scholarly journals Genetic diversity and taxonomic issues in Gastridium P.Beauv (Poaceae) inferred from plastid and nuclear DNA sequence analysis

2019 ◽  
Author(s):  
Anna Scoppola ◽  
Simone Cardoni ◽  
Mariangela Pellegrino ◽  
Javier López-Tirado ◽  
Marco Cosimo Simeone
Keyword(s):  
Nuclear Dna ◽  
Species Number ◽  
Sister Relationship ◽  
Phylogenetic Reconstructions ◽  
Grassland Ecosystems ◽  
Nucleotide Sequence Variation ◽  
Poaceae Family ◽  
Tree Topologies ◽  
Nuclear Its ◽  
Current Assessment

AbstractIncomplete taxonomic knowledge may seriously hamper biodiversity conservation efforts that are crucial in a context of global change. Gastridium P.Beauv. is a Mediterranean-Paleotropical member of the Poaceae family, inhabiting ephemeral grass habitats, whose species number and diversity are still imperfectly known. In order to progress towards a comprehensive taxonomic treatment of this genus, we examined patterns of DNA diversity in the four taxa (Gastridium lainzii, G. phleoides, G. scabrum, and G. ventricosum) that have been recently advanced by different authors, based on new morpho-ecological descriptors. We explored nucleotide sequence variation at two plastid (trnH-psbA, trnL-F) and one nuclear (ITS) DNA markers in 44 total individuals. Diversity data were treated with multiple statistical and phylogenetic tools, and integrated with available GenBank sequences of Gastridium and other closely related genera. Despite the limited variability detected, evidence of within-taxon genetic cohesion and estimates of molecular divergence comparable with those of species in the same subtribal lineage (Agrostidinae) were recovered. The identified plastid genealogies appeared congruent with a subdivision of the genus into (at least) three distinct entities, and coherent with collected morphological descriptors. Phylogenetic reconstructions with ITS were less corresponding to taxa identities, likely due to reticulation and polyploidization. Once placed in a broader taxonomic context, the investigated dataset produced plastid and nuclear tree topologies consistent with previous assessments, highlighting the overall little resolution of species and genera within Agrostidinae. In the plastid tree, a sister relationship between Gastridium and Triplachne was weakly supported. In the ITS tree, relationships among these genera were unresolved. The hypothesis of closely related but separately evolving lineages within Gastridium is discussed, suggesting a re-evaluation of its current assessment in taxonomic authorities to enhance our knowledge of the grass family, and assist future biodiversity surveys of key Mediterranean grassland ecosystems.

Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

2021 ◽  
Author(s):  
Sara Fuentes-Soriano ◽  
Elizabeth A. Kellogg
Keyword(s):  
Sequence Data ◽  
Plastid Dna ◽  
Sister Relationship ◽  
Data Set ◽  
Woody Perennial ◽  
History Of ◽  
Nuclear Its ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

scholarly journals Molecular phylogeny of Kazimierzus Plisko, 2006 (Clitellata, Kazimierzidae) from the Western and Northern Cape Province inferred from mitochondrial DNA sequences

2020 ◽  
Vol 61 (2) ◽  
pp. 83-92
Author(s):  
Thembeka Clara Nxele ◽  
Jadwiga Danuta Plisko ◽  
Tarombera Mwabvu ◽  
Oliver Tendayi Zishiri
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Integrative Taxonomy ◽  
Cryptic Diversity ◽  
Undescribed Species ◽  
Mitochondrial Marker ◽  
Phylogenetic Reconstructions ◽  
Northern Cape ◽  
Tree Building ◽  
Close Relatedness

