Molecular Data ◽  
Fusarium Avenaceum ◽  
Beta Tubulin ◽  
Separate Species ◽  
High Genetic Diversity ◽  
Wheat Seedlings ◽  
Climatic Regions

Fusarium avenaceum and closely related species are common fungi on various plants, cultivated in different climatic regions. The aim of this study was to determine the taxonomic affiliations of the F. avenaceum, Fusarium arthrosporioides, and Fusarium anguioides strains by using morphological, physiological and molecular-genetic approaches. Twenty-six single-spored morphologically identified strains, which were mainly from cereals, were investigated in order to find out, if they belong to a separate species. Pathogenicity of strains to wheat seedlings and ISSR (Inter Simple Sequence Repeats) fingerprint and beta-tubulin DNA sequence patterns were analyzed. According to phylogenetic analyses, the strains could be divided into two big groups consisting of mostly F. avenaceum or F. anguioides strains. F. arthrosporioides was not detected as a separate species by the sum of the characters. F. anguioides was characterized as a separate species, which could be identified by morphological and molecular data. High genetic diversity of the F. avenaceum species complex was revealed. One F. anguioides strain (rudbeckia, Vladivostok, Russia), had an identical beta-tubulin sequence with two previously sequenced strains of Fusarium tricinctum species complex, which were isolated from dicotyledonous plants in Asia.

Phylogeny of the water strider genus Aquarius Schellenberg (Heteroptera: Gerridae) based on nuclear and mitochondrial DNA sequences and morphology

2000 ◽  
Vol 31 (1) ◽  
pp. 71-90 ◽  
Author(s):  
Nils Møller Andersen ◽  
Jakob Damgaard ◽  
Felix A.H. Sperling
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Morphological Data ◽  
Published Data ◽  
Data Sets ◽  
Gene Encoding ◽  
Data Set

AbstractWe examined phylogenetic relationships among gerrid water striders of the genus Aquarius Schellenberg using molecular and morphological characters. The molecular data sets included 780 bp sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI), and 515 bp sequence data from the nuclear gene encoding elongation factor I alpha (EF-1α). The morphological data set was a slightly modified version of a previously published data set. We included all 17 known species and one subspecies of Aquarius as well as five species from three related genera, Gigantometra gigas, Limnoporus esakii, L. rufoscutellatus, Gerris pingreensis, and G. lacustris. Unweighted parsimony analyses of the COI data set gave a single most parsimonious tree (MPT) with a topology quite similar to the morphological tree. Parsimony analyses of the EF-1α data set gave 3 MPT's and a strict consensus of these trees gave a tree with a slightly different topology. A combined analysis of the three data sets gave a single MPT with the same topology as for the morphological data set alone. The phylogeny of Aquarius presented here supports the monophyly of the A. najas, remigis, conformis and paludum species groups as well as previous hypotheses about their relationships. On the other hand, the inclusion of molecular data weakens the support for the monophyly of the genus Aquarius, and questions the specific status of the eastern North American A. nebularis (as separate from A. conformis) and members of the Nearctic A. remigis group. Finally, we discuss the implications of the reconstructed phylogeny in the biogeography and ecological phylogenetics of Aquarius.

scholarly journals Taxonomy of dark- and white-barked birches related to Betula pendula and B. pubescens (Betulaceae) in Ukraine based on both morphological traits and DNA markers

2019 ◽  
Vol 191 (1) ◽  
pp. 142-154 ◽  
Author(s):  
Andrii Tarieiev ◽  
Igor Olshanskyi ◽  
Oliver Gailing ◽  
Konstantin V Krutovsky
Keyword(s):  
Morphological Traits ◽  
Molecular Genetic ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Betula Pubescens ◽  
Internal Transcribed Spacers ◽  
Published Data ◽  
Nucleotide Polymorphisms ◽  
Separate Species ◽  
Molecular Genetic Data

Abstract Distribution, taxonomy, nomenclature and molecular genetic data are presented for two closely related pairs of birch taxa: (1) dark-barked Betula pubescens var. sibakademica (Baran.) Kuzeneva (basionym B. sibakademica Baranov) and white-barked B. pubescens var. pubescens, and (2) dark-barked B. kotulae Zaverucha = B. pendula var. obscura (Kotula ex Fiek) Olšavská (basionym B. obscura Kotula ex Fiek, heterotypic synonym B. kotulae) and white-barked B. pendula, respectively. Using published data and sequences obtained in this study, it was found that, although these pairs can be distinguished not only by morphological characters but also by two diagnostic single nucleotide polymorphisms (SNPs) in the internal transcribed spacers ITS1 and ITS2, no sequence differences within each pair were detected. These results suggest that the colour of the bark cannot be used as a taxonomic trait at the species level, and the dark-barked birches within each pair should not be treated as separate species or varieties, but as forms, respectively. Therefore, we reassessed the taxonomic status of B. sibakademica and B. kotulae using morphological traits and molecular genetic markers and suggest that B. pubescens f. sibakademica (Baranov) Tarieiev comb. nov. and B. pendula f. obscura (Kotula ex Fiek) Tarieiev comb. nov. should be used for them, respectively. Betula pubescens f. sibakademica was described in Ukraine for the first time.

