The rise and fall of a genus: Complete mtDNA genomes shed light on the phylogenetic position of yellow-tailed woolly monkeys, Lagothrix flavicauda, and on the evolutionary history of the family Atelidae (Primates: Platyrrhini)

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.

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Systematic evidence from gene duplication and regulation

Australian Systematic Botany ◽

10.1071/sb9900145 ◽

1990 ◽

Vol 3 (1) ◽

pp. 145

Author(s):

DJ Colgan

Keyword(s):

Gene Duplication ◽

Evolutionary History ◽

Tandem Duplication ◽

Fragment Length Polymorphism ◽

Duplicate Genes ◽

Polymorphism Analysis ◽

Multiple Origins ◽

The Family ◽

History Of ◽

Phylogenetic Hypotheses

This paper is a review of the use of information regarding the presence of duplicate genes and their regulation in systematics. The review concentrates on data derived from protein electrophoresis and restriction fragment length polymorphism analysis. The appearance of a duplication in a subset of a group of species implies that the members of the subset belong to the same clade. Suppression of the duplication may render this clade apparently paraphyletic, but may itself be informative of relations within the lineage through patterns of loss of expression in all, or some tissues, or through restrictions of the formation of functional heteropolymers in polymeric enzymes. Examples are given of studies which have used such information to establish phylogenetic hypotheses at the family level, to identify an auto- or allo-polyploid origin of polyploid species and to determine whether there have been single or multiple origins of such species. The likelihood of homoplasy in the patterns of appearance and regulation of duplicates depends on the molecular basis of the duplication. In particular, the contrast between the expected consequences of tandem duplication and the expression of pseudogenes emphasises the value of determining the mechanism of the original duplication. Many instances of sporadic gene duplication are now known, and polyploidisation is a common event in the evolutionary history of both plants and animals. So the opportunities to discover duplicationrelated characters will arise in many systematic studies. A program is presented to increase the chances that such useful information will be recognisable during the studies.

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Phylogenetic position and evolutionary history of the turtle and whale barnacles (Cirripedia: Balanomorpha: Coronuloidea)

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2012.12.018 ◽

2013 ◽

Vol 67 (1) ◽

pp. 9-14 ◽

Cited By ~ 16

Author(s):

Ryota Hayashi ◽

Benny K.K. Chan ◽

Noa Simon-Blecher ◽

Hiromi Watanabe ◽

Tamar Guy-Haim ◽

...

Keyword(s):

Evolutionary History ◽

Phylogenetic Position ◽

History Of

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Three new Cenomanian conifers from El Chango (Chiapas, Mexico) offer a snapshot of the geographic mosaic of the Mesozoic conifer decline

10.1101/2021.09.01.458614 ◽

2021 ◽

Author(s):

Ixchel Gonzalez-Ramirez ◽

Sergio RS Cevallos-Ferriz ◽

Carl Rothfels

Keyword(s):

Evolutionary History ◽

Mixed Forest ◽

Freshwater Ecosystems ◽

Total Evidence ◽

Morphological Data ◽

Phylogenetic Position ◽

Dominant Group ◽

Geographic Mosaic ◽

History Of ◽

Rare Opportunity

Premise of study: El Chango is a recently discovered quarry that contains extremely well preserved fossils. The Cenomanian age of the locality corresponds to a time when the global flora was transitioning from gymnosperm- to angiosperm-dominated, yet conifers predominate in this locality. These fossils thus provide a rare opportunity to understand the replacement of conifers by angiosperms as the dominant group of plants. Methods: We collected material from El Chango in annual expeditions (2010 to 2014). We selected the three most abundant and best preserved conifer morphotypes and conducted a total-evidence (i.e., including molecular and morphological data) phylogenetic analysis of a sample of 72 extant conifer species plus the three fossils. We use these results to inform our taxonomic decisions. Results: We obtained four equally most-parsimonious trees (consistency index = 44.1%, retention index = 78.8%). Despite ambiguous relationships among some extant taxa, the three fossil conifers had the same phylogenetic position in all four most parsimonious trees; we describe these species as new: Sequoiadendron helicalancifolium sp. nov. (Cupressaceae), and Microcachrys rhomboidea sp. nov. and Dacrydium bifoliosus sp. nov (Podocarpaceae). The ecosystem is interpreted as a coastal humid mixed forest. Conclusions: Our findings contribute to the understanding of Cenomanian equatorialregions, and support the hypothesis of a geographically and ecologically structured rise of angiosperms, with conifers remaining dominant in brackish-water and angiosperms becoming dominant in freshwater-ecosystems. These fossils fill in gaps in the evolutionary history of lineages like Microcachrys, which we demonstrate occurred in the Northern hemisphere before becoming restricted to its current range (Tasmania).

