scholarly journals Neurocranial anatomy of an enigmatic Early Devonian fish sheds light on early osteichthyan evolution

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Alice M Clement ◽  
Benedict King ◽  
Sam Giles ◽  
Brian Choo ◽  
Per E Ahlberg ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Taxon ◽  
Phylogenetic Position ◽  
Micro Ct ◽  
Bayesian Analyses ◽  
Early Devonian ◽  
Precise Position ◽  
Anatomical Features ◽  
Skull Roof ◽  
Ct Data

The skull of ‘Ligulalepis’ from the Early Devonian of Australia (AM-F101607) has significantly expanded our knowledge of early osteichthyan anatomy, but its phylogenetic position has remained uncertain. We herein describe a second skull of ‘Ligulalepis’ and present micro-CT data on both specimens to reveal novel anatomical features, including cranial endocasts. Several features previously considered to link ‘Ligulalepis’ with actinopterygians are now considered generalized osteichthyan characters or of uncertain polarity. The presence of a lateral cranial canal is shown to be variable in its development between specimens. Other notable new features include the presence of a pineal foramen, the some detail of skull roof sutures, the shape of the nasal capsules, a placoderm-like hypophysial vein, and a chondrichthyan-like labyrinth system. New phylogenetic analyses place ‘Ligulalepis’ as a stem osteichthyan, specifically as the sister taxon to ‘psarolepids’ plus crown osteichthyans. The precise position of ‘psarolepids’ differs between parsimony and Bayesian analyses.

scholarly journals The systematic position of the enigmatic thyreophoran dinosaurParanthodon africanus, and the use of basal exemplifiers in phylogenetic analysis

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4529 ◽  
Author(s):  
Thomas J. Raven ◽  
Susannah C.R. Maidment
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
Lower Cretaceous ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Type Material ◽  
Sister Taxon ◽  
Phylogenetic Position ◽  
Taxonomic Assignment

The first African dinosaur to be discovered,Paranthodon africanuswas found in 1845 in the Lower Cretaceous of South Africa. Taxonomically assigned to numerous groups since discovery, in 1981 it was described as a stegosaur, a group of armoured ornithischian dinosaurs characterised by bizarre plates and spines extending from the neck to the tail. This assignment has been subsequently accepted. The type material consists of a premaxilla, maxilla, a nasal, and a vertebra, and contains no synapomorphies of Stegosauria. Several features of the maxilla and dentition are reminiscent of Ankylosauria, the sister-taxon to Stegosauria, and the premaxilla appears superficially similar to that of some ornithopods. The vertebral material has never been described, and since the last description of the specimen, there have been numerous discoveries of thyreophoran material potentially pertinent to establishing the taxonomic assignment of the specimen. An investigation of the taxonomic and systematic position ofParanthodonis therefore warranted. This study provides a detailed re-description, including the first description of the vertebra. Numerous phylogenetic analyses demonstrate that the systematic position ofParanthodonis highly labile and subject to change depending on which exemplifier for the clade Stegosauria is used. The results indicate that the use of a basal exemplifier may not result in the correct phylogenetic position of a taxon being recovered if the taxon displays character states more derived than those of the basal exemplifier, and we recommend the use, minimally, of one basal and one derived exemplifier per clade.Paranthodonis most robustly recovered as a stegosaur in our analyses, meaning it is one of the youngest and southernmost stegosaurs.

scholarly journals The systematic position of the enigmatic thyreophoran dinosaur Paranthodon africanus, and the use of basal exemplifiers in phylogenetic analysis

2018 ◽  
Author(s):  
Tom Raven ◽  
Susannah C. R. Maidment
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
Lower Cretaceous ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Type Material ◽  
Sister Taxon ◽  
Phylogenetic Position ◽  
Taxonomic Assignment

The first African dinosaur to be discovered, Paranthodon africanus was found in 1845 in the Lower Cretaceous of South Africa. Taxonomically assigned to numerous groups since discovery, in 1981 it was described as a stegosaur, a group of armoured ornithischian dinosaurs characterised by bizarre plates and spines extending from the neck to the tail. This assignment has been subsequently accepted. The type material consists of a premaxilla, maxilla, a nasal, and a vertebra, and contains no synapomorphies of Stegosauria. Several features of the maxilla and dentition are reminiscent of Ankylosauria, the sister-taxon to Stegosauria, and the premaxilla appears superficially similar to that of some ornithopods. The vertebral material has never been described, and since the last description of the specimen, there have been numerous discoveries of thyreophoran material potentially pertinent to establishing the taxonomic assignment of the specimen. An investigation of the taxonomic and systematic position of Paranthodon is therefore warranted. This study provides a detailed re-description, including the first description of the vertebra. Numerous phylogenetic analyses demonstrate that the systematic position of Paranthodon is highly labile and subject to change depending on which exemplifier for the clade Stegosauria is used. The results indicate that the use of a basal exemplifier may not result in the correct phylogenetic position of a taxon being recovered if the taxon displays character states more derived than those of the basal exemplifier, and we recommend the use, minimally, of one basal and one derived exemplifier per clade. Paranthodon is most robustly recovered as a stegosaur in our analyses, meaning it is one of the youngest and southernmost stegosaurs.

