scholarly journals Cladistic analyses of molecular characters: The good, the bad and the ugly

2002 ◽  
Vol 71 (1-3) ◽  
pp. 93-100 ◽  
Author(s):  
Maximilian J. Telford
Keyword(s):  
General Solution ◽  
Morphological Character ◽  
Morphological Characters ◽  
Molecular Characteristic ◽  
Cladistic Analyses ◽  
Molecular Characters

Molecular cladistics is an emerging discipline in which any heritable molecular characteristic can be treated in the same way that a traditional cladist would treat a morphological character. Taxa that share specific derived molecular characters (synapomorphies)are recognized as more closely related to each other than they are to other taxa without these characters. Herein, I point out that molecular characters are susceptible to the same problems of homoplasy and uncertain polarity as morphological characters and illustrate these problems (and point towards a general solution) using examples from the Metazoa.

Molecular systematics of subtribe Banksiinae (Banksia and Dryandra; Proteaceae) Based on cpDNA and nrDNA sequence data: Implications for taxonomy and biogeography

1998 ◽  
Vol 11 (4) ◽  
pp. 321 ◽  
Author(s):  
Austin R. Mast
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Base Substitution ◽  
Trnl Intron ◽  
Single Root ◽  
Cladistic Analyses ◽  
Molecular Characters

Despite considerable research interest in the subtribe Banksiinae (Banksia L.f. and Dryandra R.Br.), no strongly supported phylogenetic hypothesis for the relationship between the genera exists, nor have molecular characters been sampled for phylogenetic reconstruction at any level. In this study, DNA sequence characters were sampled from chloroplast DNA (cpDNA; the trnL intron, the trnL 3′ exon, and the spacer between the trnL 3′ exon and trnF) and nuclear ribosomal DNA (nrDNA; both internal transcribed spacers) of 18 species of Banksia and five of Dryandra, with six outgroup taxa from the subfamily Grevilleoideae. The molecular characters provided the opportunity to code taxa outside of Banksia for cladistic comparison with the genus—an opportunity not previously provided by morphological characters. Cladistic analyses, using parsimony, explored the effects of various weightings of transition to transversion events and base substitution to insertion and deletion events to determine which relationships in the cladograms were robust. The trnL/trnF and ITS characters strongly supported a paraphyletic Banksia with respect to a monophyletic Dryandra. The molecular results supported a single root for Thiele and Ladiges’(1996) unrooted morphological cladogram along the branch between the Isotylis to B. fuscolutea clade and the Grandes to B. tricuspis clade. George’s (1981) subgenus Banksia and section Banksia appeared dramatically non-monophyletic. The distribution of eastern taxa at derived positions on the molecular cladograms suggested considerable cladogenesis in the the genus prior to the formation of the Nullarbor Plain during the Tertiary.

scholarly journals Distribution and evolution of secondary metabolites in Eriocaulaceae, Lythraceae and Velloziaceae from "campos rupestres"

2000 ◽  
Vol 23 (4) ◽  
pp. 931-940 ◽  
Author(s):  
Antonio Salatino ◽  
Maria Luiza Faria Salatino ◽  
Déborah Yara A.C. dos Santos ◽  
Márcia Cristina B. Patrício
Keyword(s):  
Fatty Acids ◽  
Secondary Metabolites ◽  
Salient Feature ◽  
Morphological Characters ◽  
Epicuticular Wax ◽  
Campos Rupestres ◽  
Carbon Chains ◽  
Cladistic Analyses ◽  
Flavonoid Patterns ◽  
Molecular Characters

Hypotheses are presented on the evolution of structural patterns of secondary metabolites (flavonoids and foliar wax alkanes) and fatty acids of families of "campos rupestres". The distribution of fatty acids is given for genera of Lythraceae, with emphasis on Cuphea (supposedly more advanced) and Diplusodon. Compounds with saturated short chains represent a derived condition in Lythraceae although they are probably restricted to Cuphea. It is suggested that evolution selected for more complex flavonoid patterns in Cuphea, with the inclusion of C-glycoflavones and methoxylated flavonols (rhamnetin and isorhamnetin), which are not found in members of Diplusodon and Lafoensia. The supposedly primitive groups of Eriocaulaceae (e.g., Paepalanthus) presented more complex flavonoid patterns characterized by flavones and flavonols, the latter frequently being 6-hydroxylated or methoxylated. More advanced groups of Eriocaulaceae (e.g., Leiothrix and Syngonanthus) apparently possess only flavones, C-glycoflavones are a salient feature of species with smaller habits. In Velloziaceae, members of the primitive subfamily Vellozioideae show distribution of alkanes of foliar epicuticular wax in which C27, C29 or C31 predominate; members of the derived subfamily Barbacenioideae usually show distributions with a predominance of C33 or C35, while species of Pleurostima (Barbacenioideae) have C31 as the main homologue, thus being intermediate between the two subfamilies. It is suggested that the evolution of alkanes in Velloziaceae follows a trend toward elongation of carbon chains. The condition of advanced or primitive chemical patterns is inferred from the results of cladistic analyses based on morphological characters (Eriocaulaceae and Lythraceae), and morphological and molecular characters (Velloziaceae).

