scholarly journals Progress, pitfalls and parallel universes: a history of insect phylogenetics

2016 ◽  
Vol 13 (121) ◽  
pp. 20160363 ◽  
Author(s):  
Karl M. Kjer ◽  
Chris Simon ◽  
Margarita Yavorskaya ◽  
Rolf G. Beutel
Keyword(s):  
Morphological Evolution ◽  
Large Datasets ◽  
Phylogenetic Studies ◽  
Number Of Genes ◽  
Molecular Phylogenetic ◽  
Parallel Universes ◽  
Methodological Improvement ◽  
History Of ◽  
New Challenges

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985–2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

scholarly journals What does mitogenomics tell us about the evolutionary history of the Drosophila buzzatii cluster (repleta group)

2019 ◽  
Author(s):  
Nicolás N. Moreyra ◽  
Julián Mensch ◽  
Juan Hurtado ◽  
Francisca Almeida ◽  
Cecilia Laprida ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary Biology ◽  
Large Scale ◽  
South American ◽  
Phylogenetic Studies ◽  
Drosophila Buzzatii ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Tree Topologies ◽  
American Clade

AbstractThe Drosophila repleta group is an array of more than 100 cactophilic species endemic to the “New World”. The acquisition of the ability to utilize decaying cactus tissues as breeding and feeding sites is a key aspect that allowed the successful diversification of the repleta group in the American deserts. Within this group, the Drosophila buzzatii cluster is a South American clade of seven cactophilic closely related species in different stages of divergence, a feature that makes it a valuable model system for evolutionary research. However, even though substantial effort has been devoted to elucidating the phylogenetic relationships among members of the D. buzzatii cluster, the issue is still controversial. In effect, molecular phylogenetic studies performed to date generated ambiguous results since tree topologies depend on the kind of molecular marker employed. Curiously, even though mitochondrial DNA has become a popular marker in evolutionary biology and population genetics, none of the more than twenty Drosophila mitogenomes assembled so far belongs to this cluster. In this work we report the assembly of six complete mitogenomes of five species: D. antonietae, D. borborema, D. buzzatii, D. seriema and two strains of D. koepferae, with the aim to revisit the phylogenetic relationships and divergence times by means of a mitogenomic approach. The recovered topology using complete mitogenomes gives support to the hypothesis of the monophyly of that the D. buzzatii cluster and shows two main clades, one including D. buzzatii and D. koepferae (both strains) and the other the remaining species. These results are in agreement with previous reports based on a few mitochondrial and/or nuclear genes but in conflict with the results of a recent large-scale nuclear phylogeny, suggesting that nuclear and mitochondrial genomes depict different evolutionary histories.

scholarly journals A theory about the evolutionary history of Lachnidae and comments on the results of some molecular phylogenetic studies of aphids (Hemiptera: Aphidoidea)

2015 ◽  
Vol 84 (4) ◽  
pp. 275-287 ◽  
Author(s):  
Ole E. Heie
Keyword(s):  
Evolutionary History ◽  
Sister Group ◽  
Compound Eyes ◽  
Host Alternation ◽  
Phylogenetic Studies ◽  
The Family ◽  
Molecular Phylogenetic ◽  
History Of

Abstract Several characters of the Lachnidae are discussed, and it is explained why some of them are not plesiomorphies as previously believed, but apomorphies. This applies e.g. to the absence of host alternation in the extant genera, to the short cauda and to the presence of compound eyes in the nymphs and the apterous adults. Some characters are adaptations to attention by ants or ways of feeding. It is concluded that many characters show that the family is relatively young and probably originally had host alternation of the same kind as Aphididae, which is regarded as the sister group. The results of some molecular phylogenetic studies are discussed.

Multilocus phylogeny and a new classification for African, Asian and Indian supple and writhing skinks (Scincidae: Lygosominae)

2019 ◽  
Vol 186 (4) ◽  
pp. 1067-1096 ◽  
Author(s):  
Elyse S Freitas ◽  
Aniruddha Datta-Roy ◽  
Praveen Karanth ◽  
L Lee Grismer ◽  
Cameron D Siler
Keyword(s):  
Southeast Asia ◽  
New Genus ◽  
New Classification ◽  
African Species ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Old World Tropics ◽  
Multilocus Phylogeny

AbstractThe genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.

scholarly journals The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1032 ◽  
Author(s):  
Yulia Vakulenko ◽  
Andrei Deviatkin ◽  
Alexander Lukashev
Keyword(s):  
Evolutionary History ◽  
Large Datasets ◽  
Sequencing Errors ◽  
Sample Bias ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
History Of ◽  
Sequence Position ◽  
Annotation Errors ◽  
Selection Of

Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.

scholarly journals Morphological evolution in Hyles Hübner, 1819 hawkmoths (Lepidoptera, Sphingidae): reconstructing the ancestral Hyles habitus

2020 ◽  
Vol 43 ◽  
pp. 181-210
Author(s):  
Anna K. Hundsdoerfer ◽  
Ian J. Kitching
Keyword(s):  
Bayesian Inference ◽  
Morphological Evolution ◽  
Morphological Characters ◽  
Phylogenetic Studies ◽  
Close Phylogenetic Relationship ◽  
Molecular Phylogenetic ◽  
Ancestral States ◽  
Body Patterns ◽  
Hyles Euphorbiae ◽  
Different Parts

Molecular phylogenetic studies suggest that similar wing and body patterns in the hawkmoth genus Hyles Hübner, [1819] do not necessarily reflect a close phylogenetic relationship. To improve our understanding of morphological evolution in these organisms, 75 characters derived from the external adult morphology are explicitly coded and analysed in a maximum parsimony cladistic framework. The results corroborate the hypothesis that wing and body patterns have indeed reappeared in different parts of the phylogeny but the underlying genetic mechanism remains to be determined. By reconstructing the suite of ancestral states of the morphological characters using Bayesian inference, we derived an approximation of the appearance of the proto-Hyles species. The overall habitus of this moth does not display a combination of characters found in any extant Hyles species. Rather, the forewings are most like those of members of the Hyles euphorbiae-complex but with better developed antemedial and postmedial lines, the hindwings are typical Hyles, and the abdominal pattern most closely resembles that of Hyles euphorbiarum (Guérin-Méneville & Percheron, 1835), but with one fewer pairs of black subdorsal patches. Within the context of the subtribe Choerocampina and Sphingidae more generally, the proto-Hyles reconstruction does not resemble any other species apart from Rhodafra opheltes (Cramer, 1780), but this appears to be another instance of convergent pattern expression.

Systematics of the Gracilariales (Rhodophyta) including new subfamilies, tribes, subgenera, and two new genera, Agarophyton gen. nov. and Crassa gen. nov.

Phytotaxa ◽  
2018 ◽  
Vol 374 (1) ◽  
pp. 1 ◽  
Author(s):  
CARLOS FREDERICO D. GURGEL ◽  
JAMES N. NORRIS ◽  
WILLIAM E. SCHMIDT ◽  
HAU NHU LE ◽  
SUZANNE FREDERICQ
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
New Genera ◽  
New Classification ◽  
Free Living ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Evolutionary Lineages ◽  
Stable Classification

The Gracilariales is a red macroalgal order and the main global source of the economically important agar, a marine phycocolloid. Independent comparative morphological and molecular phylogenetic studies over the last 20 years have revealed the existence of seven major clades recognizable as distinct genera. Of these major clades only four free-living genera have been widely accepted taxonomically: Curdiea, Melanthalia, Gracilariopsis, and Gracilaria. Three other clades comprise the reinstatement of the genus Hydropuntia and the proposal of two new genera, Agarophyton and Crassa, described herein. Based on new rbcL DNA sequences, and along with a reassessment of published comparative morphological and molecular phylogenetic studies, we argue that the latter three genera represent distinct evolutionary lineages in the Gracilariaceae, and propose a new classification for the order Gracilariales. Our new proposal incorporates the most current understanding of the evolutionary history of the order, establishes a natural and stable classification system, and provides the basis for the recognization of intra-family ranks. Our classification scheme reconciles all molecular phylogenetic studies published to date.

Beérkezett könyvek

2005 ◽  
Vol 60 (3) ◽  
pp. 425-427
Author(s):  
Csaba Pléh
Keyword(s):  
Social Interaction ◽  
Cognitive Science ◽  
Evolutionary Psychology ◽  
Well Being ◽  
General Intelligence ◽  
Human Thought ◽  
Number Of Genes ◽  
History Of ◽  
Origin Of Mind ◽  
The Mind

Ádám György: A rejtozködo elme. Egy fiziológus széljegyzetei Carpendale, J. I. M. és Müller, U. (eds): Social interaction and the development of knowledge Cloninger, R. C.: Feeling good. The science of well being Dunbar, Robin, Barrett, Louise, Lycett, John: Evolutionary psychology Dunbar, Robin: The human story. A new history of makind's evolution Geary, D. C.: The origin of mind. Evolution of brain, cognition and general intelligence Gedeon Péter, Pál Eszter, Sárkány Mihály, Somlai Péter: Az evolúció elméletei és metaforái a társadalomtudományokban Harré, Rom: Cognitive science: A philosophical introduction Horváth György: Pedagógiai pszichológia Marcus, G.: The birth of the mind. How a tiny number of genes creates the complexities of human thought Solso, R. D.: The psychology of art and the evolution of the conscious brain Wray, A. (ed.): The transition to language

