Morphological characterization and molecular phylogeny of Portunoidea Rafinesque, 1815 (Crustacea Brachyura): Implications for understanding evolution of swimming capacity and revision of the family-level classification

2014 ◽  
Vol 253 (5) ◽  
pp. 404-429 ◽  
Author(s):  
Vassily A. Spiridonov ◽  
Tatiana V. Neretina ◽  
Dmitriy Schepetov
Keyword(s):  
Molecular Phylogeny ◽  
Morphological Characterization ◽  
The Family ◽  
Family Level ◽  
Swimming Capacity

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Unearthing LTR retrotransposon gag genes co-opted in the deep evolution of eukaryotes

2021 ◽  
Author(s):  
Jianhua Wang ◽  
Guan-Zhu Han
Keyword(s):  
Gene Expression ◽  
Selective Pressure ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Cellular Functions ◽  
The Family ◽  
Family Level ◽  
Gene Expression Analyses ◽  
Comprehensive Picture ◽  
Gypsy Retrotransposons

Abstract LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes, and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.

scholarly journals The Role of Botanical Families in Medicinal Ethnobotany: A Phylogenetic Perspective

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 163
Author(s):  
Airy Gras ◽  
Oriane Hidalgo ◽  
Ugo D’Ambrosio ◽  
Montse Parada ◽  
Teresa Garnatje ◽  
...  
Keyword(s):  
Diversity Indices ◽  
Specific Level ◽  
Medicinal Uses ◽  
The Family ◽  
Family Level ◽  
Phylogenetic Level ◽  
Molecular Phylogenetic ◽  
Quantitative Analyses ◽  
Medicinal Flora

Studies suggesting that medicinal plants are not chosen at random are becoming more common. The goal of this work is to shed light on the role of botanical families in ethnobotany, depicting in a molecular phylogenetic frame the relationships between families and medicinal uses of vascular plants in several Catalan-speaking territories. The simple quantitative analyses for ailments categories and the construction of families and disorders matrix were carried out in this study. A Bayesian approach was used to estimate the over- and underused families in the medicinal flora. Phylogenetically informed analyses were carried out to identify lineages in which there is an overrepresentation of families in a given category of use, i.e., hot nodes. The ethnobotanicity index, at a specific level, was calculated and also adapted to the family level. Two diversity indices to measure the richness of reported taxa within each family were calculated. A total of 47,630 use reports were analysed. These uses are grouped in 120 botanical families. The ethnobotanicity index for this area is 14.44% and the ethnobotanicity index at the family level is 68.21%. The most-reported families are Lamiaceae and Asteraceae and the most reported troubles are disorders of the digestive and nutritional system. Based on the meta-analytic results, indicating hot nodes of useful plants at the phylogenetic level, specific ethnopharmacological research may be suggested, including a phytochemical approach of particularly interesting taxa.

scholarly journals Inuit plant use in the eastern Subarctic: comparative ethnobotany in Kangiqsualujjuaq, Nunavik, and in Nain, Nunatsiavut

Botany ◽  
2019 ◽  
Vol 97 (5) ◽  
pp. 271-282
Author(s):  
Alain Cuerrier ◽  
Courtenay Clark ◽  
Christian H. Norton
Keyword(s):  
Lifestyle Changes ◽  
Ethnobotanical Knowledge ◽  
Structured Interviews ◽  
Medicinal Species ◽  
Medicinal Uses ◽  
Plant Uses ◽  
The Family ◽  
Plant Names ◽  
Family Level ◽  
Comparative Ethnobotany