scholarly journals Short Communication: Genetic diversity of lemon (Citrus spp.) from Ternate Island (Indonesia) based on morphological and molecular characters

2020 ◽  
Vol 21 (5) ◽  
Author(s):  
Abdulrasyid Tolangara ◽  
ALOYSIUS DURAN COREBIMA ◽  
ABDU MAS’UD ◽  
SUNDARI
Keyword(s):  
Genetic Diversity ◽  
Morphological Character ◽  
Short Communication ◽  
Morphological Characters ◽  
Breeding Programs ◽  
Morphometric Characters ◽  
Insight Into ◽  
Citrus Spp ◽  
Molecular Characters ◽  
Selection Of

Abstract. Tolangara A, Corebima AD, Mas'ud A, Sundari. 2020. Short Communication: Genetic diversity of lemon (Citrus spp.) from Ternate Island (Indonesia) based on morphological and molecular characters. Biodiversitas 21: 1908-1913. One effort to build the image of Indonesian lemon can be by utilizing local genetic resources of Citrus spp. One of the growth centra lemon regions in North Maluku is Ternate Island. In Ternate island, cui (C. macrocarpa) is dominantly cultivated besides that there are Suanggi (C. histryx), nipis (C. aurantiifolia), and lemon (C sinensis). The genetic diversity of these local lemons in North Maluku, especially in Ternate, has not been scientifically reported. Therefore, this study aimed to analyze the genetic diversity of local lemons found on the island of Ternate based on morphological character and RAPD molecular analyses. A total of 12 accessions of local lemons in Ternate island to studied for morphological and molecular characters. Observation of morphological and morphometric characters of the lemons on 117 characters of vegetative and generative organs in lemons. Observation of molecular characters using three primers, i.e.: OPA1, OPA 2, and OPA 3 in the RAPD technique. The morphological character and molecular character using UPGMA analysis showed similar results. Ternate Island has moderate diversity of lemon species (75% based on morphological characters and 73% based on RAPD markers). Cluster analysis indicates that cui (C. macrocarpa) has the most distinctive autapomorphic character compared to the other local lemon varieties. Nipis (C.auratiifolia) and Suanggi (C. hystrix) shared 75% synapomorphic character similarity. This genetic diversity information provides a novel insight into the lemon commodity breeding programs which can be encouraged through the selection of superior local lemons based on morphological and molecular markers.

scholarly journals Description of a new annual rivulid killifish genus from Venezuela

Zootaxa ◽  
2008 ◽  
Vol 1734 (1) ◽  
pp. 27 ◽  
Author(s):  
TOMAS HRBEK ◽  
DONALD C. TAPHORN
Keyword(s):  
New Genus ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Sister Species ◽  
Taxonomic History ◽  
Molecular Characters

We describe a new genus to accommodate the species originally described as Rivulus stellifer Thomerson & Turner, 1973, but currently referred to the genus Rachovia Myers, 1927. Rachovia stellifer has had a complicated taxonomic history and has, at various times since its description, been placed in and out of three genera: Rivulus Poey, 1860, Pituna Costa, 1989 and Rachovia. However, phylogenetic analyses using 3537 mitochondrial and nuclear characters, and 93 morphological characters indicate it is not a member of any of these genera, but place it as a deeply divergent sister species to the genus Gnatholebias Costa, 1998. In addition to molecular characters, it is distinguished from the genera Rachovia and Gnatholebias by 13 and 33 morphological character states, respectively.

scholarly journals The relative taxonomic value of morphological characters in the genus <i>Nummulites</i> (Foraminiferida)

1992 ◽  
Vol 11 (2) ◽  
pp. 197-209 ◽  
Author(s):  
Andrew Racey
Keyword(s):  
Morphological Character ◽  
Morphological Characters ◽  
Species Discrimination ◽  
Evolutionary Trends ◽  
Ontogenetic Effects

