scholarly journals Molecular approaches reveal speciation between red and blue flowered plants in the Mediterranean Lysimachia arvensis and Lysimachia monelli (Primulaceae)

2021 ◽  
Author(s):  
Francisco Javier Jimenez-Lopez ◽  
Juan Viruel ◽  
Montserrat Arista ◽  
Pedro L Ortiz ◽  
Maria Talavera
Keyword(s):  
Phylogenetic Signal ◽  
Flower Colour ◽  
New Combination ◽  
Monophyletic Clade ◽  
Molecular Approaches ◽  
Phylogenetic Resolution ◽  
Variable Species ◽  
Nuclear Its ◽  
Plastid Markers ◽  
The Mediterranean

Flower colour constitutes a pivotal evolutionary force in speciation. The Mediterranean Lysimachia arvensis and L. monelli are morphologically variable species having both blue or red flowered plants. Previous studies suggested that L. arvensis plants differing in colour are diverging lineages, but this variation has not been considered in a phylogenetic context. We reconstruct the phylogenetic signal and the ancestral states of flower colour of Mediterranean Lysimachia species by using nuclear (ITS) and three plastid markers. Blue and red specimens are nested in two independent clades in the ITS tree, thus supporting that L. arvensis and L. monelli are polyphyletic, whereas low phylogenetic resolution was found in plastid markers. Blue-flowered L. arvensis is reconstructed sister to L. talaverae in a monophyletic clade sister to the remaining Lysimachia. Red-flowered L. arvensis is reconstructed sister to red-flowered L. monelli in a monophyletic clade sister to blue-flowered L. monelli and L. foemina. Our results suggest that colour lineages in L. arvensis and L. monelli constitute different species, but flower colour did not promote the separation of these lineages. We propose a new name for blue-flowered L. arvensis (L. loeflingii) and a new combination for red-flowered L. monelli (L. collina).

Apertochrysa (Neuroptera: Chrysopidae): A heterogeneric phantom? 

Zootaxa ◽  
2017 ◽  
Vol 4238 (1) ◽  
pp. 58 ◽  
Author(s):  
ATSUSHI MOCHIZUKI ◽  
CHARLES S. HENRY ◽  
PETER DUELLI
Keyword(s):  
Type Species ◽  
Morphological Traits ◽  
New Genus ◽  
Sequence Data ◽  
New Combination ◽  
Wing Venation ◽  
Monophyletic Clade ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Group Relationships

The small lacewing genus Apertochrysa comprises species from Africa, Asia and Australia. All lack a tignum, but otherwise resemble distantly related genera. We show that Apertochrysa does not form a monophyletic clade, based on analyses of molecular sequence data and morphological traits such as the presence and shape of the male gonapsis, wing venation, and larval setae. Apertochrysa kichijoi forms a clade with Eremochrysa, Suarius and Chrysemosa, whereas A. albolineatoides belongs to a clade that includes Cunctochrysa. Apertochrysa albolineatoides should become a new combination as Cunctochrysa albolineatoides, while A. kichijoi will have to be transferred to a new genus. The Australian A. edwardsi, the African A. eurydera and the type species of the genus Apertochrysa, A. umbrosa, join the large Pseudomallada group. Relationships of A. umbrosa are less certain, because for it we could amplify only one of the three nuclear genes used in the overall analysis. However, in all morphological traits tested, that species strongly resembles A. edwardsi and A. eurydera and thus is very likely just another exceptional Pseudomallada lacking a tignum. The fate of the genus name Apertochrysa depends on additional molecular and morphological analyses of A. umbrosa. 

scholarly journals Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Francesc López-Giráldez ◽  
Andrew H. Moeller ◽  
Jeffrey P. Townsend
Keyword(s):  
Phylogenetic Signal ◽  
Simulated Data ◽  
Quantitative Measure ◽  
Data Sets ◽  
Phylogenetic Informativeness ◽  
Phylogenetic Resolution ◽  
Taxonomic Groups ◽  
Diverse Groups ◽  
Simulated Data Sets ◽  
Selection Of

Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed.

scholarly journals Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity

2019 ◽  
Vol 20 (11) ◽  
pp. 2782 ◽  
Author(s):  
Maria M. Romeiras ◽  
Ana Rita Pena ◽  
Tiago Menezes ◽  
Raquel Vasconcelos ◽  
Filipa Monteiro ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Meta Analysis ◽  
Divergence Time ◽  
Oceanic Islands ◽  
Published Data ◽  
Cabo Verde ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Macaronesian Islands ◽  
Phylogenetic Resolution

Over the previous decades, numerous studies focused on how oceanic islands have contributed to determine the phylogenetic relationships and times of origin and diversification of different endemic lineages. The Macaronesian Islands (i.e., Azores, Madeira, Selvagens, Canaries, and Cabo Verde), harbour biotas with exceptionally high levels of endemism. Within the region, the vascular plants and reptiles constitute two of the most important radiations. In this study we compare relevant published phylogenetic data and diversification rates retrieved within Cabo Verde endemic lineages and discuss the importance of choosing appropriate phylogeny-based methods to investigate diversification dynamics on islands. From this selective literature-based review, we summarize the software packages used in Macaronesian studies and discuss their adequacy considering the published data to obtain well-supported phylogenies in the target groups. We further debate the importance of Next Generation Sequencing (NGS), to investigate the evolutionary processes of diversification in the Macaronesian Islands. Analysis of genomic data provides phylogenetic resolution for rapidly evolving species radiations, suggesting a great potential to improve the phylogenetic signal and divergence time estimates in insular lineages. The most important Macaronesian reptile radiations provide good case-studies to compare classical phylogenetic methods with new tools, such as phylogenomics, revealing a high value for research on this hotspot area.

Molecular systematics of Australian Podolepis (Asteraceae: Gnaphalieae): evidence from DNA sequences of the nuclear ITS region and the chloroplast matK gene

2000 ◽  
Vol 13 (5) ◽  
pp. 709 ◽  
Author(s):  
N. Konishi ◽  
K. Watanabe ◽  
K. Kosuge
Keyword(s):  
Dna Sequences ◽  
Its Region ◽  
Chromosomal Evolution ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Base Number ◽  
Monophyletic Clade ◽  
Matk Gene ◽  
Nuclear Its ◽  
Generic Relationships

The generic circumscription and intra-generic relationships of the genus Podolepis Labill., with various chromosome numbers from n = 12 to n = 3, were examined by sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the matK gene of chloroplast DNA. The topology of the ITS tree for 17 species and the matK tree for 18 species of the genus Podolepis sensu Davis (1957) and Anderberg (1991) and 15 taxa from eight related genera (Anderberg 1989, 1991, 1994) are basically concordant. Except for P. georgei Diels andP. kendallii F.Muell., parsimony analyses support the monophyly of the genus Podolepis sensu Davis (1957) and Anderberg (1991). The genera of Asteridea Lindl. and Pterochaeta Steetz are sisters toPodolepis in the combined tree based on the ITS and matK sequences. Within the monophyletic clade of the genus Podolepis, three lineages are identified. The chromosome base number of x = 12 may be ancestral in the genus Podolepis. The dysploidal reduction in chromosome number from n = 12 to n = 10 and 9, from n = 12 to n = 8 and 7, and from n = 12 to n = 11 and 3 in three lineages, respectively, is the primary mode of chromosomal evolution in this genus. Total karyotypic length (= genome size) is much greater in perennials than in annuals within the genus Podolepis. The number of pappus bristles on outer female florets tends to decrease and they are absent in some annuals of this genus, while myxogenic cells on the pericarp become prominent.