Plants are important in traditional Inuit life. They are used for food, tea, medicine, etc. Based on semi-structured interviews with 35 informants, we documented and compared plant names and uses in Kangiqsualujjuaq, Nunavik, and in Nain, Nunatsiavut. Plant names and uses were expected to be similar between communities owing to common boreal–subarctic environments and cultural ties. Both communities reported the same number of taxa, with equivalent proportions of vascular and nonvascular plants, growth forms, use categories, and medicinal uses. Forty-three species were used in each community, for a total of 78 species from 39 families. Despite a high overlap in species distributions, only 35% of nonvascular and 56% of vascular species were used in both communities. Correspondence was higher at the family level (64% of nonvascular and 75% of vascular families shared). The Ericaceae family was the most used, followed by Rosaceae. Thirteen of 30 medicinal species were shared between communities. There was a low correspondence regarding the conditions for which the medicinal species were used. Edible taxa were shared the most (52%). Plant uses unique to either Nain or Kangiqsualujjuaq may reveal separate bodies of traditional knowledge, or may reflect an overall loss of ethnobotanical knowledge in the Subarctic due to recent lifestyle changes.

The family Amanitaceae: molecular phylogeny, higher-rank taxonomy and the species in China

2018 ◽  
Vol 91 (1) ◽  
pp. 5-230 ◽  
Author(s):  
Yang-Yang Cui ◽  
Qing Cai ◽  
Li-Ping Tang ◽  
Jian-Wei Liu ◽  
Zhu L. Yang
Keyword(s):  
Molecular Phylogeny ◽  
The Family ◽  
Higher Rank

Phanerozoic trends in the global geographic disparity of marine biotas

Paleobiology ◽  
2009 ◽  
Vol 35 (4) ◽  
pp. 612-630 ◽  
Author(s):  
Arnold I. Miller ◽  
Devin P. Buick ◽  
Katherine V. Bulinski ◽  
Chad A. Ferguson ◽  
Austin J. W. Hendy ◽  
...  
Keyword(s):  
Geographic Distance ◽  
Marine Biodiversity ◽  
Marine Animal ◽  
Animal Life ◽  
Data Repositories ◽  
Geographic Disparity ◽  
The Family ◽  
Family Level ◽  
History Of

Previous analyses of the history of Phanerozoic marine biodiversity suggested that the post-Paleozoic increase observed at the family level and below was caused, in part, by an increase in global provinciality associated with the breakup of Pangea. Efforts to characterize the Phanerozoic history of provinciality, however, have been compromised by interval-to-interval variations in the methods and standards used by researchers to calibrate the number of provinces. With the development of comprehensive, occurrence-based data repositories such as the Paleobiology Database (PaleoDB), it is now possible to analyze directly the degree of global compositional disparity as a function of geographic distance (geo-disparity) and changes thereof throughout the history of marine animal life. Here, we present a protocol for assessing the Phanerozoic history of geo-disparity, and we apply it to stratigraphic bins arrayed throughout the Phanerozoic for which data were accessed from the PaleoDB. Our analyses provide no indication of a secular Phanerozoic increase in geo-disparity. Furthermore, fundamental characteristics of geo-disparity may have changed from era to era in concert with changes to marine venues, although these patterns will require further scrutiny in future investigations.

Contributions to Molecular Phylogeny of Lichen-Forming Fungi 2. Review of Current Monophyletic Branches of the Family Physciaceae

2021 ◽  
Vol 63 (3-4) ◽  
pp. 351-390
Author(s):  
S. Y. Kondratyuk ◽  
L. Lőkös ◽  
I. Kärnefelt ◽  
A. Thell ◽  
M.-H. Jeong ◽  
...  
Keyword(s):  
Costa Rica ◽  
Molecular Phylogeny ◽  
Type Species ◽  
Lichen Species ◽  
New Combinations ◽  
Phylogeny Analysis ◽  
The Family ◽  
Crustose Lichens ◽  
First Time ◽  
Combined Matrix

