scholarly journals The PhyloCode applied to Cintractiellales, a new order of smut fungi with unresolved phylogenetic relationships in the Ustilaginomycotina

2020 ◽  
Vol 6 (1) ◽  
pp. 55-64
Author(s):  
A.R. McTaggart ◽  
C.J. Prychid ◽  
J.J. Bruhl ◽  
R.G. Shivas
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
New Order ◽  
Smut Fungi ◽  
Systematic Relationship ◽  
Most Recent Common Ancestor

The PhyloCode is used to classify taxa based on their relation to a most recent common ancestor as recovered from a phylogenetic analysis. We examined the first specimen of Cintractiella (Ustilaginomycotina) collected from Australia and determined its systematic relationship to other Fungi. Three ribosomal DNA loci were analysed both with and without constraint to a phylogenomic hypothesis of the Ustilaginomycotina. Cintractiella did not share a most recent common ancestor with other orders of smut fungi. We used the PhyloCode to define the Cintractiellales, a monogeneric order with four species of Cintractiella, including C. scirpodendri sp. nov. on Scirpodendron ghaeri. The Cintractiellales may have shared a most recent common ancestor with the Malasseziomycetes, but are otherwise unresolved at the rank of class.

scholarly journals RootDigger: a root placement program for phylogenetic trees

2020 ◽  
Author(s):  
Ben Bettisworth ◽  
Alexandros Stamatakis
Keyword(s):  
Phylogenetic Analysis ◽  
Markov Model ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Markov Models ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Root Position ◽  
Confidence Value ◽  
Root Location

AbstractSummaryIn phylogenetic analysis, it is common to infer unrooted trees. Thus, it is unknown which node is the most recent common ancestor of all the taxa in the phylogeny. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as midpoint rooting or rooting the tree at an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position. We present a software called RootDigger which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement.Availability and implementationRootDigger is available under the MIT licence at https://github.com/computations/root_digger

scholarly journals A territory-wide study of early COVID-19 outbreak in Hong Kong community: A clinical, epidemiological and phylogenomic investigation

2020 ◽  
Author(s):  
Kenneth Siu-Sing Leung ◽  
Timothy Ting-Leung Ng ◽  
Alan Ka-Lun Wu ◽  
Miranda Chong-Yee Yau ◽  
Hiu-Yin Lao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hong Kong ◽  
Local Community ◽  
Common Ancestor ◽  
Evolutionary Rate ◽  
Reproduction Number ◽  
Epidemiological Data ◽  
Recent Common Ancestor ◽  
Common Mutation ◽  
Most Recent Common Ancestor

AbstractInitial cases of COVID-19 reported in Hong Kong were mostly imported from China. However, most cases reported in February 2020 were locally-acquired infections, indicating local community transmissions. We extracted the demographic, clinical and epidemiological data from 50 COVID-19 patients, who accounted for 53.8% of the cases in Hong Kong by February 2020. Whole-genome sequencing of the SARS-CoV-2 were conducted to determine the phylogenetic relatedness and transmission dynamics. Only three (6.0%) patients required ICU admission. Phylogenetic analysis identified six transmission clusters. All locally-acquired cases harboured a common mutation Orf3a G251V and were clustered in two subclades in global phylogeny of SARS-CoV-2. The estimated time to the most recent common ancestor of local COVID-2019 outbreak was December 24, 2019 with an evolutionary rate of 3.04×10−3 substitutions per site per year. The reproduction number value was 1.84. Social distancing and vigilant epidemiological control are crucial to the containment of COVID-19 transmission.Article summary linesA combined epidemiological and phylogenetic analysis of early COVID-19 outbreak in Hong Kong revealed that a SARS-CoV-2 variant with ORF3a G251V mutation accounted for all locally acquired cases, and that asymptomatic carriers could be a huge public health risk for COVID-19 control.

