scholarly journals Analogy, Homology, and Rhythmic Phylogeny: Commentary on Adrian Poole's "Comparing Timeline Rhythms in Pygmy and Bushmen Music"

2018 ◽  
Vol 12 (3-4) ◽  
pp. 194
Author(s):  
Justin London
Keyword(s):  
Phylogenetic Analysis ◽  
Convergent Evolution ◽  
Common Origin ◽  
Musical Cultures ◽  
Musical Practices

In his article "Comparing Timeline Rhythms in Pygmy and Bushmen Music," Adrian Poole uses computational phylogenetic analysis to assess the similarity between canonical rhythmic patterns from two African musical cultures. He then uses these analyses to evaluate previous claims of a common origin for their (now) distinct musical practices. Poole was unable to find clear evidence of a common origin, and here I provide additional analyses of these timelines casting further doubt on such claims. Instead, I offer a perspective from convergent evolution/sociobiology which can account for the broad similarities that exist between these two sets of timelines. I conclude with a critique of the claim of Poole and others that African timelines and the musical cultures in which they appear are especially resistant to change.

scholarly journals Jaw elements in Plumulites bengtsoni confirm that machaeridians are extinct armoured scaleworms

2019 ◽  
Vol 286 (1907) ◽  
pp. 20191247 ◽  
Author(s):  
Luke A. Parry ◽  
Gregory D. Edgecombe ◽  
Dan Sykes ◽  
Jakob Vinther
Keyword(s):  
Phylogenetic Analysis ◽  
Early Evolution ◽  
The Body ◽  
Common Origin ◽  
Discrete Elements ◽  
Crown Group ◽  
Total Group ◽  
Early Ordovician ◽  
Jaw Apparatus ◽  
Competing Hypotheses

Machaeridians are Palaeozoic animals that are dorsally armoured with serialized, imbricating shell plates that cover or enclose the body. Prior to the discovery of an articulated plumulitid machaeridian from the Early Ordovician of Morocco that preserved unambiguous annelid characters (segmental parapodia with chaetae), machaeridians were a palaeontological mystery, having been previously linked to echinoderms, barnacles, tommotiids (putative stem-group brachiopods) or molluscs. Although the annelid affinities of machaeridians are now firmly established, their position within the phylum and relevance for understanding the early evolution of Annelida is less secure, with competing hypotheses placing Machaeridia in the stem or deeply nested within the crown group of annelids. We describe a scleritome of Plumulites bengtsoni from the Fezouata Formation of Morocco that preserves an anterior jaw apparatus consisting of at least two discrete elements that exhibit growth lines. Although jaws have multiple independent origins within the annelid crown group, comparable jaws are present only within Phyllodocida, the clade that contains modern aphroditiforms (scaleworms and relatives). Phylogenetic analysis places a monophyletic Machaeridia within the crown group of Phyllodocida in total-group Aphroditiformia, consistent with a common origin of machaeridian shell plates and scaleworm elytrae. The inclusion of machaeridians in Aphroditiformia truncates the ghost lineage of Phyllodocida by almost a hundred million years.

scholarly journals Evolutionary convergence in lignin-degrading enzymes

2018 ◽  
Vol 115 (25) ◽  
pp. 6428-6433 ◽  
Author(s):  
Iván Ayuso-Fernández ◽  
Francisco J. Ruiz-Dueñas ◽  
Angel T. Martínez
Keyword(s):  
Phylogenetic Analysis ◽  
Convergent Evolution ◽  
Acid Level ◽  
Lignin Degradation ◽  
Amino Acid Level ◽  
Surface Oxidation ◽  
Phenotypic Trait ◽  
Limiting Step ◽  
Powerful Strategy

The resurrection of ancestral enzymes of now-extinct organisms (paleogenetics) is a developing field that allows the study of evolutionary hypotheses otherwise impossible to be tested. In the present study, we target fungal peroxidases that play a key role in lignin degradation, an essential process in the carbon cycle and often a limiting step in biobased industries. Ligninolytic peroxidases are secreted by wood-rotting fungi, the origin of which was recently established in the Carboniferous period associated with the appearance of these enzymes. These first peroxidases were not able to degrade lignin directly and used diffusible metal cations to attack its phenolic moiety. The phylogenetic analysis of the peroxidases of Polyporales, the order in which most extant wood-rotting fungi are included, suggests that later in evolution these enzymes would have acquired the ability to degrade nonphenolic lignin using a tryptophanyl radical interacting with the bulky polymer at the surface of the enzyme. Here, we track this powerful strategy for lignin degradation as a phenotypic trait in fungi and show that it is not an isolated event in the evolution of Polyporales. Using ancestral enzyme resurrection, we study the molecular changes that led to the appearance of the same surface oxidation site in two distant peroxidase lineages. By characterization of the resurrected enzymes, we demonstrate convergent evolution at the amino acid level during the evolution of these fungi and track the different changes leading to phylogenetically distant ligninolytic peroxidases from ancestors lacking the ability to degrade nonphenolic lignin.