Species identification of earthworms using morphology can be challenging and inconclusive as homoplasy in many characters is high. The use of molecular DNA technology, such as the use of conserved regions in mtDNA and nuclear DNA has unravelled the phylogenetic background of several earthworm species. The current study utilised the cytochrome c oxidase subunit I (COI) mitochondrial marker to reconstruct the phylogeny of Kazimierzus Plisko, 2006 species from the Western and Northern Cape provinces of South Africa. Phylogenetic reconstructions were implemented using Bayesian Inference, as well as Maximum Likelihood. Both tree building methods adhered to the monophyly of the majority of the taxa. Results showed that species fell into two clades and validated eleven currently known Kazimierzus species (K. circulatus (Plisko, 1998), K. franciscus (Pickford, 1975), K. guntheri (Pickford, 1975), K. hamerae (Plisko, 1998), K. kleinoodi Nxele & Plisko, 2017, K. nietvoorbiji Nxele & Plisko, 2017, K. nieuwoudtvillensis Nxele & Plisko, 2017, K. occidualis (Plisko, 1998), K. pearsonianus (Pickford, 1975), K. phumlani Nxele & Plisko, 2017, K. sophieae (Plisko, 2002)). Cryptic diversity is evident in K. occidualis with genetic divergence greater than 12% amongst populations. Kazimierzus franciscus and K. ljungstroemi (Pickford, 1975) have a low genetic variability suggesting close relatedness or probably conspecificity. A group of specimens from Clanwilliam are morphologically identical to K. sophieae, but are genetically distinct and may belong to undescribed species. This study demonstrates the importance of integrative taxonomy in earthworms in order to present reliable taxonomic and biogeographic data.

scholarly journals Phylogenetics of extant and fossil Pinaceae: methods for increasing topological stability

Botany ◽  
2016 ◽  
Vol 94 (9) ◽  
pp. 863-884 ◽  
Author(s):  
David S. Gernandt ◽  
Garth Holman ◽  
Christopher Campbell ◽  
Matthew Parks ◽  
Sarah Mathews ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Consensus Methods ◽  
Topological Stability ◽  
Branch Support ◽  
Tree Topologies ◽  
Cone Scale

Relationships of living and fossil Pinaceae were inferred using parsimony and Bayesian inference of morphological characters and plastid and nuclear DNA sequences. When considering extant taxa only, adding molecular to morphological characters resulted in markedly increased resolution and branch support compared with analysis of morphology alone. Including 45 fossil taxa resulted in drastically decreased resolution in morphology-based consensus trees. We evaluated the effect on branch support and resolution of including DNA sequences, deleting fossils lacking information for cone scale apices and seeds, using reduced consensus methods, and using implied weighting, and found that the greatest improvements were found by including DNA sequences and using implied weighting. The tree topologies from parsimony and Bayesian inference confirm previous findings that the fossil genus Pseudoaraucaria and a few species of Pityostrobus from the Lower Cretaceous are related to abietoid genera, and that other species of Pityostrobus are pinoid and closely related to Pinus. Focusing phylogenetic analyses on the most complete fossil cones, specifically those that are anatomically preserved and include both cone scale apices and seeds, and taking into account homoplasy, resulted in the clearest hypotheses for the timing and sequence of diversification in the family.

scholarly journals Contribution to Globularia phylogeny based on nuclear ribosomal spacer and two chloroplast DNA regions

2017 ◽  
Vol 118 (4) ◽  
Author(s):  
Kroata Hazler Pilepić ◽  
Maja Friščić ◽  
Ahmet Duran ◽  
Semir Maslo ◽  
Rade Garić ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Leaf Tissue ◽  
Molecular Data ◽  
Rbcl Gene ◽  
Nuclear Its ◽  
Cellular Dna ◽  
Chloroplast Dna Regions