The anatomy and phylogenetic position of the Triassic dinosaur Staurikosaurus pricei Colbert, 1970

Zootaxa ◽  
2009 ◽  
Vol 2079 (1) ◽  
pp. 1-56 ◽  
Author(s):  
JONATHAS DE SOUZA BITTENCOURT ◽  
ALEXANDER WILHELM ARMIN KELLNER
Keyword(s):  
Morphological Characters ◽  
Late Triassic ◽  
Sister Taxon ◽  
Phylogenetic Position ◽  
Southern Brazil ◽  
Anatomical Features ◽  
Phylogenetic Studies ◽  
Caudal Vertebrae ◽  
Close Relationship ◽  
Santa Maria

We redescribe the holotype of the saurischian dinosaur Staurikosaurus pricei Colbert, 1970 from Late Triassic Santa Maria Formation (southern Brazil), following additional preparation that revealed new anatomical features. A revised diagnosis is proposed and the published synapomorphies for Dinosauria and less inclusive clades (e.g. Saurischia) are evaluated for this species. Some characters previously identified as present in the holotype, including the intramandibular joint, hyposphene-hypantrum articulations in dorsal vertebrae, and a cranial trochanter and trochanteric shelf on the femur, cannot be confirmed due to poor preservation or are absent in the available material. In addition, postcranial characters support a close relationship between S. pricei and Herrerasaurus ischigualastensis Reig, 1963 (Late Triassic, Argentina), forming the clade Herrerasauridae. Several pelvic and vertebral characters support the placement of S. pricei as a saurischian dinosaur. Within Saurischia, characters observed in the holotype, including the anatomy of the dentition and caudal vertebrae, support theropod affinities. However, the absence of some characters observed in the clades Theropoda and Sauropodomorpha suggests that S. pricei is not a member of Eusaurischia. Most morphological characters discussed in previous phylogenetic studies cannot be assessed for S. pricei because of the incompleteness of the holotype and only known specimen. The phylogenetic position of S. pricei is constrained by that of its sister taxon H. ischigualastensis, which is known from much more complete material.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

scholarly journals Evolutionary significance of the blastozoan Eumorphocystis and its pseudo-arms

2020 ◽  
pp. 1-17
Author(s):  
Thomas E. Guensburg ◽  
James Sprinkle ◽  
Rich Mooi ◽  
Bertrand Lefebvre
Keyword(s):  
Phylogenetic Analysis ◽  
Sister Taxon ◽  
Evolutionary Significance ◽  
Coelomic Cavity ◽  
Anatomical Features ◽  
New Findings ◽  
Solid Block ◽  
Cover Plates

Abstract Twelve specimens of Eumorphocystis Branson and Peck, 1940 provide the basis for new findings and a more informed assessment of whether this blastozoan (a group including eocrinoids, blastoids, diploporites, rhombiferans) constitutes the sister taxon to crinoids, as has been recently proposed. Both Eumorphocystis and earliest-known crinoid feeding appendages express longitudinal canals, a demonstrable trait exclusive to these taxa. However, the specimen series studied here shows that Eumorphocystis canals constrict proximally and travel within ambulacrals above the thecal cavity. This relationship is congruent with a documented blastozoan pattern but very unlike earliest crinoid topology. Earliest crinoid arm cavities lie fully beneath floor plates; these expand and merge directly with the main thecal coelomic cavity at thecal shoulders. Other associated anatomical features echo this contrasting comparison. Feeding appendages of Eumorphocystis lack two-tiered cover plates, podial basins/pores, and lateral arm plating, all features of earliest crinoid ‘true arms.’ Eumorphocystis feeding appendages are buttressed by solid block-like plates added during ontogeny at a generative zone below floor plates, a pattern with no known parallel among crinoids. Eumorphocystis feeding appendages express brachioles, erect extensions of floor plates, also unknown among crinoids. These several distinctions point to nonhomology of most feeding appendage anatomy, including longitudinal canals, removing Eumorphocystis and other blastozoans from exclusive relationship with crinoids. Eumorphocystis further differs from crinoids in that thecal plates express diplopores, respiratory structures not present among crinoids, but ubiquitous among certain groups of blastozoans. Phylogenetic analysis places Eumorphocystis as a crownward blastozoan, far removed from crinoids.

