scholarly journals ULASAN Kajian Filogenetika Molekuler dan Peranannya dalam Menyediakan Informasi Dasar untuk Meningkatkan Kualitas Sumber Genetik Anggrek

2016 ◽  
Vol 4 (1) ◽  
pp. 35 ◽  
Author(s):  
Topik Hidayat ◽  
Adi Pancoro
Keyword(s):  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Biochemical Properties ◽  
Intergeneric Hybrids ◽  
Basic Knowledge ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Ornamental Crops

<p>Early information<br />resulted from molecular phylogenetic studies of many important<br />ornamental crops is often less attention to many<br />growers and farmers. Phylogenetics is one of the most preferable<br />method in systematics to reconstruct evolutionary<br />relationships of groups of biological organisms in order to<br />understand their biodiversities. This has been revolutionized<br />by DNA sequences data. In this method, a group of organisms<br />that shares many identical characteristics are considered<br />to be closely related; deriving from a common<br />ancestor and is assumed to have similar genetic patterns<br />and biochemical properties. By these basic principles,<br />molecular phylogenetics plays important roles in revealing a<br />basic knowledge on pattern of relationships to which<br />genetic resources can be improved. Over the past decade,<br />botanists have done several thousand phylogenetic analyses<br />based on molecular data of economically and horticulturally<br />important crops. Orchids are the best example for this.<br />There is no doubt that most orchid plants had played roles in<br />horticulture and hybridization. At present, many infrageneric<br />and intergeneric hybrids are available commercially. Successful<br />hybridization can be achieved if two or more individual<br />plants understudy are closely related in respect to their<br />genetics and evolution.</p>

scholarly journals The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

2015 ◽  
Vol 46 (3) ◽  
pp. 269-290 ◽  
Author(s):  
Ian J. Kitching ◽  
C. Lorna Culverwell ◽  
Ralph E. Harbach
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Set ◽  
Generic Status ◽  
Strong Signal ◽  
Phylogenetic Studies ◽  
Data Support

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

Additional data on Iranian trichodorids (Triplonchida: Trichodoridae) and first record of a rare species, Trichodorus variabilis Roca, 1998

Nematology ◽  
2017 ◽  
Vol 19 (2) ◽  
pp. 121-129 ◽  
Author(s):  
Majid Pedram ◽  
Ali Roshan-Bakhsh ◽  
Ebrahim Pourjam ◽  
Mohammad Reza Atighi ◽  
Wilfrida Decraemer ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
First Record ◽  
Molecular Data ◽  
Slight Variation ◽  
Natural Forests ◽  
Northern Iran ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
First Time ◽  
Of Greece

Trichodorus variabilis, recovered from three separate locations in natural forests of northern Iran, was studied using morphological, morphometric and molecular data. Variation in position of the ventromedian cervical papillae (CP1 and CP2) with respect to the onchiostyle base in the resting position, and spicule characters (having or lacking striation in distal blade region and bristles in proximal blade region) were observed. Variation was also observed in the nature of the pharyngo-intestinal junction (offset to slight overlapping). The secretory-excretory pore of females also showed slight variation in placement. Molecular phylogenetic studies, using partial 28S rDNA D2-D3 sequences of three studied populations and one sequenced isolate of the species from Greece, revealed T. variabilis has variation in the sequences of this genomic fragment. The similarity percent of four sequences ranged from 96.7 to 99.7%. The species was found for the first time outside of Greece, the country from which it was originally described. A newly recovered population of T. persicus, originally described from Iran, was also included in the molecular phylogenetic analyses.

Floral ontogeny and anatomy of the shrub Gaiadendron punctatum and a comparison of floral characters in the tribes Gaiadendrinae and Nuytsiae (Loranthaceae)

2021 ◽  
Vol 69 (3) ◽  
Author(s):  
Hernán Darío Suárez ◽  
Camila Robayo ◽  
Xavier Marquínez ◽  
Lauren Raz
Keyword(s):  
Vascular Tissue ◽  
Developmental Stages ◽  
Floral Anatomy ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Inflorescence Development ◽  
Mountainous Regions ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Floral Characters