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Systematics and biogeography of the “Metacryphaeus group” Calmoniidae (Trilobita, Devonian), with comments on adaptive radiations and the geological history of the Malvinokaffric Realm

Journal of Paleontology ◽

10.1017/s0022336000024902 ◽

1993 ◽

Vol 67 (4) ◽

pp. 549-570 ◽

Cited By ~ 27

Author(s):

Bruce S. Lieberman

Keyword(s):

New Species ◽

South African ◽

Evolutionary History ◽

Geological History ◽

Parsimony Analysis ◽

Evolutionary Patterns ◽

The Family ◽

History Of ◽

Adaptive Radiations ◽

Rapid Diversification

Phylogenetic parsimony analysis was used to classify the Siegenian–Eifelian “Metacryphaeus group” of the family Calmoniidae. Thirty-eight exoskeletal characters for 16 taxa produced a shortest-length cladogram with a consistency index of 0.49. A classification based on retrieving the structure of this cladogram recognizes nine genera: Typhloniscus Salter, Plesioconvexa n. gen., Punillaspis Baldis and Longobucco, Eldredgeia n. gen., Clarkeaspis n. gen., Malvinocooperella n. gen., Wolfartaspis Cooper, Plesiomalvinella Lieberman, Edgecombe, and Eldredge (used to represent the malvinellid clade), and Metacryphaeus Reed. The malvinellid clade is most closely related to a revised monophyletic Metacryphaeus. Typhloniscus is the basal member of the “Metacryphaeus group,” and the monotypic Wolfartaspis is sister to the clade containing the malvinellids and Metacryphaeus. Six new species are diagnosed: Punillaspis n. sp. A, “Clarkeaspis” gouldi, Clarkeaspis padillaensis, Malvinocooperella pregiganteus, Metacryphaeus curvigena, and Metacryphaeus branisai. Primitively, this group has South African and Andean affinities, and its evolutionary history suggests rapid diversification. In addition, evolutionary patterns in this group, and the distribution of character reversals, call into question certain notions about the nature of adaptive radiations. The distributions of taxa may answer questions about the number of marine transgressive/regressive cycles in the Emsian–Eifelian of the Malvinokaffric Realm.

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Adaptive convergent evolution of genome proofreading in SARS-CoV2: insights into the Eigen’s paradox

10.1101/2021.09.11.459886 ◽

2021 ◽

Author(s):

Keerthic Aswin ◽

Srinivasan Ramachandran ◽

Vivek T Natarajan

Keyword(s):

Convergent Evolution ◽

Genome Stability ◽

Evolutionary History ◽

Rna Binding ◽

Phylogenetic Analyses ◽

Comparative Genome Analysis ◽

The Family ◽

History Of ◽

Key Residues

AbstractEvolutionary history of coronaviruses holds the key to understand mutational behavior and prepare for possible future outbreaks. By performing comparative genome analysis of nidovirales that contain the family of coronaviruses, we traced the origin of proofreading, surprisingly to the eukaryotic antiviral component ZNFX1. This common recent ancestor contributes two zinc finger (ZnF) motifs that are unique to viral exonuclease, segregating them from DNA proof-readers. Phylogenetic analyses indicate that following acquisition, genomes of coronaviruses retained and further fine-tuned proofreading exonuclease, whereas related families harbor substitution of key residues in ZnF1 motif concomitant to a reduction in their genome sizes. Structural modelling followed by simulation suggests the role of ZnF in RNA binding. Key ZnF residues strongly coevolve with replicase, and the helicase involved in duplex RNA unwinding. Hence, fidelity of replication in coronaviruses is a result of convergent evolution, that enables maintenance of genome stability akin to cellular proofreading systems.

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Phylogenetic position and taxonomy of Cycloseris explanulata and C. wellsi (Scleractinia: Fungiidae): lost mushroom corals find their way home

Contributions to Zoology ◽

10.1163/18759866-08103001 ◽

2012 ◽

Vol 81 (3) ◽

pp. 125-146 ◽

Cited By ~ 57

Author(s):

Francesca Benzoni ◽

Roberto Arrigoni ◽

Fabrizio Stefani ◽

Bastian T. Reijnen ◽

Simone Montano ◽

...