Seven genera new to science, i.e.: Helmutiopsis, Huriopsis, Johnsheardia, Klauskalbia, Kudratovia, Kurokawia and Poeltonia of the Physciaceae are proposed for the ‘Rinodina’ atrocinerea, the ‘Rinodina’ xanthophaea, the ‘Rinodina’ cinnamomea, the ‘Heterodermia’ obscurata, the ‘Rinodina’ straussii, the ‘Anaptychia’ isidiata and the ‘Physconia’ grisea groups consequently that all form strongly supported monophyletic branches in a phylogeny analysis based on a combined matrix of nrITS and mtSSU sequences. Phylogenetic positions of species belonging to the genera Kashiwadia s. l., Leucodermia, Mischoblastia,Oxnerella, Phaeorrhiza s. l., Polyblastidium and Rinodinella s. l. are discussed. Oxnerella afghanica which for the first time recorded as parasitic lichen species from both epiphytic and saxicolous crustose lichens is designated as type species for the genus Oxnerella. Sequences of the recently described Physcia orientostellaris as well as Huriopsis xanthophaea and additional sequences of Kashiwadia aff. orientalis and Mischoblastia aff. oxydata are submitted to the GenBank. The positions of Polyblastidium casaterrinum from Costa Rica, ‘Rinodina’ efflorescens from Białowieża, Poland, and ‘Mischoblastia’ confragosula from Cambodia in the Physciaceae are confirmed in a phylogeny analysis based on the nrITS sequences. The presence of ‘extraneous mycobiont DNA’ in lichen associations is exemplified with earlier incorrect identifications of Heterodermia, Kashiwadia, Kurokawia,Oxnerella and Poeltonia specimens. Fifty-six new combinations are presented: Helmutiopsis alba (for Rinodina alba Metzler ex Arn.), Helmutiopsis aspersa (for Lecanora aspersa Borrer), Helmutiopsis atrocinerea (for Parmelia atrocinerea Fr.), Huriopsis chrysidiata (for Rinodina chrysidiata Sheard), Huriopsis chrysomelaena (for Rinodina chrysomelaena Tuck.), Huriopsis lepida (for Lecanora lepida Nyl.), Huriopsis luteonigra (for Rinodina luteonigra Zahlbr.), Huriopsis plana (for Rinodina plana H. Magn.), Huriopsis thiomela (for Lecanora thiomela Nyl.), Huriopsis xanthomelana (for Rinodina xanthomelana Müll. Arg.), Huriopsis xanthophaea (for Lecanora xanthophaea Nyl.), Johnsheardia cinnamomea (for Rinodina mniaroea var. cinnamomea Th. Fr.), Johnsheardia herteliana (for Rinodina herteliana Kaschik), Johnsheardia jamesii (for Rinodina jamesii H. Mayrhofer), Johnsheardia reagens (for Rinodina reagens Matzer et H. Mayrhofer), Johnsheardia zwackhiana (for Lecanora zwackhiana Kremp.), Kashiwadia austrostellaris (for Physcia austrostellaris Elix), Kashiwadia jackii (for Physcia jackii Moberg), Kashiwadia littoralis for Physcia littoralis Elix), Kashiwadia nubila (for Physcia nubila Moberg), and Kashiwadia tropica (for Physcia tropica Elix), Klauskalbia crocea (for Heterodermia crocea R. C. Harris), Klauskalbia flabellata (for Parmelia flabellata Fée), Klauskalbia obscurata (for Physcia speciosa (Wulfen) Nyl. *obscurata Nyl.), Klauskalbia paradoxa (for Heterodermia paradoxa Schumm et Schäfer-Verwimp), Kudratovia bohlinii (for Rinodina bohlinii H. Magn.), Kudratovia candidogrisea (for Rinodina candidogrisea Hafellner, Muggia et Obermayer), Kudratovia luridata (for Buellia luridata Körb.), Kudratovia metaboliza (for Rinodina metaboliza Vain.), Kudratovia pycnocarpa (for Rinodina pycnocarpa H. Magn.), Kudratovia roscida (for Lecanora roscida Sommerf.), Kudratovia straussii (for Rinodina straussii J. Steiner), Kudratovia terrestris (for Rinodina terrestris Tomin), Kurokawia bryorum (for Anaptychia bryorum Poelt), Kurokawia isidiata (for Anaptychia isidiata Tomin), Kurokawia mereschkowskii (for Physcia mereschkowskii Tomin), Kurokawia palmulata (for Psoroma palmulatum Michx.), Kurokawia runcinata (for Lichen runcinatus With.), Kurokawia stippea (for Parmelia aquila var. stippea Ach.), Lecania safavidiorum (for Oxnerella safavidiorum S. Y. Kondr., Zarei-Darki, Lőkös et Hur), Leucodermia erinacea (for Lichen erinaceus Ach.), Mischoblastia confragosula (for Lecanora confragosula Nyl.), Mischoblastia destituta (for Lecidea destituta Nyl.), Mischoblastia moziana (for Lecanora moziana Nyl.), Mischoblastia moziana subsp. parasitica (comb. et stat. nova for Rinodina moziana var. parasitica Kaschik et H. Mayrhofer), Mischoblastia ramboldii (for Rinodina ramboldii Kaschik), Mischoblastia vezdae (for Rinodina vezdae H. Mayrhofer), Oxnerella afghanica (for Rinodina afghanica M. Steiner et Poelt), Oxnerella castanomelodes (for Rinodina castanomelodes H. Mayrhofer et Poelt), Physciella nigricans (for Lecanora nigricans Flörke), Poeltonia elegantula (for Physconia elegantula Essl.), Poeltonia grisea (for Lichen griseus Lam.), Poeltonia isidiomuscigena (for Physconia isidiomuscigena Essl.), Poeltonia perisidiosa (for Physcia perisidiosa Erichsen), Poeltonia venusta (for Parmelia venusta Ach.), and Polyblastidium albicans (for Parmelia albicans Pers.) are proposed.