Introducction: Gaiadendron punctatum is a hemiparasitic species of Loranthaceae (Tribe Gaiadendreae) that is widely distributed in mountainous regions of Central and South America. Embryological and phylogenetic studies in the family indicate a trend towards reduction of the gynoecium and ovules, the morphology of which supports the current circumscription of Tribe Gaiadendreae (Gaiadendron and Atkinsonia). Molecular phylogenetic studies suggest that Nuytsia, Atkinsonia and Gaiadendron diverged successively, forming a grade at the base of the Loranthaceae, but support values are low. Objetive: In the present study, the floral anatomy of Gaiadendron punctatum was investigated in order to provide additional data to permit comparisons among the three basal-most genera in the Loranthaceae and reevaluate their relationships. Methods: Flowers of G. punctatum were collected at different developmental stages and serial sections were prepared and analyzed by light microscopy. Results: Inflorescence development is acropetal; the flowers are bisexual with an inferior ovary surmounted by a calyculus, a ring-shaped structure lacking vascular tissue; the ovary is comprised of seven basal locules, each with an ategmic, tenuinucellate ovule. Above the locules is a mamelon that is fused with the adjacent tissues. The androecium is comprised of seven epipetalous stamens, the anthers with fibrous endothecium dehiscence through a single longitudinal slit, releasing tricolpated pollen. Conclusions: The results of this study show that Gaiadendron and Atkinsonia share versatile, dorsifixed anthers, while Gaiadendron and Nuytsia share the same mode of anther dehiscence. On the other hand, Gaiadendron shares with members of Tribe Elytrantheae an amyliferous mamelon and an unvascularized calyculus. Combined phylogenetic analyses of morphological and molecular data are desirable to determine whether Tribe Gaiadendreae comprises a clade, a grade or if the two genera are more distantly related.

Disentangling the taxonomy of the Galactia-Camptosema- Collaea complex with new generic circumscriptions in the Galactia clade (Leguminosae, Diocleae)

Neodiversity ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 56-94
Author(s):  
Luciano P. Queiroz ◽  
◽  
Ana C.S. Oliveira ◽  
Cristiane Snak
Keyword(s):  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
New Genera ◽  
Genus Level ◽  
Phylogenetic Studies ◽  
Taxonomic History ◽  
Molecular Phylogenetic

The Galactia clade is one of three major lineages of the papilionoid legume tribe Diocleae. It comprises eight genera and approximately 140 species almost entirely restricted to the Americas. Establishing stable generic boundaries within this clade has been a challenge because of its tortuous taxonomic history and the broad polyphyly of the genera of the so-called Galactia-Camptosema-Collaea complex. Previous molecular phylogenetic studies revealed some well-supported lineages, but did not advance towards any new taxonomic arrangements. We carried out maximum parsimony and Bayesian phylogenetic analyses of a combined dataset including our previously published multilocus molecular data (nrITS and ETS and plastid trnK/matK and trnT-Y regions) and 82 morphological characters. The resulting topologies largely concur with those previously reported based on molecular data only, where Camptosema and Galactia appear as broadly polyphyletic, with species scattered among five (Camptosema) and seven (Galactia) of the twelve lineages that are newly recognized here at genus level. We are therefore proposing the following new taxonomic rearrangements within the Galactia clade: descriptions of the new genera Caetangil, Cerradicola, Mantiqueira, and Nanogalactia; resurrection of Betencourtia; and the subsuming of Neorudolphia into Rhodopis and of Camptosema sect. Macropetalum into Cratylia.

A new pratylenchid nematode, Hoplotylus japonicus n. sp. (Tylenchina: Pratylenchidae) from the rhizosphere of Japanese maple, Acer palmatum (Thumb.)

Nematology ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. 1131-1140
Author(s):  
Jianfeng Gu ◽  
Munawar Maria ◽  
Yiwu Fang ◽  
Majid Pedram
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Anterior Margin ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Dorsal Side ◽  
Lateral View ◽  
Molecular Phylogenetic ◽  
A New Species

Summary During quarantine inspections, a new species of Hoplotylus was detected from the rhizosphere of the Japanese maple, Acer palmatum, imported into China from Japan. Hoplotylus japonicus n. sp. is characterised by a stout 431-602 μm long body, well-developed 20.0-24.5 μm long stylet with tulip-shaped knobs having rounded sides in lateral view and a rounded anterior margin, excretory pore located slightly posterior to the hemizonid, usually empty, spermatheca, conical tail with a spike-like projection, which is distally smooth on the dorsal side, and males not found. It was morphologically compared with four currently known species of the genus, viz., H. femina, H. montanus, H. silvaticus, and H. sjacobi. In molecular phylogenetic analyses using 18S, 28S and internal transcribed spacer (ITS) ribosomal DNA sequences, the new species formed a clade with the only currently sequenced species of the genus, H. femina, in all phylogenies. This is the second species of the genus characterised by molecular data and the second species recovered from Japan.