Probiotics in gastroenterology – from a different angle

2013 ◽  
Vol 154 (8) ◽  
pp. 294-304 ◽  
Author(s):  
György Miklós Buzás
Keyword(s):  
Side Effects ◽  
Beneficial Effect ◽  
Analytical Data ◽  
Well Being ◽  
Gastrointestinal Diseases ◽  
Convincing Evidence ◽  
Probiotic Treatment ◽  
History Of ◽  
Irritable Bowel

After a short overview of the history of probiotics, the author presents the development of human intestinal microflora based on the newest genetic data and the microbiological features of main probiotics. The indications of probiotic administration have been defined and extended in recent years. The author reviews significant results of probiotic treatment in some gastrointestinal diseases based on meta-analytical data. Probiotics are useful in preventing and treating diarrhoea caused by antibiotics and Clostridium difficile caused diarrhoea. In the treatment of Helicobacter pylori infection, preparations containing certain Lactobacillus,Bifidobacterium strains or Saccaromyces boulardii could enhance by 5–10% the rate of successful eradication and reduce the incidence and severity of the side effects. Some symptoms of irritable bowel syndrome and thus the quality of life can be improved by probiotics. Their beneficial effect in ulcerative colitis was proven, while in Crohn’s disease has not yet been defined. The use of probiotics is not included in guidelines, with the exception of the Maastricht IV/Florence consensus. For each disease it is advisable to use probiotics containing strains only with proven beneficial effect. The efficiency of preparations containing mixed strains has not yet been properly investigated. The author reviews the rare but potentially serious side effects of probiotics. In Hungary, there are many probiotic preparations available which can be purchased in pharmacies without prescription: their use is more empirical than evidence-based. The European Food Safety Authority has recently rejected claims for probiotics to be classed as medicines given the lack of convincing evidence on the effects of probiotics on human health and well-being. Clearly, further research is needed to collect evidence which could be incorporated into the international guidelines. Orv. Hetil., 2013, 154, 294–304.

Consortium of European Research Libraries 2008: New Challenges

2009 ◽  
pp. 80-84
Author(s):  
Nailya F. Verbina ◽  
Andrei C. Masevich
Keyword(s):  
International Organizations ◽  
International Research ◽  
Book History ◽  
Bibliographic Database ◽  
European Research ◽  
Research Libraries ◽  
International Research Institute ◽  
History Of ◽  
New Challenges ◽  
History Of Culture

On the activities of one of the most significant international organizations connected with research of book history - Consortium of European Research Libraries. The creation of a bibliographic database of the printed book from 1452 to 1830, which was supposed to collect materials from libraries of Europe, was the goal of Consortium since the beginning of its foundation. The authors of the article write that today the activities of the Consortium is much broader, it turns into international research institute on the history of culture.

EXPLORING HEALTHCARE ARCHITECTURE THROUGH THE MEDIUM OF FILM: Motives and Techniques

2014 ◽  
Vol 8 (1) ◽  
pp. 29
Author(s):  
Stephen Verderber
Keyword(s):  
Real World ◽  
The Real ◽  
Healthcare Settings ◽  
Interdisciplinary Field ◽  
Body Of Knowledge ◽  
Behavior Setting ◽  
Physical Environments ◽  
Scant Attention ◽  
History Of

The interdisciplinary field of person-environment relations has, from its origins, addressed the transactional relationship between human behavior and the built environment. This body of knowledge has been based upon qualitative and quantitative assessment of phenomena in the “real world.” This knowledge base has been instrumental in advancing the quality of real, physical environments globally at various scales of inquiry and with myriad user/client constituencies. By contrast, scant attention has been devoted to using simulation as a means to examine and represent person-environment transactions and how what is learned can be applied. The present discussion posits that press-competency theory, with related aspects drawn from functionalist-evolutionary theory, can together function to help us learn of how the medium of film can yield further insights to person-environment (P-E) transactions in the real world. Sampling, combined with extemporary behavior setting analysis, provide the basis for this analysis of healthcare settings as expressed throughout the history of cinema. This method can be of significant aid in examining P-E transactions across diverse historical periods, building types and places, healthcare and otherwise, otherwise logistically, geographically, or temporally unattainable in real time and space.

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