Background and Purpose: Molecular approach has a major impact on phylogenetic studies of plants, considering that it gives useful information about evolutionary events and relations on all taxonomic levels. The sequence data of the nuclear ITS and of two chloroplast regions, trnL-trnF spacer and rbcL gene, obtained from thirteen Globularia L. taxa, including five Anatolian endemics, representing six sections altogether, were analyzed in order to determine the relations between the European and the Anatolian species and get a better insight into the phylogeny of several closely related Globularia taxa.  Materials and Methods: Total cellular DNA was extracted from fresh or frozen leaf tissue of thirteen Globularia samples. The ITS regions of nuclear DNA and two chloroplast DNA regions were amplified and sequenced. Obtained nuclear and combined plastid data matrices were subjected to Maximum Parsimony analyses. Results and Conclusions: Molecular data that were obtained in this study indicate the existence of separate centers of diversification for the European and the Anatolian Globularia. The results provide support for relationships among the studied Anatolian endemic species and indications for a redefinition of affinities of some of the European species. The results presented herein are discussed along with available morphological, karyological, phytogeographical and molecular data. Keywords: Globularia, ITS, trnL-trnF, rbcL, Maximum Parsimony, Quaternary

Teuvoa, a new lichen genus inMegasporaceae(Ascomycota:Pertusariales), includingTeuvoa junipericolasp. nov.

2013 ◽  
Vol 45 (3) ◽  
pp. 347-360 ◽  
Author(s):  
Mohammad SOHRABI ◽  
Steven D. LEAVITT ◽  
Víctor J. RICO ◽  
Mehmet G. HALICI ◽  
Gajendra SHRESTHA ◽  
...  
Keyword(s):  
North America ◽  
Central Asia ◽  
New Genus ◽  
Sequence Data ◽  
Morphological Characters ◽  
Sister Relationship ◽  
New Synonyms ◽  
Nuclear Its ◽  
Relationship Of ◽  
The Relationship

AbstractThe relationship ofAspicilia uxoriswithinMegasporaceaeis assessed within a phylogenetic context. ‘Aspicilia’uxorisand other related species are recovered as sister to the genusLobothallias. str. and described here as a new genus.Teuvoa(Ascomycota,Megasporaceae) is erected based on nuclear ITS and LSU sequence data and morphological characters. In addition toTeuvoa uxoris, a second species,T. junipericola,is added to the new genus based on material collected from North America.Teuvoa junipericola, T. uxorisandT. tibeticaform a group with 8-spored asci, absence of extrolites, rather short-sized conidia and ascospores, lack of a subhypothecial algal layer, and different substratum preferences (on organic substratum) with a sister relationship to genusLobothallias. lat. (AspiciliasubgenusPachyothalliaClauzade & C. Roux). Based on spore measurements of the holotypes,Lecanora ferganensisTomin from central Asia (Kyrgyzstan, Tajikistan and Uzbekistan),Lecanora atrodiscataGintovt, from Tajikistan andLecanora takyroidesDzhur. from Turkmenistan are new synonyms toT. uxoris. A lectotype forLecanora ferganensisis designated, expanding the known distribution ofT. uxorisfrom Algeria, Morocco and Spain, into Central Asia.

scholarly journals Phylogeny and Systematics of Ground Rollers (Brachypteraciidae) of Madagascar

The Auk ◽  
2001 ◽  
Vol 118 (4) ◽  
pp. 849-863 ◽  
Author(s):  
Jeremy J. Kirchman ◽  
Shannon J. Hackett ◽  
Steven M. Goodman ◽  
John M. Bates ◽  
R. Prum
Keyword(s):  
Ribosomal Rna ◽  
Nadh Dehydrogenase ◽  
Sequence Divergence ◽  
Museum Specimens ◽  
Sister Relationship ◽  
Data Set ◽  
Phylogenetic Reconstructions ◽  
The Family ◽  
Two Parameter ◽  
Combined Data

