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#phylogenetic

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Niklas Hohmann

🚨R package StratPal update🚨
Full integration with the FossilSim package to study effects of #taphonomy and #ecology on #phylogenetic trees with sampled ancestors, and simplified handling of categorical niche models 😁
#stratigraphy
mindthegap-erc.github.io/Strat

mindthegap-erc.github.ioStratigraphic Paleobiology Modeling PipelinesThe fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes, which can be used as a template to set up one's own simulation.
Public
Teresita Porter 🙋🏻‍♀️

Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales

biorxiv.org/content/10.1101/20

bioRxiv · Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order LobulomycetalesFungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens, and endophytes, yet their significance in marine environments is often understudied. Seagrasses, as globally distributed marine flowering plants, have critical ecological functions, but knowledge about their associated fungal communities remains relatively limited. Previous amplicon surveys of the fungal community associated with the seagrass, Zostera marina have revealed an abundance of potentially novel chytrids. In this study, we employed deep metagenomic sequencing to extract metagenome-assembled genomes (MAGs) from these chytrids and other microbial eukaryotes associated with Z. marina leaves. Our efforts resulted in the recovery of five eukaryotic MAGs, including a single fungal MAG in the order Loubulomycetales (65% BUSCO completeness), three MAGs representing diatoms in the family Bacillariaceae (93%, 70% and 31% BUSCO completeness) and a single MAG representing a haptophyte algae in the genus Prymnesium (40% BUSCO completeness). Whole-genome phylogenomic assessment of these MAGs suggests they all largely represent under sequenced, and possibly novel eukaryotic lineages. Of particular interest, the chytrid MAG was placed within the order Lobulomycetales, consistent with the identity of the dominant chytrid from previous Z. marina amplicon survey results. Annotation of this MAG yielded 5,650 gene models of which 77% shared homology to current databases. With-in these gene models, we predicted 121 carbohydrate-active enzymes and 393 secreted proteins (103 cytoplasmic effectors, 30 apoplastic effectors). Exploration of orthologs between the Lobulomycetales MAG and existing Chytridiomycota genomes have revealed a landscape of high-copy gene families related to host recognition and interaction. Further machine learning analyses based on carbohydrate-active enzyme composition predict that this MAG is a symbiont. Overall, these five eukaryotic MAGs represent substantial genomic novelty and valuable community resources, contributing to a deeper understanding of the roles of fungi and other microbial eukaryotes in the larger seagrass ecosystem. ### Competing Interest Statement Jonathan A. Eisen is on the Scientific Advisory Board of Zymo Research, Inc. Jason E. Stajich is a scientific consultant for Michroma, Inc.
#MAGs#phylogenetic#chytrid
Continued thread
Public
grimmiges

That would have been enough for a #phylogenetic #ResearchPaper. But one problem with classic German coauthors is that we don't scratch surfaces.

A new animal was found. A British researcher writes a half-page abstract a month later: The elephant, a new animal from Africa.
One year later, a French writes a 5 pp. long paper, content: The elephant, a new animal from Africa.
Five years later a 500 pp. German book is published: The Elephant. Part 1: Its trunk.

(5/)

Public
Giuseppe Michieli

An #epizootic of highly pathogenic avian #influenza virus #H7N3 in a #Mexican ecological #reserve, Arch Virol.: link.springer.com/article/10.1

#Phylogenetic #analysis revealed that the HPAI H7N3 virus detected in affected birds shared a close genetic relationship with Mexican H7N3 isolates from 2012.

SpringerLinkAn epizootic of highly pathogenic avian influenza virus H7N3 in a Mexican ecological reserve - Archives of VirologyIn this case study, we describe an outbreak of highly pathogenic avian influenza (HPAI) virus subtype H7N3 in an ecological reserve in Chiapas, Mexico, affecting captive and wild birds. The virus was detected mainly in plain chachalacas displaying respiratory and gastrointestinal clinical signs and death within 24 hours. Mortality in white-fronted parrots and a clay-colored thrush was also recorded. We describe control strategies implemented to prevent virus dissemination and active surveillance within the risk area. Phylogenetic analysis revealed that the HPAI H7N3 virus detected in affected birds shared a close genetic relationship with Mexican H7N3 isolates from 2012.
Public
Julien M.
#Pasta #Evolution #Science #Italia #Sardinia
Evolution of the Italian #PastaRipiena: the first steps toward a scientific classification

In this study, #phylogenetic and #biogeographic methods are used to investigate the evolutionary relationships between various types of Italian pasta ripiena (filled pasta) and related representatives from across #Eurasia, using information from their geography, shape, content and cooking methods. Our results showed that, with the exception of the Sardinian #Culurgiones, all the other pasta ripiena from Italy likely had a single origin in the northern parts of the country. Based on the proposed evolutionary hypothesis, the Italian pasta are divided into two main clades: a #ravioli clade mainly characterized by a more or less flat shape, and a #tortellini clade mainly characterized by a three-dimensional shape. The implications of these findings are further discussed.
https://link.springer.com/article/10.1007/s44187-024-00136-1
Phylogeny of pasta ripiena. Pie charts show ancestral distribution probabilities inferred by BioGeoBEARS
Public
Giuseppe Michieli

#Phylogenetic Characterization of Novel #Reassortant 2.3.4.4b #H5N8 Highly Pathogenic Avian #Influenza Viruses Isolated from Domestic #Ducks in #Egypt During the Winter Season 2021–2022

Source: Viruses, AbstractAvian influenza (AI) is an extremely contagious viral disease of domestic and wild birds that can spread rapidly among bird populations, inducing serious economic losses in the poultry industry. During the winter season 2021–2022, we isolated seventeen highly…

etidioh.wordpress.com/2024/10/

ETIDIoH · #Phylogenetic Characterization of Novel #Reassortant 2.3.4.4b #H5N8 Highly Pathogenic Avian #Influenza Viruses Isolated from Domestic #Ducks in #Egypt During the Winter Season 2021–2022Source: Viruses, AbstractAvian influenza (AI) is an extremely contagious viral disease of domestic and wild birds that can spread rapidly among bird populations, inducing serious economic losses in…
Public
Giuseppe Michieli

#Phylogenetic Insights into #H7Nx #Influenza Viruses: Uncovering #Reassortment #Patterns and Geographic Variability

Source: Viruses, AbstractInfluenza A viruses (IAVs), which belong to the Orthomyxoviridae family, are RNA viruses characterized by a segmented genome that allows them to evolve and adapt rapidly. These viruses are mainly transmitted by wild waterfowl. In this study, we investigated the evolutionary processes of H7Nx (H7N1, H7N2, H7N3, H7N4, H7N5, H7N6,…

etidioh.wordpress.com/2024/10/

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Stefan F. Wirth

The largest #cartilaginousfish is the #whaleshark, the largest/heaviest Actinopterygii is the sunfish. Due to the #phylogenetic situation in early #vertebrates, when using the general term "#fish", one should be aware that this is a #paraphyletic group.
© #StefanFWirth Berlin

My article on X
x.com/wirthstef/status/1843663

Photos
#sunfish, Denmark, by Per-Ola Norman, 2009, the © holder published into pub. domain

Whale Shark, by Sh.
ElkCloner, 2012, licensed  Cr. Commons Attr-ShareAlike 3.0 Unp.

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