Molecular phylogenetics provides new insights into the systematics of Pimelea and Thecanthes (Thymelaeaceae)

2016 ◽  
Vol 29 (3) ◽  
pp. 185 ◽  
Author(s):  
Charles S. P. Foster ◽  
David J. Cantrill ◽  
Elizabeth A. James ◽  
Anna E. Syme ◽  
Rebecca Jordan ◽  
...  
Keyword(s):  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Distinct Species ◽  
Flowering Plants ◽  
New Combination ◽  
Evolutionary Relationships ◽  
Toxic Compounds ◽  
Biogeographic History ◽  
Plastid Markers

Pimelea Banks & Sol. ex Gaertn. is a genus of flowering plants comprising an estimated 90 species in Australia and ~35 species in New Zealand. The genus is economically important, with the inflorescences of some species having floricultural applications, and the presence of toxic compounds in several species proving poisonous to livestock. Pimelea grows in a variety of habitats ranging from arid to alpine, suggesting a complicated biogeographic history. The relationships within Pimelea remain largely uncertain, despite previous attempts at clarification using molecular phylogenetics. However, it is clear that Pimelea is closely related to Thecanthes Wikstr., with the two genera comprising the subtribe Pimeleinae. We used Bayesian and maximum-likelihood phylogenetic analyses of four plastid markers (matK, rbcL, rps16, trnL–F) and one nuclear ribosomal marker (ITS) to examine the evolutionary relationships within Pimeleinae. We found strong support for the monophyly of Pimeleinae but, similar to previous studies, Pimelea was paraphyletic with respect to Thecanthes. Our results also indicated that P. longiflora R.Br. subsp. longiflora and P. longiflora subsp. eyrei (F.Muell.) Rye are best considered as distinct species. Therefore, we reduce Thecanthes to synonymy with Pimelea, making the necessary new combination Pimelea filifolia (Rye) C.S.P.Foster et M.J.Henwood (previously Thecanthes filifolia Rye), and also reinstate Pimelea eyrei F.Muell.

scholarly journals A New Combination in Holodiscus (Rosaceae, Amygdaloideae, Spiraeeae)

Phytotaxa ◽  
2020 ◽  
Vol 477 (2) ◽  
pp. 284-290
Author(s):  
DANIEL POTTER ◽  
ROGER RAICHE
Keyword(s):  
Genetic Data ◽  
New Combination ◽  
Serpentine Soils ◽  
Variable Species ◽  
Sonoma County ◽  
Coast Ranges ◽  
Distinct Morphology ◽  
Outer Coast

Holodiscus dumosus var. cedrorum, The Cedars oceanspray, was described in 2011 in recognition of the distinct morphology of populations occurring on serpentine soils in The Cedars area in the Outer Coast Ranges of Sonoma County, California. Morphological and genetic data suggest that this taxon should instead be treated as a variety of Holodiscus discolor, here interpreted broadly as a widespread and highly variable species with several taxonomic varieties that intergrade. The new combination Holodiscus discolor var. cedrorum is made and a key to the varieties that occur in California is provided.

scholarly journals Phylogenetic Signal and Bias in Paleontology

2021 ◽  
Author(s):  
Robert J Asher ◽  
Martin R Smith
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Tree Of Life ◽  
Morphological Data ◽  
Phylogenetic Resolution ◽  
Phylogeny Estimation ◽  
Better Than

Abstract An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.

scholarly journals The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences

PhytoKeys ◽  
2019 ◽  
Vol 125 ◽  
pp. 1-112 ◽  
Author(s):  
James A. Compton ◽  
Brian D. Schrire ◽  
Kálmán Könyves ◽  
Félix Forest ◽  
Panagiota Malakasi ◽  
...  
Keyword(s):  
East Asia ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
New Combination ◽  
New Combinations ◽  
New Genera ◽  
Infraspecific Taxa ◽  
Nuclear Its ◽  
Single Genus ◽  
Chloroplast Dna Sequences