scholarly journals Phylogenetic analysis of Andinia (Pleurothallidinae; Orchidaceae) and a systematic re-circumscription of the genus

Phytotaxa ◽  
2017 ◽  
Vol 295 (2) ◽  
pp. 101 ◽  
Author(s):  
MARK WILSON ◽  
GRAHAM S. FRANK ◽  
LOU JOST ◽  
ALEC M. PRIDGEON ◽  
SEBASTIAN VIEIRA-URIBE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Convergent Evolution ◽  
Type Species ◽  
Floral Morphology ◽  
Phylogenetic Analyses ◽  
Evolutionary Diversification ◽  
The Andes ◽  
Deceit Pollination ◽  
Nuclear Its ◽  
The Individual

Most of the species studied in this paper have previously been placed in either Pleurothallis or Lepanthes. However, at one time or another, members of the group have also been placed in the genera Andinia, Brachycladium, Lueranthos, Masdevalliantha, Neooreophilus, Oreophilus, Penducella, Salpistele and Xenosia. Phylogenetic analyses of nuclear ITS and plastid matK sequences indicate that these species form a strongly supported clade that is only distantly related to Lepanthes and is distinct from Pleurothallis and Salpistele. Since this clade includes the type species of Andinia, A. dielsii, and it has taxonomic precedence over all other generic names belonging to this group, Andinia is re-circumscribed and expanded to include 72 species segregated into five subgenera: Aenigma, Andinia, Brachycladium, Masdevalliantha and Minuscula. The required taxonomic transfers are made herein. We hypothesize that convergent evolution towards a similar pollinator syndrome involving deceit pollination via pseudocopulation by Diptera resulted in a similar floral morphology between species of subgenus Brachycladium and species of Lepanthes; hence the prior placement of the species of subgenus Brachycladium in Lepanthes. Species of the re-circumscribed Andinia are confined exclusively to the Andes, ranging from about 1,200 to 3,800 m, from Colombia south to Bolivia, making the generic name very apt. Elevational distributions of the individual clades are discussed in relation to the possible evolutionary diversification of the most species-rich clade, subgenus Brachycladium.

scholarly journals Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1583 ◽  
Author(s):  
William G. Parker
Keyword(s):  
Phylogenetic Analysis ◽  
Convergent Evolution ◽  
Morphological Character ◽  
Late Triassic ◽  
Parsimony Analysis ◽  
Weak Support ◽  
Selective Pressures ◽  
Body Regions ◽  
High Species Diversity ◽  
First Time

Aetosauria is an early-diverging clade of pseudosuchians (crocodile-line archosaurs) that had a global distribution and high species diversity as a key component of various Late Triassic terrestrial faunas. It is one of only two Late Triassic clades of large herbivorous archosaurs, and thus served a critical ecological role. Nonetheless, aetosaur phylogenetic relationships are still poorly understood, owing to an overreliance on osteoderm characters, which are often poorly constructed and suspected to be highly homoplastic. A new phylogenetic analysis of the Aetosauria, comprising 27 taxa and 83 characters, includes more than 40 new characters that focus on better sampling the cranial and endoskeletal regions, and represents the most comprenhensive phylogeny of the clade to date. Parsimony analysis recovered three most parsimonious trees; the strict consensus of these trees finds an Aetosauria that is divided into two main clades: Desmatosuchia, which includes the Desmatosuchinae and the Stagonolepidinae, and Aetosaurinae, which includes the Typothoracinae. As defined Desmatosuchinae now containsNeoaetosauroides engaeusand several taxa that were previously referred to the genusStagonolepis, and a new clade, Desmatosuchini, is erected for taxa more closely related toDesmatosuchus. Overall support for some clades is still weak, and Partitioned Bremer Support (PBS) is applied for the first time to a strictly morphological dataset demonstrating that this weak support is in part because of conflict in the phylogenetic signals of cranial versus postcranial characters. PBS helps identify homoplasy among characters from various body regions, presumably the result of convergent evolution within discrete anatomical modules. It is likely that at least some of this character conflict results from different body regions evolving at different rates, which may have been under different selective pressures.

scholarly journals A comprehensive phylogenetic analysis of the serpin superfamily

2020 ◽  
Author(s):  
Matthew A. Spence ◽  
Matthew D. Mortimer ◽  
Ashley M. Buckle ◽  
Bui Quang Minh ◽  
Colin J. Jackson
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Convergent Evolution ◽  
Alternative Hypothesis ◽  
Structural Alignment ◽  
High Homology ◽  
Physiological Processes ◽  
New Directions ◽  
Hub Proteins

Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer (HGT) due to their unexpectedly high homology. Here we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of HGT. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.