Arnebolagus, the oldest eulagomorph, and phylogenetic relationships within the Eocene Eulagomorpha new clade (Mammalia, Duplicidentata)

2020 ◽  
pp. 1-12
Author(s):  
Alexey V. Lopatin ◽  
Alexander O. Averianov
Keyword(s):  
Phylogenetic Relationships ◽  
Common Ancestor ◽  
Morphological Characters ◽  
Recent Common Ancestor ◽  
Early Eocene ◽  
Modern Aspect ◽  
Most Recent Common Ancestor ◽  
Single Tooth ◽  
Land Mammal ◽  
First Time

Abstract Arnebolagus leporinus Lopatin and Averianov, 2008, known previously from a single tooth (P3) from the early Eocene Bumban Member of Naran Bulak Formation at Tsagan-Khushu locality in Mongolia, is redescribed based on additional specimens from the type locality. Phylogenetic relationships of Eocene stem lagomorphs from Asia and North America are reconstructed for the first time based on a parsimony analysis of 54 morphological characters and 32 taxa. Two new node-based clades are proposed, stemming from the most-recent common ancestor of Lepus Linnaeus, 1758 and Dawsonolagus Li, Meng, and Wang, 2007 (Eulagomorpha new clade, ‘lagomorphs of the modern aspect’) and from the most-recent common ancestor of Lepus and Gobiolagus Burke, 1941 (Epilagomorpha new clade). Arnebolagus Lopatin and Averianov, 2008 is geologically oldest and the most plesiomorphic eulagomorph, similar to Dawsonolagus from the early Eocene Arshanto Formation of China in its weakly pronounced, unilateral hypsodonty of the upper cheek teeth and its brachyodont lower cheek teeth with separate roots. Arnebolagus is more plesiomorphic than Dawsonolagus in having two roots of P4. Arnebolagus is the oldest known eulagomorph, the only taxon known from the earliest Eocene Bumbanian Asiatic Land Mammal Age (ALMA). The other Asiatic early Eocene eulagomorphs (Dawsonolagus, Aktashmys Averianov, 1994, and Romanolagus Shevyreva, 1995) come from the Arshantan ALMA.

scholarly journals An ancient clade of Penelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genomes

2021 ◽  
Author(s):  
Rory J. Craig ◽  
Irina A. Yushenova ◽  
Fernando Rodriguez ◽  
Irina R. Arkhipova
Keyword(s):  
Ribosomal Dna ◽  
Structural Organization ◽  
Common Ancestor ◽  
Hammerhead Ribozyme ◽  
Recent Common Ancestor ◽  
Ltr Retrotransposons ◽  
Phylogenetic Distribution ◽  
Reverse Transcriptases ◽  
Most Recent Common Ancestor ◽  
Green Lineage

ABSTRACTPenelope-like elements (PLEs) are an enigmatic clade of retroelements whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical EN+ PLEs encodes RT and a C-terminal GIY-YIG endonuclease (EN) that enables intrachromosomal integration, while EN–PLEs lack endonuclease and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, while EN–PLEs occur in several kingdoms. Here we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY-YIG endonuclease is linked to a C-terminal RT by a short domain with a characteristic Zn-finger-like motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune and Nematis clades, and show insertion bias for microsatellites, but lack hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiad clade is found in numerous invertebrate phyla, where they can reach tens of thousands of copies per genome. Naiads in spiders and clams independently evolved to encode selenoproteins. Chlamys, which lack the CCHH motif universal to PLE endonucleases, occur in green algae, spike mosses (targeting ribosomal DNA) and the slime mold Physarum. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain, strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, distribution and abundance is comparable to non-LTR and LTR-retrotransposons.

scholarly journals Affinities and class-level systematics of the phylum Cnidaria

1992 ◽  
Vol 6 ◽  
pp. 297-297
Author(s):  
Heyo Van Iten
Keyword(s):  
Phylogenetic Relationships ◽  
Common Ancestor ◽  
Prey Capture ◽  
Soft Part ◽  
Sister Group ◽  
Monophyletic Group ◽  
Recent Common Ancestor ◽  
Single Pair ◽  
Most Recent Common Ancestor ◽  
Alternative Hypotheses