Abstract We studied relationships of five extant members of the endemic Malagasy family Brachypteraciidae, the ground rollers, using several mitochondrial genes (cytochrome-b, NADH dehydrogenase 2, 12S ribosomal RNA, and cytochrome oxidase I). As outgroups, we used other coraciiforms including the Cuckoo Roller (Family Leptosomatidae, Leptosomus discolor), several true rollers (Corcaciidae) and a tody (Todidae). Partial sequences of the Long-tailed Ground Roller (Uratelornis chimaera) were obtained from toe pad samples taken off museum specimens. For a combined data set of all genes, Kimura two-parameter distances between sequences of the five ground roller species were high, averaging 11% divergence. For several species, samples were available from widely separated geographic regions and intraspecific sequence divergence was low (≤0.8%). Unweighted and weighted parsimony and maximum-likelihood analyses consistently recovered monophyly of the family, a sister relationship between Brachypteraciidae and Coraciidae, and monophyly of one of three currently recognized ground roller genera (Atelornis). At the base of the Brachypteraciidae clade, we could not fully resolve relationships between Uratelornis and two species currently placed in Brachypteracias. Because of the uncertainty of basal nodes in our phylogenetic reconstructions, we recommend returning B. squamigera to the monotypic genus Geobiastes. High levels of divergence among ground rollers are similar to levels found in other avian groups endemic to Madagascar. However, we suggest that molecular divergences appear far too low to be consistent with mid-Eocene fossils attributed to the family.

scholarly journals A new phylogenetic analysis of Phytosauria (Archosauria: Pseudosuchia) with the application of continuous and geometric morphometric character coding

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5901 ◽  
Author(s):  
Andrew S. Jones ◽  
Richard J. Butler
Keyword(s):  
Phylogenetic Analyses ◽  
Late Triassic ◽  
Morphometric Character ◽  
Sister Relationship ◽  
Geometric Morphometric ◽  
Variable Position ◽  
Basal Clade ◽  
Discrete Character ◽  
Tree Topologies ◽  
Character Matrix

Phytosauria is a clade of large, carnivorous, semi-aquatic archosauromorphs which reached its peak diversity and an almost global distribution in the Late Triassic (c. 230–201 Mya). Previous phylogenetic analyses of Phytosauria have either focused primarily on the relationships of specific subclades, or were limited in taxonomic scope, and no taxonomically comprehensive dataset is currently available. We here present the most taxonomically comprehensive cladistic dataset of phytosaurs to date, based on extensive first-hand study, identification of novel characters and synthesis of previous matrices. This results in an almost twofold increase in phylogenetic information scored per taxon over previous analyses. Alongside a traditional discrete character matrix, three variant matrices were analysed in which selected characters were coded using continuous and landmarking methods, to more rigorously explore phytosaur relationships. Based on these four data matrices, four tree topologies were recovered. Relationships among non-leptosuchomorph phytosaurs are largely consistent between these four topologies, whereas those of more derived taxa are more variable. Rutiodon carolinensis consistently forms a sister relationship with Angistorhinus. In three topologies Nicrosaurus nests deeply within a group of traditionally non-Mystriosuchini taxa, leading us to redefine Mystriosuchini by excluding Nicrosaurus as an internal specifier. Two distinct patterns of relationships within Mystriosuchini are present in the four topologies, distinguished largely by the variable position of Mystriosuchus. In two topologies Mystriosuchus forms the most basal clade in Mystriosuchini, whilst in the others it occupies a highly derived position within the Machaeroprosopus clade. ‘Redondasaurus’ is consistently recovered as monophyletic; however, it also nests within the Machaeroprosopus clade. The greatest impact on tree topology was associated with the incorporation of continuous data into our matrices, with landmark characters exerting a relatively modest influence. All topologies correlated significantly with stratigraphic range estimates. Topological variability in our results highlights clades in which further investigation may better elucidate phytosaur relationships.

scholarly journals Una especie nueva de rana del género Chiasmocleis (Microhylidae: Gastrophryninae) de la Cordillera del Cóndor, Ecuador

2017 ◽  
Vol 57 (10) ◽  
pp. 119 ◽  
Author(s):  
Ana De Lourdes Almendáriz Cabezas ◽  
Jorge Brito M. ◽  
Diego Alejandro Batallas Revelo ◽  
Jorge Vaca-Guerrero ◽  
Santiago R. Ron
Keyword(s):  
New Species ◽  
Nuclear Dna ◽  
Ecological Data ◽  
Sister Relationship ◽  
White Spots ◽  
Close Relationship ◽  
Especie Nueva ◽  
Hands And Feet ◽  
A New Species ◽  
Yellowish White