Phylogenetic analysis of longitudinal melanoma samples to reveal convergent evolution and markers of immunotherapy resistance.

2018 ◽  
Vol 36 (15_suppl) ◽  
pp. 9581-9581
Author(s):  
David Liu ◽  
Gao Zhang ◽  
Alvin Shi ◽  
Benjamin Izar ◽  
Alexander Heyde ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Convergent Evolution

scholarly journals A Comprehensive Phylogenetic Analysis of the Serpin Superfamily

2021 ◽  
Author(s):  
Matthew A Spence ◽  
Matthew D Mortimer ◽  
Ashley M Buckle ◽  
Bui Quang Minh ◽  
Colin J Jackson
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Convergent Evolution ◽  
Alternative Hypothesis ◽  
Structural Alignment ◽  
High Homology ◽  
Physiological Processes ◽  
New Directions ◽  
Hub Proteins

Abstract Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer due to their unexpectedly high homology. Here, we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of horizontal gene transfer. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.

Musical Cultures of the Ibero-American Borderlands

2019 ◽  
pp. 524-543
Author(s):  
Kristin Dutcher Mann ◽  
Drew Edward Davies
Keyword(s):  
Musical Instruments ◽  
Colonial Period ◽  
Urban Life ◽  
Orchestral Music ◽  
Music Making ◽  
Rural And Urban ◽  
Musical Cultures ◽  
Musical Practices ◽  
Liturgical Chant ◽  
Political Realities

Music and dance were key elements of culture in the Ibero-American borderlands that served to reflect, shape, and express cultural and political realities. From colonizers’ perspectives, proficiency in Western musical practices equaled acculturation to Catholic norms and civilized, sedentary society. At the same time, performances of music and dance articulated changing native identities. There was no single borderlands music or dance, and evidence in the form of music manuscripts, eyewitness accounts, and musical instruments remains fragmented and scattered among periods and locations. Practices such as liturgical chant, bell ringing, religious songs, communal dance, orchestral music, and other musical arts formed integral parts of mission and urban life in the borderlands throughout the colonial period. Whereas the interior church spaces such as Durango Cathedral, were dominated by performative music genres, music making in rural and urban exterior spaces included participatory activities that produced diverse ambient soundscapes.

scholarly journals An early chondrichthyan and the evolutionary assembly of a shark body plan

2018 ◽  
Vol 285 (1870) ◽  
pp. 20172418 ◽  
Author(s):  
Michael I. Coates ◽  
John A. Finarelli ◽  
Ivan J. Sansom ◽  
Plamen S. Andreev ◽  
Katharine E. Criswell ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Middle Devonian ◽  
Convergent Evolution ◽  
Feeding Habits ◽  
Suspension Feeding ◽  
Gill Slit ◽  
Crown Group ◽  
Skeletal Morphology ◽  
Histological Techniques ◽  
Condition Characteristic

Although relationships among the major groups of living gnathostomes are well established, the relatedness of early jawed vertebrates to modern clades is intensely debated. Here, we provide a new description of Gladbachus , a Middle Devonian (Givetian approx. 385-million-year-old) stem chondrichthyan from Germany, and one of the very few early chondrichthyans in which substantial portions of the endoskeleton are preserved. Tomographic and histological techniques reveal new details of the gill skeleton, hyoid arch and jaws, neurocranium, cartilage, scales and teeth. Despite many features resembling placoderm or osteichthyan conditions, phylogenetic analysis confirms Gladbachus as a stem chondrichthyan and corroborates hypotheses that all acanthodians are stem chondrichthyans. The unfamiliar character combination displayed by Gladbachus , alongside conditions observed in acanthodians, implies that pre-Devonian stem chondrichthyans are severely under-sampled and strongly supports indications from isolated scales that the gnathostome crown group originated at the latest by the early Silurian (approx. 440 Ma). Moreover, phylogenetic results highlight the likely convergent evolution of conventional chondrichthyan conditions among earliest members of this primary gnathostome division, while skeletal morphology points towards the likely suspension feeding habits of Gladbachus , suggesting a functional origin of the gill slit condition characteristic of the vast majority of living and fossil chondrichthyans.

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