Phylogenetic relationships among the cnidarian classes Anthozoa, Hydrozoa and Scyphozoa, and between Cnidaria and other metazoan phyla, continue to be subject to widely divergent interpretations. Also controversial are the affinities of numerous fossil groups, including Byronia Bischoff, Sphenothallus Hall and conulariids, that have been interpreted as extinct cnidarians. Currently favored interpretations of evolution within Cnidaria are generally consistent with one of two alternative hypotheses of phylogenetic relationships: scyphozoans and anthozoans are members of a monophylclic group that excludes hydrozoans; or scyphozoans and hydrozoans are members of a monophyletic group that excludes anthozoans. Putative anthozoan-scyphozoan synapomorphies include (1) gastric septa present; (2) cnidae present in both ectoderm and gastroderm; (3) sex cells gastrodermal; and (4) mesoglea contains amoeboid cells. Putative hydrozoan-scyphozoan synapomorphies include (1) medusa present; (2) tetraradial symmetry; (3) rhopaloid nematocysts; and (4) similarities in sperm structure.Evaluation of alternative hypotheses of relationships within Cnidaria is complicated by uncertainty surrounding relationships between this and other metazoan phyla. While some investigators have interpreted Cnidaria and Ctenophora as members of a monophyletic group that excludes other phyla, others have argued that ctenophorans are more closely related to platyhelminths than they are to cnidarians. Putative cnidarian-ctenophoran synapomorphies include (1) production of cells modified for prey capture; and (2) presence of a medusa. Putative ctenophoran-platyhelminth synapomorphies include (1) presence of gonoducts; (2) ciliated cells with several to many cilia; (3) determinate cleavage; and (4) muscle cells developed from mesoderm. Comparisons of these and other phyla indicate that the strongest hypotheses of synapomorphy are those between cnidarians and ctenophorans. Ctenophorans do not have a mesoderm, and they lack complex reproductive structures that can be homologized with platyhelminth gonoducts. Similarities between ctenophorans and platyhelminths in ciliation and cleavage type are either non-homologous or shared primitive. The most recent common ancestor of ctenophorans and cnidarians was probably a medusa-like animal with circular and meridional muscle fibers and a non-septate digestive cavity having four radial canals. This cavity probably lacked cells specialized for prey capture, but glutinant prey-capture structures may have been present on tentacles. Sperm produced by this common ancestor were most similar to sperm of extant ctenophorans, hydrozoans and scyphozoans. Anatomical features unique to ctenophorans or cnidarians, regarded by some investigators as evidence against a close relationship between these two groups, are autapomorphies. These interpretations imply that putative hydrozoan-scyphozoan synapomorphies are actually shared primitive, and that the presence of gastric septa and cnidae-bearing gastric filaments in scyphozoans and anthozoans is shared derived. This would mean that the most parsimonious hypothesis of phylogenetic relationships within Cnidaria is that anthozoans and scyphozoans are members of a monophyletic group that excludes hydrozoans.Debate over relationships among these extant taxa has heightened interest in the affinities of prominent groups of problematic fossil cnidarians. Byronia Bischoff, Sphenothallus Hall and conulariids, all characterized by an apatitic, multilamellar theca, show detailed anatomical similarities to hydrozoans and/or scyphozoans. Putative synapomorphies linking Byronia and coronatid scyphozoans include the presence of multiple whorls of thorn-like nodes projecting into the thecal cavity, with each whorl consisting of eight nodes arranged in two sets of four nodes each. Sphenothallus, characterized by a pair of tentacles and, in some species, multiple branching, is most similar to hydrozoan and scyphozoan polyps, many of which are colonial or exhibit a single pair of tentacles early in their development. Similarities in hard- and soft-part anatomy between scyphozoans and conulariids suggest that conulariids, like scyphozoans, possessed four gastric septa and produced medusae through polydisc strobilation. Although conulariids have been interpreted as ancestral to extant cnidarians, they are more likely either a sister group to Scyphozoa or members of this class.

scholarly journals Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants

Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 1187-1198 ◽  
Author(s):  
Mikkel H Schierup ◽  
Xavier Vekemans ◽  
Freddy B Christiansen
Keyword(s):  
Dominance Hierarchy ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Self Incompatibility ◽  
Most Recent Common Ancestor ◽  
Dominance Interactions ◽  
Turnover Process ◽  
Neutral Gene ◽  
Interspecific Comparisons ◽  
Coalescence Times

Abstract Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

scholarly journals Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018

2021 ◽  
Author(s):  
Wenjun Cheng ◽  
Tianjiao Ji ◽  
Shuaifeng Zhou ◽  
Yong Shi ◽  
Lili Jiang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Mainland China ◽  
Recent Common Ancestor ◽  
Genetic Characteristics ◽  
Most Recent Common Ancestor ◽  
Significant Difference ◽  
Echovirus 6 ◽  
Epidemiological Characteristics ◽  
Highest Posterior Density ◽  
Genotype F

AbstractEchovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.

scholarly journals The Ancestry of a Sample of Sequences Subject to Recombination

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1217-1228 ◽  
Author(s):  
Carsten Wiuf ◽  
Jotun Hein
Keyword(s):  
Genetic Distance ◽  
Population Size ◽  
Upper Bound ◽  
Recombination Rate ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Sequence Length ◽  
Most Recent Common Ancestor ◽  
The Mean ◽  
Mean Time

Abstract In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.