We describe a new species of frog of the genus Chiasmocleis from the montane forests of southeastern Ecuador, at the western slopes of Cordillera del Cóndor, between 1,224‑1,630 m of elevation. Based on new sequences of mitochondrial and nuclear DNA we present phylogenetic relationships of the new species and its congeners. The phylogeny shows a close relationship to C. antenori, C. carvalhoi, C. magnova and C. tridactyla. The new species is part of a clade of species that were previously assigned to the genus Syncope. This clade has a sister relationship to a clade that contains all remaining species of Chiasmocleis. The new species differs from its congeners by its reddish-brown to dark-brown (sepia) dorsum with minute yellowish-white spots. Chiasmocleis parkeri sp. nov. is similar to Chiasmocleis antenori in lacking digit I of both hands and feet but Chiasmocleis parkeri differs in coloration, arrangement and size of pale spots, and the absence of a pale line in the canthal region. We describe the calls, which are characterized by having non-pulsed notes, and we provide ecological data from the type locality and adjacent areas.

Comparative phylogeography between parasitic sucking lice and their host the Namaqua rock mouse, Micaelamys namaquensis (Rodentia: Muridae)

2020 ◽  
Author(s):  
Johannes C Bothma ◽  
Sonja Matthee ◽  
Conrad A Matthee
Keyword(s):  
Nuclear Dna ◽  
Sequence Data ◽  
Strong Support ◽  
Dna Sequence Data ◽  
Geographic Patterns ◽  
Phylogenetic Reconstructions ◽  
Geographic Populations ◽  
Louse Species ◽  
Species Specific ◽  
Host Parasite

Abstract To gain a deeper understanding of the mechanisms affecting parasite gene dispersal and subsequent evolution, we investigated mitochondrial and nuclear DNA phylogeographic structures of two ectoparasitic louse species, Polyplax praomydis and Hoplopleura patersoni, and compared this to their host Micaelamys namaquensis. Analyses of mitochondrial and nuclear DNA sequence data derived from 13 geographic populations resulted in the detection of distinct phylogenetic clades within the parasite and host species. Strong support for host–parasite co-divergence was found over larger geographic scales but failed to show complete co-divergence over fine geographic scales. This finding led to the partial rejection of the hypothesis that the evolution of species-specific permanent parasites will mirror the phylogeographic pattern of their host. JANE co-phylogenetic reconstructions support the notion that host switching best explains the discrepancies in geographic patterns. We conclude that host specificity and permanency on the host only plays a partial role in maintaining co-divergences between parasites and their hosts.

scholarly journals An annotated key to the species of Gastridium (Poaceae) with distributional novelties to the Italian territory

2019 ◽  
Vol 6 (2) ◽  
Author(s):  
Anna Scoppola
Keyword(s):  
Related Species ◽  
Molecular Basis ◽  
Mediterranean Region ◽  
Species Number ◽  
Herbarium Specimens ◽  
Present Contribution ◽  
Closely Related Species ◽  
Poaceae Family ◽  
Italian Territory

Gastridium is a Mediterranean-paleotropical genus of the Poaceae family, native to Italy. Species number and diversity were imperfectly known until recent taxonomic updates on morphological and molecular basis that enhanced our knowledge of this taxon. The present contribution provides a complete key of the genus, encompassing the four currently known closely related species, G. lainzii, G. phleoides, G. scabrum, and G. ventricosum. The essential features of panicle, spikelets, and florets are specified and briefly discussed. Revisions of ancient and recent herbarium specimens provided three Italian distributional novelties for G. phleoides concerning Liguria, Campania, and Puglia and two for G. scabrum concerning Liguria and Basilicata. In contrast, the distributional ranges of G. scabrum and G. lainzii in the W Mediterranean region remain poorly known and await further investigations.

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