scholarly journals A Micro-Computed Tomography Comparison of the Porosity in Additively Fabricated CuCr1 Alloy Parts Using Virgin and Surface-Modified Powders

Materials ◽  
2021 ◽  
Vol 14 (8) ◽  
pp. 1995
Author(s):  
Mirko Sinico ◽  
Suraj Dinkar Jadhav ◽  
Ann Witvrouw ◽  
Kim Vanmeensel ◽  
Wim Dewulf
Keyword(s):  
High Energy ◽  
High Energy Density ◽  
Micro Ct ◽  
Micro Computed Tomography ◽  
Powder Bed ◽  
Metallurgical Defects ◽  
Ct Analysis ◽  
Ct Data ◽  
Surface Modified ◽  
Fusion Pores

Recently, the use of novel CuCr1 surface-modified powder for reliable laser powder-bed fusion (LPBF) manufacturing has been proposed, enabling a broader LPBF processing window and longer powder storage life. Nevertheless, virgin CuCr1 powder is also LPBF processable, on the condition that a high-energy density is employed. In this work, we compare two dense specimens produced from virgin and surface-modified CuCr1 powder. Furthermore, a third sample fabricated from surface-modified powder is characterized to understand an abnormal porosity content initially detected through Archimedes testing. Utilizing high-resolution micro-CT scans, the nature of the defects present in the different samples is revealed. Pores are analyzed in terms of size, morphology and spatial distribution. The micro-CT data reveal that the virgin CuCr1 dense specimen displays keyhole pores plus pit cavities spanning multiple layer thicknesses. On the other hand, the sample fabricated with the surface-modified CuCr1 powder mainly contains small and spherical equi-distributed metallurgical defects. Finally, the CT analysis of the third specimen reveals the presence of a W contamination, favoring lack-of-fusion pores between subsequent LPBF layers. The LPBF melting mode (keyhole or conductive), the properties of the material, and the potential presence of contaminants are connected to the different porosity types and discussed.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

scholarly journals Phenotypically and Genotypically Heterogeneous Strains of Pseudomonas syringae Associated With Alfalfa Leaf Spot Disease in Iran

Plant Disease ◽  
2019 ◽  
Vol 103 (12) ◽  
pp. 3199-3208 ◽  
Author(s):  
Maryam Ansari ◽  
S. Mohsen Taghavi ◽  
Sadegh Zarei ◽  
Soraya Mehrb-Moghadam ◽  
Hamzeh Mafakheri ◽  
...  
Keyword(s):  
Host Range ◽  
Pseudomonas Syringae ◽  
Leaf Spot ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Pcr Primers ◽  
Phylogenetic Position ◽  
Leaf Spot Disease ◽  
Bacterial Strains ◽  
Alfalfa Leaf

In this study, we provide a polyphasic characterization of 18 Pseudomonas spp. strains associated with alfalfa leaf spot symptoms in Iran. All of the strains were pathogenic on alfalfa, although the aggressiveness and symptomology varied among the strains. All strains but one were pathogenic on broad bean, cucumber, honeydew, and zucchini, whereas only a fraction of the strains were pathogenic on sugar beet, tomato, and wheat. Syringomycin biosynthesis genes (syrB1 and syrP) were detected using the corresponding PCR primers in all of the strains isolated from alfalfa. Phylogenetic analyses using the sequences of four housekeeping genes (gapA, gltA, gyrB, and rpoD) revealed that all of the strains except one (Als34) belong to phylogroup 2b of P. syringae sensu lato, whereas strain Als34 placed within phylogroup 1 close to the type strain of P. syringae pv. apii. Among the phylogroup 2b strains, nine strains were phylogenetically close to the P. syringae pv. aptata clade, whereas the remainder were scattered among P. syringae pv. atrofaciens and P. syringae pv. syringae strains. Pathogenicity and host range assays of the bacterial strains evaluated in this study on a set of taxonomically diverse plant species did not allow us to assign a “pathovar” status to the alfalfa strains. However, these results provide novel insight into the host range and phylogenetic position of the alfalfa-pathogenic members of P. syringae sensu lato, and they reveal that phenotypically and genotypically heterogeneous strains of the pathogen cause bacterial leaf spot of alfalfa.

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