Fossils, homology, and “Phylogenetic Paleo-ontogeny”: a reassessment of primary posterior plate homologies among fossil and living crinoids with insights from developmental biology

Paleobiology ◽  
2015 ◽  
Vol 41 (4) ◽  
pp. 570-591 ◽  
Author(s):  
David F. Wright
Keyword(s):  
Developmental Biology ◽  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
A Priori ◽  
Evolutionary Developmental Biology ◽  
Phylogeny Reconstruction ◽  
Phylogenetic Systematics ◽  
Developmental Patterns ◽  
Single Plate ◽  
Homology Recognition

AbstractPaleobiologists must propose a priori hypotheses of homology when conducting a phylogenetic analysis of extinct taxa. The distributions of such “primary” homologies among species are fundamental to phylogeny reconstruction because they reflect a prior belief in what constitutes comparable organismal elements and are the principal determinants of the outcome of phylogenetic analysis. Problems arise when fossil morphology presents seemingly equivocal hypotheses of homology, herein referred to as antinomies. In groups where homology recognition has been elusive, such as echinoderms, these problems are commonly accompanied by the presence (and persistence) of poor descriptive terminology in taxonomic literature that confounds an understanding of characters and stymy phylogenetic research. This paper combines fossil morphology, phylogenetic systematics, and insights from evolutionary developmental biology to outline a research program in Phylogenetic Paleo-ontogeny. A “paleo” ontogenetic approach to character analysis provides a logical basis for homology recognition and discerning patterns of character evolution in a phylogenetic context. To illustrate the utility of the paleo-ontogenetic approach, I present a reassessment of historically contentious plate homologies for “pan-cladid” crinoids (Cladida, Flexibilia, Articulata). Developmental patterns in living crinoids were combined with the fossil record of pan-cladid morphologies to investigate primary posterior plate homologies. Results suggest the sequence of morphologic transitions unfolding during the ontogeny of extant crinoids are developmental relics of their Paleozoic precursors. Developmental genetic modules controlling posterior plate development in pan-cladid crinoids have likely experienced considerable constraint for over 250 million years and limited morphologic diversity in the complexity of calyx characters. Future phylogenetic analyses of pan-cladids are recommended to consider the presence of a single plate in the posterior region homologous with the radianal, rather than the anal X, as is commonly assumed.

scholarly journals A phylogenomic framework and timescale for comparative studies of tunicates

2017 ◽  
Author(s):  
Frédéric Delsuc ◽  
Hervé Philippe ◽  
Georgia Tsagkogeorga ◽  
Paul Simion ◽  
Marie-Ka Tilak ◽  
...  
Keyword(s):  
Developmental Biology ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Sister Group ◽  
Evolutionary Developmental Biology ◽  
Sequence Evolution ◽  
Precise Position ◽  
Representative Species ◽  
Vertebrate Model ◽  
Phylogenetic Framework

AbstractBackgroundTunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species.ResultsPhylogenetic analyses using site-heterogeneous CAT mixture models of amino acid sequence evolution resulted in a strongly supported tree topology resolving the relationships among four major tunicate clades: 1) Appendicularia, 2) Thaliacea + Phlebobranchia + Aplousobranchia, 3) Molgulidae, and 4) Styelidae + Pyuridae. Notably, the morphologically derived Thaliacea are confirmed as the sister-group of the clade uniting Phlebobranchia + Aplousobranchia within which the precise position of the model ascidian genus Ciona remains uncertain. Relaxed molecular clock analyses accommodating the accelerated evolutionary rate of tunicates reveal ancient diversification (~450-350 million years ago) among the major groups and allow comparing their evolutionary age with respect to the major vertebrate model lineages.ConclusionsOur study represents the most comprehensive phylogenomic dataset for the main tunicate lineages. It offers a reference phylogenetic framework and first tentative timescale for tunicates, allowing the direct comparison with vertebrate model species in comparative genomics and evolutionary developmental biology studies.

Evo-Devo and the Structure(s) of Evolutionary Theory

2017 ◽  
Author(s):  
Alan C. Love
Keyword(s):  
Developmental Biology ◽  
Evolutionary Theory ◽  
Mechanistic Explanation ◽  
Evolutionary Developmental Biology ◽  
Primary Concern ◽  
Adaptive Function ◽  
Specific Content ◽  
Central Location ◽  
Developmental Form ◽  
Evo Devo

Many researchers have argued that evolutionary developmental biology (evo-devo) constitutes a challenge to standard evolutionary theory, requiring the explicit inclusion of developmental processes that generate variation and attention to organismal form (rather than adaptive function). An analysis of these developmental-form challenges indicates that the primary concern is not the inclusion of specific content but the epistemic organization or structure of evolutionary theory. Proponents of developmental-form challenges favor moving their considerations to a more central location in evolutionary theorizing, in part because of a commitment to the value of mechanistic explanation. This chapter argues there are multiple legitimate structures for evolutionary theory, instead of a single, overarching or canonical organization, and different theory presentations can be understood as idealizations that serve different investigative and explanatory goals in evolutionary inquiry.