The evolutionary history and conservation value of disjunct Bartonia paniculata subsp. paniculata (Branched Bartonia) populations in Canada

Botany ◽  
2013 ◽  
Vol 91 (9) ◽  
pp. 605-613 ◽  
Author(s):  
Claudia Ciotir ◽  
Chris Yesson ◽  
Joanna Freeland
Keyword(s):  
Great Lakes ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Great Lakes Region ◽  
Conservation Value ◽  
Most Recent Common Ancestor ◽  
Disjunct Populations ◽  
Management Plans ◽  
Global Status

Understanding the spatial distribution of genetic diversity and its evolutionary history is an essential part of developing effective biodiversity management plans. This may be particularly true when considering the value of peripheral or disjunct populations. Although conservation decisions are often made with reference to geopolitical boundaries, many policy-makers also consider global distributions, and therefore a species’ global status may temper its regional status. Many disjunct populations can be found in the Great Lakes region of North America, including those of Bartonia paniculata subsp. paniculata, a species that has been designated as threatened in Canada but globally secure. We compared chloroplast sequences between disjunct (Canada) and core (USA) populations of B. paniculata subsp. paniculata separated by 600 km, which is the minimum distance between disjunct and core populations in this subspecies. We found that although lineages within the disjunct populations shared a relatively recent common ancestor, the genetic divergence between plants from Ontario and New Jersey was substantially greater than expected for a consubspecific comparison. A coalescence-based analysis dated the most recent common ancestor of the Canadian and US populations at approximately 534 000 years ago with the lower confidence estimate at 226 000 years ago. This substantially predates the Last Glacial Maximum and suggests that disjunct and core populations have followed independent evolutionary trajectories throughout multiple glacial–interglacial cycles. Our findings provide important insight into the diverse processes that have resulted in numerous disjunct species in the Great Lakes region and highlight a need for additional work on Canadian B. paniculata subsp. paniculata taxonomy prior to a reevaluation of its conservation value.

Whole-genome analysis-based phylogeographic investigation of Streptococcus pneumoniae serotype 19A sequence type 320 isolates in Japan.

2021 ◽  
Author(s):  
Satoshi Nakano ◽  
Takao Fujisawa ◽  
Bin Chang ◽  
Yutaka Ito ◽  
Hideki Akeda ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Sampling Bias ◽  
Health Concern ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Identification Rate ◽  
Most Recent Common Ancestor ◽  
The Common ◽  
The U.S

After the introduction of the seven-valent pneumococcal conjugate vaccine, the global spread of multidrug resistant serotype 19A-ST320 strains became a public health concern. In Japan, the main genotype of serotype 19A was ST3111, and the identification rate of ST320 was low. Although the isolates were sporadically detected in both adults and children, their origin remains unknown. Thus, by combining pneumococcal isolates collected in three nationwide pneumococcal surveillance studies conducted in Japan between 2008 and 2020, we analyzed 56 serotype 19A-ST320 isolates along with 931 global isolates, using whole-genome sequencing to uncover the transmission route of the globally distributed clone in Japan. The clone was frequently detected in Okinawa Prefecture, where the U.S. returned to Japan in 1972. Phylogenetic analysis demonstrated that the isolates from Japan were genetically related to those from the U.S.; therefore, the common ancestor may have originated in the U.S. In addition, Bayesian analysis suggested that the time to the most recent common ancestor of the isolates form Japan and the U.S. was approximately the 1990s to 2000, suggesting the possibility that the common ancestor could have already spread in the U.S. before the Taiwan 19F-14 isolate was first identified in a Taiwanese hospital in 1997. The phylogeographical analysis supported the transmission of the clone from the U.S. to Japan, but the analysis could be influenced by sampling bias. These results suggested the possibility that the serotype 19A-ST320 clone had already spread in the U.S. before being imported into Japan.

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