scholarly journals APLIKASI ZERO WASTE DALAM LINGKUNGAN MASYARAKAT DESA TUMPUKRENTENG DENGAN PENDEKATAN ASET BASE COMMUNITY DEVELOPMENT THEORY

2019 ◽  
Vol 1 (1) ◽  
pp. 28-32
Author(s):  
Evawati Alisah
Keyword(s):  
Community Development ◽  
Plastic Waste ◽  
Solution Model ◽  
Development Theory ◽  
Zero Waste ◽  
The Family ◽  
Family Level ◽  
Small Things

Constructing dreams together with discovering a unique and communally defined design in a particular place destination in overcoming the problem of waste is an achievement that should be appreciated. Go to Zero Waste must indeed be raised in all circles so that the predicate of producing plastic waste is no longer attached to Indonesia.Inorganic waste from family level activities, whose sustainability is maintained because of adat: is managed together with a simple organization and the amount is limited eventually if accumulated will become a mountain of problems that are resolved, even into results that can be utilized. The solution model can be applied elsewhere in order to solve the problem of garbage from the family level during the celebration. RT 13 RW 03 neighborhood of Tumpukrenteng Village, Turen District, Malang Regency has proven that it can mobilize assets for small things, such as garbage so that it becomes a blessing. 

scholarly journals A revised taxonomy of Asian snail-eating snakes Pareas (Squamata, Pareidae): evidence from morphological comparison and molecular phylogeny

ZooKeys ◽  
2020 ◽  
Vol 939 ◽  
pp. 45-64
Author(s):  
Ping Wang ◽  
Jing Che ◽  
Qin Liu ◽  
Ke Li ◽  
Jie Qiong Jin ◽  
...  
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Morphological Data ◽  
Multivariate Morphometrics ◽  
Cryptic Diversity ◽  
Cyt B ◽  
Morphological Comparison ◽  
The Family ◽  
Two New Species

The Asian snail-eating snakes Pareas is the largest genus of the family Pareidae (formerly Pareatidae), and widely distributed in Southeast Asia. However, potential diversity remains poorly explored due to their highly conserved morphology and incomplete samples. Here, on basis of more extensive sampling, interspecific phylogenetic relationships of the genus Pareas were reconstructed using two mitochondrial fragments (cyt b and ND4) and two nuclear genes (c-mos and Rag1), and multivariate morphometrics conducted for external morphological data. Both Bayesian Inference and Maximum Likelihood analyses consistently showed that the genus Pareas was comprised of two distinct, monophyletic lineages with moderate to low support values. Based on evidences from molecular phylogeny and morphological data, cryptic diversity of this genus was uncovered and two new species were described. In additional, the validity of P. macularius is confirmed.

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