Keyword(s):

Molecular Study ◽

Molecular Data ◽

Phylogenetic Position ◽

Distribution Data ◽

Data Sets ◽

Free Living ◽

New Findings ◽

The Family ◽

Ecological Implications ◽

History Of

The scleractinian species Psammocora explanulata and Coscinaraea wellsi were originally classified in the family Siderastreidae, but in a recent morpho-molecular study it appeared that they are more closely related to each other and to the Fungiidae than to any siderastreid taxon. A subsequent morpho-molecular study of the Fungiidae provided new insights regarding the phylogenetic relationships within that family. In the present study existing molecular data sets of both families were analyzed jointly with those of new specimens and sequences of P. explanulata and C. wellsi. The results indicate that both species actually belong to the Cycloseris clade within the family Fungiidae. A reappraisal of their morphologic characters based on museum specimens and recently collected material substantiate the molecular results. Consequently, they are renamed Cycloseris explanulata and C. wellsi. They are polystomatous and encrusting like C. mokai, another species recently added to the genus, whereas all Cycloseris species were initially thought to be monostomatous and free-living. In the light of the new findings, the taxonomy and distribution data of C. explanulata and C. wellsi have been updated and revised. Finally, the ecological implications of the evolutionary history of the three encrusting polystomatous Cycloseris species and their free-living monostomatous congeners are discussed.

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Origin of raptorial feeding in juvenile euarthropods revealed by a Cambrian radiodontan

National Science Review ◽

10.1093/nsr/nwy057 ◽

2018 ◽

Vol 5 (6) ◽

pp. 863-869 ◽

Cited By ~ 12

Author(s):

Jianni Liu ◽

Rudy Lerosey-Aubril ◽

Michael Steiner ◽

Jason A Dunlop ◽

Degan Shu ◽

...

Keyword(s):

Evolutionary History ◽

Feeding Habits ◽

Phylogenetic Position ◽

Early Developmental Stage ◽

Rapid Rise ◽

Juvenile Instar ◽

History Of ◽

Dietary Ecology ◽

Chengjiang Biota ◽

Early Developmental

Abstract The rapid rise of arthropods during the Cambrian quickly established some clades, such as the euarthropod stem-group called Radiodonta, as the dominant and most diverse predators in marine ecosystems. Recent discoveries have shown that the size and dietary ecology of radiodontans are far more diverse than previously thought, but little is known about the feeding habits of juveniles. Here, we document a very small (∼18-mm-long), near-complete specimen of the radiodontan Lyrarapax unguispinus from the early Cambrian Chengjiang Biota of China. This specimen is the smallest radiodontan individual known, representing a juvenile instar. Its adult-like morphology—especially the fully developed spinose frontal appendages and tetraradial oral cone—indicates that L. unguispinus was a well-equipped predator at an early developmental stage, similar to modern raptorial euarthropods, such as mantises, mantis shrimps and arachnids. This evidence, coupled with the basal phylogenetic position of radiodontans, confirms that raptorial feeding habits in juvenile euarthropods appeared early in the evolutionary history of the group.

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Human Evolution

Notes for a Short Course: Studies in Geology ◽

10.1017/s0271164800000968 ◽

1984 ◽

Vol 8 ◽

pp. 182-198

Author(s):

Catherine Badgley

Keyword(s):

Human Evolution ◽

Evolutionary History ◽

Pan Paniscus ◽

Homo Sapiens ◽

Great Apes ◽

Sister Group ◽

The Family ◽

History Of ◽

Living Species ◽

Single Living

The evolutionary history of humans is well understood in outline, compared to that of many other groups of mammals. But human evolution remains enigmatic in its details, and these are compelling both scientifically and personally because they relate to the biological uniqueness of humans. Humans are placed in the primate family Hominidae, which, in traditional classifications, contains a single living species, Homo sapiens. The closest living relatives of humans are great apes: the chimpanzees Pan paniscus and Pan troglodytes, the gorilla Gorilla gorilla, and the orangutan Pongo pygmaeus. These apes have traditionally been placed in the family Pongidae as the sister group of Hominidae. Living Hominidae and Pongidae, together with Hylobatidae (gibbons) comprise the modern representatives of the primate suborder Hominoidea.

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Monsignor Lord William Joseph Petre (1847–93): A Pillar of Downside

Recusant History ◽

10.1017/s0034193200001795 ◽

1994 ◽

Vol 22 (1) ◽

pp. 88-101

Author(s):

Stewart Foster

Keyword(s):

Liberal Education ◽

Focal Point ◽

Periodical Literature ◽

House Of Lords ◽

The Reformation ◽

The Family ◽

History Of ◽

The Church ◽

Shed Light

Ever since the purchase of the Manor of Ingatestone in 1539, the Petre family has played a prominent part not only in the history of the Catholic community in Essex, but in the life of the Church further afield. Sir William Petre, the founder of the Essex line, and two of his descendants have merited the attention of a biographer, while there has also been a substantial periodical literature associated with the family. However, no such detailed study has yet been written on perhaps the most intriguing member of the family, the little-known thirteenth Baron of Writtle, Monsignor Lord William Joseph Petre. The present article seeks to shed light on the early part of the career of this pioneer of Catholic liberal education and the first Catholic priest to take his seat in the House of Lords since the Reformation. The focal point of Petre's earlier years was the monastery and school of St. Gregory's, Downside.

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