scholarly journals Evidence from the resurrected family Polyrhabdinidae Kamm, 1922 (Apicomplexa: Gregarinomorpha) supports the epimerite, an attachment organelle, as a major eugregarine innovation

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11912
Author(s):  
Gita G. Paskerova ◽  
Tatiana S. Miroliubova ◽  
Andrea Valigurová ◽  
Jan Janouškovec ◽  
Magdaléna Kováčiková ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Light Microscopy ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Molecular Data ◽  
Lsu Rdna ◽  
The Family ◽  
Molecular Phylogenetic ◽  
And Function

Background Gregarines are a major group of apicomplexan parasites of invertebrates. The gregarine classification is largely incomplete because it relies primarily on light microscopy, while electron microscopy and molecular data in the group are fragmentary and often do not overlap. A key characteristic in gregarine taxonomy is the structure and function of their attachment organelles (AOs). AOs have been commonly classified as “mucrons” or “epimerites” based on their association with other cellular traits such as septation. An alternative proposal focused on the AOs structure, functional role, and developmental fate has recently restricted the terms “mucron” to archigregarines and “epimerite” to eugregarines. Methods Light microscopy and scanning and transmission electron microscopy, molecular phylogenetic analyses of ribosomal RNA genes. Results We obtained the first data on fine morphology of aseptate eugregarines Polyrhabdina pygospionis and Polyrhabdina cf. spionis, the type species. We demonstrate that their AOs differ from the mucron in archigregarines and represent an epimerite structurally resembling that in other eugregarines examined using electron microscopy. We then used the concatenated ribosomal operon DNA sequences (SSU, 5.8S, and LSU rDNA) of P. pygospionis to explore the phylogeny of eugregarines with a resolution superior to SSU rDNA alone. The obtained phylogenies show that the Polyrhabdina clade represents an independent, deep-branching family in the Ancoroidea clade within eugregarines. Combined, these results lend strong support to the hypothesis that the epimerite is a synapomorphic innovation of eugregarines. Based on these findings, we resurrect the family Polyrhabdinidae Kamm, 1922 and erect and diagnose the family Trollidiidae fam. n. within the superfamily Ancoroidea Simdyanov et al., 2017. Additionally, we re-describe the characteristics of P. pygospionis, emend the diagnoses of the genus Polyrhabdina, the family Polyrhabdinidae, and the superfamily Ancoroidea.

Phylogenetic studies in the South American tribe Dichroplini (Orthoptera: Acrididae: Melanoplinae): is the Paranaense-Pampeano informal genus group a natural clade?

Zootaxa ◽  
2009 ◽  
Vol 2174 (1) ◽  
pp. 51-62 ◽  
Author(s):  
P. A. DINGHI ◽  
V. CONFALONIERI ◽  
M. M. CIGLIANO
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Morphological Characters ◽  
Molecular Data ◽  
South American ◽  
Male And Female ◽  
Weak Support ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Group A

The Dichroplini genera Scotussa, Leiotettix, Ronderosia, Atrachelacris, Chlorus, Eurotettix and Dichromatos have been grouped into the “Paranaense-Pampeano” informal genus group, based on characters of the male genitalia. However, recent molecular phylogenetic analyses showed weak support values or no support at all for this group. In this study, we used molecular and morphological characters to test the monophyly of this informal genus group. Morphological characters included aspects of the general morphology, and male and female genitalia as well. Whereas the molecular data was based on one mitochondrial gene: cytochrome oxidase I. Independent and combined phylogenetic analyses of the data were performed under both unweighted and implied weighting parsimony. Our results showed that, when only molecular data is considered, the “Paranaense-Pampeano” informal genus group is not recovered. However, the group is monophyletic according to morphological and combined analyses. The “Paranaense-Pampeano” informal genus group is considered to be a natural clade; therefore, we propose the genus group name Scotussae. As a final remark, the molecular data provided in most cases the same evidence of relationships as morphology.