The Tribe Wisterieae (Zhu 1994), founded on the single genus Wisteria, is emended and recircumscribed based on morphology and data from nuclear ITS and ndhJ-trnF, matK and rbcL chloroplast DNA sequences. This newly enlarged tribe comprises 36 species and 9 infraspecific taxa within 13 described genera. Six genera are new, two are reinstated and five were previously placed in Tribe Millettieae. The genus Adinobotrys is also reinstated comprising two species including the new combination A.vastus. Other reinstated genera include Whitfordiodendron, with four species, and Padbruggea, with three species, including the reinstatement of P.filipes and the new combination P.filipesvar.tomentosa. The existing genera Afgekia, Callerya, Endosamara (with the new combination E.racemosavar.pallida), Sarcodum and Wisteria, with the new combinations W.frutescenssubsp.macrostachya are evaluated. The new genera comprise three Australasian species in Austrocallerya: A.australis, A.megasperma and A.pilipes; Wisteriopsis with five species from east Asia has six new combinations: W.japonica, W.kiangsiensis, W.championii, W.eurybotrya, W.reticulata and W.reticulatavar.stenophylla. Two species comprise the new Thai genus Kanburia: K.tenasserimensis and K.chlorantha. Nanhaia comprises the two species: N.fordii and N.speciosa and the monotypic genera Sigmoidala and Serawaia are based respectively on the species S.kityana and S.strobilifera. Lectotypes are designated for the names Adinobotrysfilipes, A.myrianthus, Millettiabonatiana, Millettiabracteosa, Millettiachampionii, Millettiacinerea, Millettiadielsiana, Millettiakityana, M.maingayi, Millettianitida, Millettiaoocarpa, Millettiapurpurea, M.reticulata, M.reticulatavar.stenophylla, Padbruggeadasyphylla, Pterocarpusaustralis, Robiniaracemosa, Whitfordiodendronscandens, W.sumatranum and Wisteriapallida. A neotype is designated for the name Millettialeiogyna.

scholarly journals An Elegy to Rangaeris, Including a Description of Two New Genera in the Cyrtorchis–Tridactyle Clade (Orchidaceae, Angraecinae)

2020 ◽  
Vol 105 (3) ◽  
pp. 300-322
Author(s):  
João N. M. Farminhão ◽  
Tania D'haijère ◽  
Vincent Droissart ◽  
Landry Dumbo Isonga ◽  
Ling Dong ◽  
...  
Keyword(s):  
Conservation Status ◽  
Intergenic Spacer ◽  
Phylogenetic Position ◽  
Morphological Evidence ◽  
New Genera ◽  
Representative Sampling ◽  
Distribution Maps ◽  
Nuclear Its ◽  
Plastid Markers ◽  
Angraecoid Orchids

The phylogenetic position of Rangaeris (Schltr.) Summerh. has been one of the most problematic issues of angraecoid orchid taxonomy. A recently published phylogenetic tree with nearly comprehensive taxon sampling of African angraecoid orchids suggested that this genus was polyphyletic, as its species appear nested within different subclades of the Cyrtorchis–Tridactyle clade. However, the lack of DNA data for the generic type, R. muscicola (Rchb. f.) Summerh., and for the little-known species R. longicaudata (Rolfe) Summerh. and R. trilobata Summerh., has precluded an integrative reappraisal of the delimitation of this genus. Here we present the results of a new phylogenetic analysis of one nuclear (ITS) and five plastid markers (matK, rps16, trnC-petN intergenic spacer, trnL-trnF intergenic spacer, ycf1) for all six species of Rangaeris, including those recently transferred to Podangis Schltr. and Ypsilopus Summerh., together with a representative sampling of 14 other species of the genera Cyrtorchis Schltr., Listrostachys Rchb. f., Plectrelminthus Raf., Summerhayesia P. J. Cribb, Tridactyle Schltr., and Ypsilopus. Based on molecular and morphological evidence, R. muscicola is transferred to Podangis, where Rangaeris is reduced to the rank of section. In addition, R. longicaudata and R. trilobata are each moved to new monotypic genera, Planetangis Stévart & Farminhão and Aziza Farminhão & D’haijère, respectively. An identification key for all genera of the Cyrtorchis–Tridactyle clade is presented, together with one for the three species of recircumscribed Podangis. Finally, taxonomic accounts of the new genera are presented, including amended descriptions, illustrations, distribution maps, and preliminary conservation status assessments of their species.

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