Abstract. The main evolutionary trends in the nummulites are briefly summarised and the value of certain morphological characters in species discrimination are summarised. The degree of interdependence of each morphological character on all other characters is assessed and the characters are weighted in order of importance. Environmental and ontogenetic effects on each character are then reviewed and the characters reweighted in order of importance.

scholarly journals Morphological Character of Local Irrigated Rice on Farmer Field in North Sulawesi

2018 ◽  
Vol 24 (1) ◽  
pp. 1
Author(s):  
Janne H.W. Rembang ◽  
Abdul W. Rauf ◽  
Joula O.M. Sondakh
Keyword(s):  
Qualitative Method ◽  
Morphological Character ◽  
Grain Morphology ◽  
Morphological Characters ◽  
Leaf Sheath ◽  
Rice Cultivars ◽  
Rice Varieties ◽  
Irrigated Rice ◽  
North Sulawesi ◽  
Leaf Character

<p>Local rice is a potential germplasm as a source of genes that control important properties in rice plants. The research aimed to characterize the morphological character of local rice cultivars of North Sulawesi. The research was conducted from January to June 2015 in North Sulawesi. The method used was the descriptive qualitative method. Exploration was done by collecting samples of local rice cultivars in North Sulawesi. Each cultivar was characterized its morphological characters according to the Characterization and Evaluation Guidelines of Rice Germplasm. The local rice found in North Sulawesi were 10 varieties, namely Pulo Sawah, Superwin, CK, Serwo, Pilihan, Sako, Sito Merah, Sito Putih, TB, and Serayu. There were similarities of the characters from all local rice varieties of North Sulawesi, such as culm (culm strength and culm habit), leaf character (basal leaf sheath color, leaf blade color, collar color, and auricle color), and flower character (panicle exsertion and panicle attitude of branches). The character of grain morphology was very diverse for all local rice varieties of North Sulawesi.</p>

scholarly journals Karakterisasi Morfologi dan Sifat Kuantitatif Gandum (Triticum aestivum L.) di Dataran Menengah

2016 ◽  
Vol 44 (2) ◽  
pp. 162
Author(s):  
Sartika Widowati ◽  
Nurul Khumaida ◽  
Sintho Wahyuning Ardie ◽  
Dan Trikoesoemaningtyas
Keyword(s):  
Morphological Character ◽  
Plant Biomass ◽  
Block Design ◽  
Triticum Aestivum L ◽  
Morphological Characters ◽  
Environmental Condition ◽  
Harvest Time ◽  
Wheat Growth ◽  
Randomized Complete Block Design ◽  
Weight Number

ABSTRACT<br /><br />Indonesia is one of the largest wheat importers. Suitable environmental condition for wheat needs to be studied if wheat is going to be widely cultivated in Indonesia. The adaptability of wheat grown in various climates and altitudes is one of the important aspects. The objective of this experiment was to study the quantitative and morphological character of wheat grown in middle land (540 m asl) in Bogor, West Java. The experiment was arranged in randomized complete block design with three replications. Wheat genotypes used were three national varieties (Nias, Selayar, and Dewata), four new improved varieties (Guri 3 Agritan, Guri 4 Agritan, Guri 5 Agritan, and Guri 6 Unand), and one introduced genotype (SBD). Data were collected for several quantitative variables and seventeen morphological characters based on UPOV descriptor. The result showed that wheat growth was restricted in Bogor. Genotype determined plant height, leaf number, ear length, root length, number of spikelet, harvest time, seed weight, number of tillers, and plant biomass. Based on ear length, grain weight, and plant biomass, Guri 3 Agritan had the highest production than the other genotypes.<br /><br />Keywords: diversity, genetic relationship, high temperature, introduced genotype, phylogenetic<br /><br />

scholarly journals A new species of Galleria Fabricius (Lepidoptera, Pyralidae) from Korea based on molecular and morphological characters

ZooKeys ◽  
2020 ◽  
Vol 970 ◽  
pp. 51-61
Author(s):  
Seung Jin Roh ◽  
Haechul Park ◽  
Seong-Hyun Kim ◽  
So-Yun Kim ◽  
Yong-Su Choi ◽  
...  
Keyword(s):  
New Species ◽  
Honey Bees ◽  
Galleria Mellonella ◽  
Morphological Characters ◽  
Taxonomic Study ◽  
Greater Wax Moth ◽  
Lepidoptera Pyralidae ◽  
A New Species ◽  
Molecular Characters ◽  
Wax Moth