Morphological data, molecular data, and total evidence in phylogenetic analysis

1995 ◽  
Vol 73 (S1) ◽  
pp. 667-676 ◽  
Author(s):  
Anders Tehler
Keyword(s):  
Molecular Phylogeny ◽  
Sequence Data ◽  
Molecular Data ◽  
Sister Species ◽  
Total Evidence ◽  
Morphological Data ◽  
Data Sets ◽  
Data Set ◽  
Morphological And Molecular Data ◽  
Congruence Test

Two data sets, one morphological and one molecular, for ascolocular fungi have been analysed separately for taxonomic congruence and in combination for total evidence. Data were analysed with cladistic parsimony, the total support test, and the congruence test. The morphological data set comprised 15 characters and four species, Arthonia radiata, Dendrographa leucophaea, Lecanactis abietina, and Schismatomma pericleum (Arthoniales). The molecular data include the same species and comprised sequence data with 21 informative sites from approximately half of the 18S ribosomal RNA gene. The morphological phylogeny is corroborated by the molecular phylogeny with regard to relationships of Arthonia radiata, Schismatomma pericleum, and Dendrographa leucophaea. But in the molecular phylogeny Lecanactis abietina is placed as a sister species to the former three species. In the phylogeny inferred from morphological data Lecanactis abietina and Dendrographa leucophaea constitute a sister pair with Schismatomma pericleum followed by Arthonia radiata as subsequent sister taxa. The consensus obtained from the taxonomic congruence method was fully collapsed and uninformative. The combined morphological and molecular data in total evidence produced one most parsimonious cladogram. In total evidence Lecanactis abietina is placed as sister species to Schismatomma pericleum and Dendrographa leucophaea all with Arthonia radiata as sister species. The most resolved and phylogenetically informative hypothesis was obtained from cladistic parsimony analysis using total evidence. A review of congruence between morphological and molecular data in determining gross relationships within the Eumycota and Ascomycetes is also given. Key words: Ascomycetes, Arthoniales, phylogeny, cladistics, taxonomic congruence, total evidence, 18SrDNA.

scholarly journals Molecular phylogeny and morphological revision of the Ctenotus labillardieri (Reptilia: Squamata: Scincidae) species group and a new species of immediate conservation concern in the southwestern Australian biodiversity hotspot

Zootaxa ◽  
2012 ◽  
Vol 3390 (1) ◽  
pp. 1 ◽  
Author(s):  
GEOFFREY M. KAY ◽  
J. SCOTT KEOGH
Keyword(s):  
New Species ◽  
Nuclear Dna ◽  
Molecular Data ◽  
Species Group ◽  
Biodiversity Hotspot ◽  
Entire Group ◽  
Data Sets ◽  
Data Set ◽  
Conservation Concern ◽  
A New Species

Ctenotus is the largest and most diverse genus of skinks in Australia with at least 97 described species. We generated largemitochondrial and nuclear DNA data sets for 70 individuals representing all available species in the C. labillardieri species-group to produce the first comprehensive phylogeny for this clade. The widespread C. labillardieri was sampled extensively toprovide the first detailed phylogeographic data set for a reptile in the southwestern Australian biodiversity hotspot. Wesupplemented our molecular data with a comprehensive morphological dataset for the entire group, and together these data areused to revise the group and describe a new species. The morphologically highly variable species C. labillardieri comprisesseven well-supported genetic clades that each occupy distinct geographic regions. The phylogeographic patterns observed inthis taxon are consistent with studies of frogs, plants and invertebrates, adding strength to emerging biogeographic hypothesesin this iconic region. The species C. catenifer, C. youngsoni, and C. gemmula are well supported, and despite limited samplingboth C. catenifer and C. gemmula show substantial genetic structure. The threatened C. lancelini from Lancelin Island and theadjacent mainland is the sister taxon to a new species from the Swan Coastal Plain, which we describe as C. ora sp. nov. Thisspecies is a habitat specialist, occurring primarily in sandy regions south of Perth that currently are under intense development. Ctenotus ora sp. nov. should be considered for conservation attention immediately.

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