scholarly journals Molecular phylogenetics of swimming crabs (Portunoidea Rafinesque, 1815) supports a revised family-level classification and suggests a single derived origin of symbiotic taxa

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4260 ◽  
Author(s):  
Nathaniel Evans
Keyword(s):  
16S Rrna ◽  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Taxonomic Diversity ◽  
Molecular Data ◽  
28S Rrna ◽  
Single Clade ◽  
Molecular Phylogenetic ◽  
Phylogenetic Origin ◽  
New Diagnosis

Portunoidea is a diverse lineage of ecologically and economically important marine crabs comprising 8 families and 14 subfamilies. Closely related portunid subfamilies Caphyrinae and Thalamitinae constitute some of this group’s greatest morphological and taxonomic diversity, and are the only known lineages to include symbiotic taxa. Emergence of symbiosis in decapods remains poorly studied and portunoid crabs provide an interesting, but often overlooked example. Yet the paucity of molecular phylogenetic data available for Portunoidea makes it challenging to investigate the evolution and systematics of the group. Phylogenetic analyses, though limited, suggest that many putative portunoid taxa are para- or polyphyletic. Here I augment existing molecular data—significantly increasing taxon sampling of Caphyrinae, Thalamitinae, and several disparate portunoid lineages—to investigate the phylogenetic origin of symbiosis within Portunoidea and reevaluate higher- and lower-level portunoid classifications. Phylogenetic analyses were carried out on sequences of H3, 28S rRNA, 16S rRNA, and CO1 for up to 168 portunoid taxa; this included, for the first time, molecular data from the generaAtoportunus,Brusinia,Caphyra,Coelocarcinus,Gonioinfradens,Raymanninus, andThalamonyx. Results support the placement of all symbiotic taxa (Caphyra,Lissocarcinus, and twoThalamita) in a single clade derived within the thalamitine genusThalamita. Caphyrina Paulson, 1875, nom. trans. is recognized here as a subtribe within the subfamily Thalamitinae. Results also support the following taxonomic actions:Croniusis reclassified as a thalamitine genus;Thalamonyxis reestablished as a valid genus;Goniosupradensis raised to the generic rank; and three new genera (Zygitagen. nov.,Thranitagen. nov., andTrierarchusgen. nov.) are described to accommodate someThalamitas.l. taxa rendered paraphyletic by Caphyrina. A new diagnosis of Thalamitinae is provided. Results also support a more conservative classification of Portunoidea comprising three instead of eight extant families: Geryonidae (Geryonidae + Ovalipidae; new diagnosis provided), Carcinidae (Carcinidae + Pirimelidae + Polybiidae + Thiidae +Coelocarcinus; new diagnosis provided) and Portunidae. Finally, 16s rRNA data suggests family Brusiniidae might not be a portunoid lineage.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

scholarly journals Polulichloris henanensis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga

Phytotaxa ◽  
2015 ◽  
Vol 218 (2) ◽  
pp. 137 ◽  
Author(s):  
Huiyin Song ◽  
Qi Zhang ◽  
Guoxiang Liu ◽  
Zhengyu Hu
Keyword(s):  
Green Alga ◽  
New Genus ◽  
Cultured Cells ◽  
Phylogenetic Analyses ◽  
Light And Electron Microscopy ◽  
Molecular Data ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Molecular Phylogenetic ◽  
18S Rdna Gene

Coccoid green algae are abundant in subaerial habitats, but they are largely unexplored because of their morphological uniformity. Several new genus-level lineages have recently been described on the basis of molecular data. In this study, a coccoid green alga was isolated from surface soil in Zhoukou, Henan Province, China, and the cultured cells were described using light and electron microscopy. The ellipsoidal cell had smooth cell wall and parietal chloroplast with a pyrenoid surrounded by a starch envelope. Reproduction occurred by formation of 2‒16 autospores. Molecular phylogenetic analyses based on the nuclear 18S rDNA gene and the chloroplast ribulose-bisphosphate carboxylase gene (rbcL) indicated that this coccoid green alga represents a new lineage of the Watanabea clade (Trebouxiophyceae, Chlorophyta). Here, we describe this organism as a new genus and species, Polulichloris henanensis, gen. et sp. nov.

Sign in / Sign up

Export Citation Format

Share Document