Molecular trees

Nature ◽  
1977 ◽  
Vol 270 (5637) ◽  
pp. 547-547
Author(s):  
Thomas H. Jukes
Keyword(s):  
Molecular Trees

Electron-Reservoir Sandwich Complexes: From Mono- and Bimetallic Complexes to Molecular Trees

1996 ◽  
pp. 107-127 ◽  
Author(s):  
D. Astruc ◽  
C. Valério ◽  
J.-L. Fillaut ◽  
J. Ruiz ◽  
J.-R. Hamon ◽  
...  
Keyword(s):  
Bimetallic Complexes ◽  
Sandwich Complexes ◽  
Molecular Trees

scholarly journals Opening Pandora’s Molecular Box

Zootaxa ◽  
2011 ◽  
Vol 2946 (1) ◽  
pp. 60 ◽  
Author(s):  
MALTE C. EBACH ◽  
MARCELO R. DE CARVALHO ◽  
DAVID M. WILLIAMS
Keyword(s):  
Dna Barcoding ◽  
Molecular Systematics ◽  
Molecular Data ◽  
Supporting Evidence ◽  
Dna Taxonomy ◽  
Theoretical Position ◽  
Conflicting Evidence ◽  
Original Question ◽  
Molecular Homology ◽  
Molecular Trees

Mooi & Gill (2010) have prised open the cap of the molecular systematics vial and caused a debate to take-off in the ichthyological community. Molecular trees and their supporting evidence are the first two items to leave this Pandora’s box, closely followed by DNA barcoding and DNA taxonomy. In short, the debate is fuelled by the nature of molecular data: can nucleotide sequences provide the necessary evidence for relationship? The majority (Wiley et al., 2011) believe that DNA contains informative data; however, in our view, they have failed to ascertain the truth of their claim. Not all data are informative. Data may provide supporting evidence, conflicting evidence, or no evidence at all. Assuming that all data are informative apriori to analysis is a theoretical position, not an empirical one. We claim that systematics is, quite the contrary, empirical, and relies on evidence rather than on implicit measurements of data. Consequently, this assertion leads back to the original question of evidence in molecular systematics, namely molecular homology.

ChemInform Abstract: Electron-Reservoir Sandwich Complexes: From Mono- and Bimetallic Complexes to Molecular Trees

ChemInform ◽  
2010 ◽  
Vol 28 (22) ◽  
pp. no-no
Author(s):  
D. ASTRUC ◽  
C. VALERIO ◽  
J.-L. FILLAUT ◽  
J. RUIZ ◽  
J.-R. HAMON ◽  
...  
Keyword(s):  
Bimetallic Complexes ◽  
Sandwich Complexes ◽  
Molecular Trees

scholarly journals Two new generic names for dinophytes harbouring a diatom as an endosymbiont, Blixaea and Unruhdinium (Kryptoperidiniaceae, Peridiniales)

Phytotaxa ◽  
2017 ◽  
Vol 306 (4) ◽  
pp. 296 ◽  
Author(s):  
MARC GOTTSCHLING ◽  
ANŽE ŽERDONER ČALASAN ◽  
JULIANE KRETSCHMANN ◽  
HAIFENG GU
Keyword(s):  
Small Group ◽  
Habitat Preference ◽  
Sister Group ◽  
Monophyletic Group ◽  
Unique Type ◽  
Molecular Trees

Kryptoperidiniaceae are a small group of dinophytes hosting a tertiary endosymbiont derived from a diatom (Tomas et al. 1973, Horiguchi & Pienaar 1994). Those so called ‘dinotoms’ (Imanian et al. 2011) include Dinothrix, Durinskia, Galeidinium, Kryptoperidinium (= Phyllodinium) and some species currently assigned to “Peridiniopsis” and “Peridinium” (Tamura et al. 2005, Horiguchi & Takano 2006, Hansen et al. 2007, Zhang et al. 2011). Besides ‘possessing a diatom endosymbiont’ as a highly derived trait, the monophyly of Kryptoperidiniaceae is also supported by a unique type of eyespot that has possibly derived from the original chloroplast (Moestrup & Daugbjerg 2007). In molecular trees, Kryptoperidiniaceae constitute a well supported monophyletic group (Kretschmann et al. unpubl.), but it is not finally resolved at present, whether they are embedded in the Thoracosphaeraceae or constitute their sister group (Gottschling & McLean 2013). Regarding habitat preference, molecular trees further indicate at least two independent marine→freshwater transitions in the Kryptoperidiniaceae during the late Paleogene at the latest (Žerdoner Čalasan et al. unpubl.).

scholarly journals Spines and homologues in ‘araphid’ diatoms

2019 ◽  
Vol 152 (2) ◽  
pp. 150-162 ◽  
Author(s):  
David M. Williams
Keyword(s):  
Morphological Characters ◽  
Comparative Biology ◽  
Molecular Trees ◽  
As If

Background and aims – Many diatoms have spines on the surface of their valves. These structures differ from one taxon to another. Are all these spines the same? Are they homologues of one another? This paper sets out to explore some of the issues surrounding the determination of homologues with reference to members of Fragilariaceae. Methods – A variety of spines from species in Fragilariaceae are examined (in the SEM) and position on the valve documented relative to those already recorded in the literature. Key results – Spines that occur on the valves of some ‘araphid’ diatoms in Fragilariaceae can be interpreted in the light of where they are found. Spines that occur on the virgae can be thought of as modifications of that structure; spines that occur on the vimines can be thought of as modifications of that structure – the two kinds of spines are not homologues of each other. The term ‘spine’, on its own, is not useful for understanding taxon relationships; the term ‘spine’ is not even a character in the comparative biology sense but a descriptive catch-all for something that simply ‘sticks out from a surface’. Conclusions – Systematic characters, those applicable to comparative biology, are modifications of other characters and so are, in one sense, like taxonomies: hierarchical. A consequence of this is that plotting morphological characters on molecular trees of relationships is a futile endeavour – treating characters and their modifications, as if they are static (unit) features of a non-changing entity, is book-keeping not science.