The greater wax moth, Galleria mellonella Linnaeus, is well known as a pest of honey bees and for the biodegradation of wax and polyethylene by their larvae. The genus Galleria has long been considered monotypic and found worldwide. A taxonomic study of the genus Galleria is presented based on morphological and molecular characters (COI, CAD, wg). A new species (Galleria similis Roh &amp; Song, sp. nov.) is recognized on the Korean peninsula. The new species is superficially similar to G. mellonella but they can be separated by the structures of hindwing venation and male genitalia. Habitus photographs and illustrations of diagnostic characters are provided.

scholarly journals Karakter Morfologi dan Identifikasi Molekuler dengan Menggunakan Marka Gen 12S rRNA pada Ikan Baronang (Siganus spp.) di Perairan Laut Selatan Pulau Lombok

2020 ◽  
Vol 6 (1) ◽  
pp. 105
Author(s):  
Mahrus Mahrus ◽  
Abdul Syukur
Keyword(s):  
Fragment Size ◽  
Morphological Characters ◽  
Rrna Genes ◽  
12S Rrna ◽  
Morphological Classification ◽  
Number Of Species ◽  
South Sea ◽  
Random Method ◽  
Molecular Characters

This study aims to obtain the certainty of the number of species of baronang fish (Siganus spp.) Siganidae family in the waters of the south sea of Lombok Island.  This study used a sample of 90 fish from the fishermen's catch. Sampling used a random method three times. Observation of morphological characters used 90 and nine fishes for molecular characters-12S rRNA genes. The study used a descriptive technique for data analysis. The results showed that the fish is only one species and suspected consists of 3 variants. Three variants of fish have the same 12S rRNA genes with a fragment size of approximately 1000 bp. The morphological classification of the three groups of fish does not indicate the number of species, but no more as genetic variants.

scholarly journals Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical reappraisal of cladistic characters

2004 ◽  
Vol 73 (1-2) ◽  
pp. 3-163 ◽  
Author(s):  
Ronald A. Jenner
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Total Evidence ◽  
Morphological Data ◽  
Future Research ◽  
Sister Group Relationship ◽  
Cladistic Analyses ◽  
Phylogenetic Hypotheses ◽  
Data Matrices

This paper critically assesses all morphological cladistic analyses of the Metazoa that were published during the last one and a half decades. Molecular and total evidence analyses are also critically reviewed. This study focuses on evaluating alternative phylogenetic positions of the ‘acoelomate’ worms: Platyhelminthes, Nemertea, and Gnathostomulida. This paper consists of two parts. In Part I, all recently proposed sister group hypotheses and the supporting synapomorphies for these phyla are evaluated. Discrepancies in the treatment of corresponding characters in different cladistic analyses are identified, and where possible, resolved. In Part II, the overall phylogenetic significance across the Metazoa of all characters relevant for placing the ‘acoelomate’ worms is examined. The coding and scoring of these characters for other phyla are evaluated, and uncertainties in our understanding are pointed out in order to guide future research. The characters discussed in this paper are broadly categorized as follows: epidermis and cuticle, reproduction and sexual condition, development, larval forms, coeloms and mesoderm source, nervous system and sensory organs, nephridia, musculature, digestive system, and miscellaneous characters. Competing phylogenetic hypotheses are compared in terms of several criteria: 1) taxon sampling and the fulfillment of domain of definition for each character; 2) character sampling; 3) character coding; 4) character scoring and quality of primary homology; 5) quality of the proposed diagnostic synapomorphies as secondary homologies. On the basis of this study I conclude that a sister group for the Platyhelminthes has not yet been unambiguously established. A clade minimally composed of Neotrochozoa (Mollusca, Sipuncula, Echiura, Annelida) emerges as the most likely sister group of the Nemertea on the basis of morphological and total evidence analyses. Finally, morphological data currrently favor a sister group relationship of Gnathostomulida and Syndermata (probably plus Micrognathozoa). In contrast, molecular or total evidence analyses have not identified a reliable sister group of Gnathostomulida.Further progress in our understanding of metazoan phylogeny crucially depends on the improvement of the quality of currently adopted cladistic data matrices. A thorough reassessment of many of the more than 70 morphological characters discussed here is necessary. Despite the recent compilation of comprehensive data matrices, the power to test competing hypotheses of higher-level metazoan relationships is critically compromised due to uncritical data selection and poor character study in even the most recently published cladistic analyses.

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