scholarly journals Molecular record for the first authentication of Isaria cicadae from Vietnam

2021 ◽  
Vol 16 (1) ◽  
pp. 711-718
Author(s):  
Thuan Duc Lao ◽  
Hanh Van Trinh ◽  
Loi Vuong ◽  
Luyen Tien Vu ◽  
Thuy Ai Huyen Le ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Pcr Assay ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Cordyceps Cicadae ◽  
High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

scholarly journals Black spicules from a new interstitial opheliid polychaete Thoracophelia minuta sp. nov. (Annelida: Opheliidae)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Naoto Jimi ◽  
Shinta Fujimoto ◽  
Mami Takehara ◽  
Satoshi Imura
Keyword(s):  
Developmental Biology ◽  
Phylogenetic Analysis ◽  
New Species ◽  
Morphological Diversity ◽  
The Body ◽  
Evolutionary Significance ◽  
Research Subject ◽  
Ecological Diversity ◽  
Coelomic Cavity ◽  
Molecular Phylogenetic

AbstractThe phylum Annelida exhibits high morphological diversity coupled with its extensive ecological diversity, and the process of its evolution has been an attractive research subject for many researchers. Its representatives are also extensively studied in fields of ecology and developmental biology and important in many other biology related disciplines. The study of biomineralisation is one of them. Some annelid groups are well known to form calcified tubes but other forms of biomineralisation are also known. Herein, we report a new interstitial annelid species with black spicules, Thoracophelia minuta sp. nov., from Yoichi, Hokkaido, Japan. Spicules are minute calcium carbonate inclusions found across the body and in this new species, numerous black rod-like inclusions of calcium-rich composition are distributed in the coelomic cavity. The new species can be distinguished from other known species of the genus by these conspicuous spicules, shape of branchiae and body formula. Further, the new species’ body size is apparently smaller than its congeners. Based on our molecular phylogenetic analysis using 18S and 28S sequences, we discuss the evolutionary significance of the new species’ spicules and also the species' progenetic origin.

scholarly journals Molecular and phylogenetic analysis reveals new diversity of Dunaliella salina from hypersaline environments

2021 ◽  
pp. 1-11
Author(s):  
Andrea Highfield ◽  
Angela Ward ◽  
Richard Pipe ◽  
Declan C. Schroeder
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Dunaliella Salina ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
Lsu Rdna ◽  
Hypersaline Environments ◽  
Rdna Its ◽  
Β Carotene ◽  
Selection Of

Abstract Twelve hyper-β carotene-producing strains of algae assigned to the genus Dunaliella salina have been isolated from various hypersaline environments in Israel, South Africa, Namibia and Spain. Intron-sizing of the SSU rDNA and phylogenetic analysis of these isolates were undertaken using four commonly employed markers for genotyping, LSU rDNA, ITS, rbcL and tufA and their application to the study of Dunaliella evaluated. Novel isolates have been identified and phylogenetic analyses have shown the need for clarification on the taxonomy of Dunaliella salina. We propose the division of D. salina into four sub-clades as defined by a robust phylogeny based on the concatenation of four genes. This study further demonstrates the considerable genetic diversity within D. salina and the potential of genetic analyses for aiding in the selection of prospective economically important strains.

New olenelline trilobites from the Northwest Territories, Canada, and the phylogenetic placement of Judomia absita Fritz, 1973

Zootaxa ◽  
2011 ◽  
Vol 2918 (1) ◽  
pp. 15 ◽  
Author(s):  
I. WESLEY GAPP ◽  
BRUCE S. LIEBERMAN ◽  
MICHAEL C. POPE ◽  
KELLY A. DILLIARD
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Northwest Territories ◽  
Phylogenetic Analyses ◽  
Geographic Range ◽  
Early Cambrian ◽  
Phylogenetic Placement ◽  
The Subject ◽  
Three New Species ◽  
One New Species

The Early Cambrian olenelline trilobites are a diverse clade and have been the subject of several phylogenetic analyses. Here, three new species of Bradyfallotaspis Fritz, 1972 (B. coriae, B. nicolascagei, and B. sekwiensis) and one new species of Nevadia Walcott, 1910 (N. saupeae) are described from the Sekwi Formation of the Mackenzie Mountains, Northwest Territories, Canada. In addition, new specimens potentially referable to Nevadia ovalis McMenamin, 1987 were recovered that may expand that species’ geographic range, which was thought to be restricted to Sonora, Mexico. The results of a phylogenetic analysis incorporating several olenelline taxa, including Judomia absita Fritz, 1973 from the Sekwi Formation, are also presented herein. This species has been assigned to various olenelline genera, including Judomia Lermontova, 1951 and Paranevadella Palmer & Repina, 1993. Phylogenetic analysis suggests this species is closely related to Judomia tera Lazarenko, 1960 from Siberia. This phylogenetic relationship provides further support for the hypothesis that a close biogeographic relationship existed between Laurentia and Siberia during the Cambrian.

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