Phylogenetic revision of the shrimp genera Ephyrina, Meningodora and Notostomus (Acanthephyridae: Caridea)

2020 ◽  
Author(s):  
Anastasiia A Lunina ◽  
Dmitry N Kulagin ◽  
Alexander L Vereshchaka
Keyword(s):  
Molecular Markers ◽  
Morphological Characters ◽  
Valid Species ◽  
Phylogenetic Study ◽  
Forward Motion ◽  
Molecular Analyses ◽  
Phylogenetic Revision ◽  
Molecular Trees

Abstract The shrimp genera Ephyrina, Meningodora and Notostomus have an unusual carapace strengthened with carinae and a half-serrated mandible, which may suggest a possible monophyly of this group. Here we test this hypothesis and present the first phylogenetic study of these genera based on 95 morphological characters (all valid species coded) and six molecular markers (71% of valid species sequenced). Representatives of all genera of Oplophoridae (sister to Acanthephyridae) were outgroups, 32 species belonging to all genera and potentially different clades of Acanthephyridae were ingroups. Both morphological and molecular analyses retrieve trees with similar topology. Our results reject the hypothesis of a clade formed by Ephyrina + Meningodora + Notostomus. We show that Ephyrina and Notostomus are monophyletic, both on morphological and on molecular trees, Meningodora gains support only on morphological trees. Evolutionary traits in the Ephyrina and Meningodora + Notostomus clades are different. Synapomorphies are mostly linked to adaptations to forward motion in Ephyrina (oar-like meri and ischia of pereopods, stempost-like rostrum) and to progressive strengthening of the carapace and pleon in Meningodora and Notostomus (net of sharp carinae). Unusual mandibles evolved in the clades independently and represent convergent adaptations to feeding on gelatinous organisms.

scholarly journals The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the Southern Cassowary, Casuarius casuarius (Aves, Palaeognathae)

2019 ◽  
Author(s):  
Phoebe Louise McInerney ◽  
Michael S. Y. Lee ◽  
Alice M. Clement ◽  
Trevor H. Worthy
Keyword(s):  
Morphological Traits ◽  
Evolutionary History ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Evidence ◽  
Functional Roles ◽  
Phylogenetic Studies ◽  
Basal Clade ◽  
Casuarius Casuarius ◽  
Molecular Trees

Abstract Background: The Palaeognathae are a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern Cassowary, Casuarius casuarius, for which information on the skeletal systems of the syrinx, hyoid and larynx is lacking - despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus suggest they would also be informative for palaeognath phylogenetic analyses, which still exhibits strong conflict between morphological and molecular trees. Results: The morphology of the syrinx, hyoid and larynx of C. casuarius is described from CT scans. The syrinx is of the simple tracheo-bronchial syrinx type, lacking specialised elements such as the pessulus; the hyoid is relatively short with longer ceratobranchials compared to epibranchials; and the larynx is comprised of entirely cartilaginous, standard avian anatomical elements including a concave, basin-like cricoid and fused cricoid wings. As in the larynx, both the syrinx and hyoid lack ossification and all three structures were most similar to Dromaius. We documented substantial variation across palaeognaths in the skeletal character states of the syrinx, hyoid, and larynx, using both the literature and novel observations (e.g. of C. casuarius). Notably, new synapomorphies linking Dinornithiformes and Tinamidae are identified, consistent with the molecular evidence for this clade. These shared morphological character traits include the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla. Conclusion: Syrinx, hyoid and larynx characters of palaeognaths display greater concordance with molecular trees than do other morphological traits. These structures might therefore be less prone to homoplasy related to flightlessness and gigantism, compared to typical morphological traits emphasised in previous phylogenetic studies. Key Words: Palaeognathae, Cassowary, Syrinx, Hyoid, Larynx, Morphology, Phylogenetics, Optimisation

scholarly journals The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the Southern Cassowary, Casuarius casuarius (Aves, Palaeognathae)

2019 ◽  
Author(s):  
Phoebe Louise McInerney ◽  
Michael S. Y. Lee ◽  
Alice M. Clement ◽  
Trevor H. Worthy
Keyword(s):  
Evolutionary History ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationships ◽  
Functional Roles ◽  
Basal Clade ◽  
Data Topology ◽  
Combined Data ◽  
Casuarius Casuarius ◽  
Molecular Trees

Abstract The Palaeognathae are a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern cassowary, Casuarius casuarius , for which information on the skeletal systems of the syrinx, hyoid and larynx is lacking despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus be informative for palaeognath phylogenetic analyses, which still exhibits strong conflict between morphological and molecular trees. We documented variation across palaeognaths in the skeletal character states of the syrinx, hyoid, and larynx, using both the literature and novel observations (e.g. of cassowary). Notably the molecular moa-tinamou clade was found to share morphological character traits including the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla. These findings contributed to optimisation of syrinx, hyoid and larynx characters showing increased phylogenetic support for palaeognath relationships derived from a molecular and morphological combined-data topology.

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