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#phylogenetics

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naturepoker<p>Does anyone know of a good tanglegram/cophylogram generator in Python? The only option I see is pretty minimal - not really up to par against the R version in features or visual quality. </p><p><a href="https://genomic.social/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a> <a href="https://genomic.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>dataviz</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
American Naturalist<p>Januario et al. found no correlation between sexual selection intensity &amp; speciation rates or proxy traits. Because sexual selection intensity has high intraspecific variation and low phylogenetic signal, its macroevolutionary impacts are weak. Read now!<br><a href="https://www.journals.uchicago.edu/doi/10.1086/734457" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">journals.uchicago.edu/doi/10.1</span><span class="invisible">086/734457</span></a> </p><p><a href="https://ecoevo.social/tags/sexualSelection" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>sexualSelection</span></a> <a href="https://ecoevo.social/tags/speciation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>speciation</span></a> <a href="https://ecoevo.social/tags/intraspecificVariation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>intraspecificVariation</span></a> <a href="https://ecoevo.social/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a> <a href="https://ecoevo.social/tags/macroevolution" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>macroevolution</span></a></p>
0xC0DEC0DE07E9<p>Wait, ants started farming when the dinosaurs were still around?!<br><a href="https://www.science.org/content/article/asteroid-impact-may-have-turned-ants-fungus-farmers-66-million-years-ago" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">science.org/content/article/as</span><span class="invisible">teroid-impact-may-have-turned-ants-fungus-farmers-66-million-years-ago</span></a><br><a href="https://hachyderm.io/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>science</span></a> <a href="https://hachyderm.io/tags/ants" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ants</span></a> <a href="https://hachyderm.io/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a></p>
Giuseppe Michieli<p>Analyses of <a href="https://mstdn.science/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a>, natural <a href="https://mstdn.science/tags/selection" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>selection</span></a>, and <a href="https://mstdn.science/tags/protein" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>protein</span></a> structure of clade 2.3.4.4b <a href="https://mstdn.science/tags/H5N1" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>H5N1</span></a> <a href="https://mstdn.science/tags/Influenza" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Influenza</span></a> A reveal that recent viral lineages have evolved promiscuity ..., <a href="https://etidiohnew.blogspot.com/2025/03/analyses-of-phylogenetics-natural.html" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">etidiohnew.blogspot.com/2025/0</span><span class="invisible">3/analyses-of-phylogenetics-natural.html</span></a></p>
naturepoker<p>A question while writing up a study proposal:</p><p>What are characters of a good prokaryotic gene alignment?</p><p>The way I learned it from no-one is a good alignment gives well-scoring inferred tree later, but that feels a bit iffy and takes too long to confirm. Any great articles/insights on this would be appreciated!</p><p><a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a> <a href="https://genomic.social/tags/microbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>microbiology</span></a> <a href="https://genomic.social/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a></p>
nf-core<p>Pipeline release! nf-core/phyloplace v2.0.0 - Phylosearch release!</p><p>Please see the changelog: <a href="https://github.com/nf-core/phyloplace/releases/tag/2.0.0" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/nf-core/phyloplace/</span><span class="invisible">releases/tag/2.0.0</span></a></p><p><a href="https://mstdn.science/tags/evolution" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>evolution</span></a> <a href="https://mstdn.science/tags/evolutionarytree" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>evolutionarytree</span></a> <a href="https://mstdn.science/tags/phylogeneticplacement" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogeneticplacement</span></a> <a href="https://mstdn.science/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a> <a href="https://mstdn.science/tags/sequenceclassification" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>sequenceclassification</span></a> <a href="https://mstdn.science/tags/taxonomyassignment" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>taxonomyassignment</span></a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nfcore</span></a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nextflow</span></a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
grimmiges<p>With the limited resources, Cecilia Banag and Sigrid Liede-Schumann, put together a nice set of classic gene markers from two of a flowering plant's genomes: rDNA spacer data from the biparentally inherited nucleome, and prospective intergenic spacer data from the (mostly) maternally inherited plastome. Which are here in a relative good fit, for a plant (plants never heard of Hennig, Platnick or Farris)<br><a href="https://ecoevo.social/tags/Phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Phylogenetics</span></a> <a href="https://ecoevo.social/tags/Tanglegrams" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Tanglegrams</span></a> <br>(2/)</p>
SIB Swiss Bioinformatics<p>PhyloSIB, our annual workshop about molecular evolution, phylogenetics, and comparative phylogenomics took place Wednesday in Lausanne as a satellite event preceding Biology25.</p><p>15 SIB Groups gave presentations on recent developments in the field. We had a full house with 80 participants. A lively and fruitful open discussion forum concluded the workshop.</p><p><span class="h-card" translate="no"><a href="https://mstdn.science/@richardneher" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>richardneher</span></a></span>, <span class="h-card" translate="no"><a href="https://ecoevo.social/@marcrr" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>marcrr</span></a></span>, <span class="h-card" translate="no"><a href="https://mstdn.science/@dessimoz" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>dessimoz</span></a></span>, <span class="h-card" translate="no"><a href="https://mstdn.science/@mariedangles" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>mariedangles</span></a></span>, <span class="h-card" translate="no"><a href="https://ecoevo.social/@rmwaterhouse" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>rmwaterhouse</span></a></span> </p><p><a href="https://mstdn.science/tags/PhyloSIB" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PhyloSIB</span></a> <a href="https://mstdn.science/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a> <a href="https://mstdn.science/tags/Phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Phylogenetics</span></a> <a href="https://mstdn.science/tags/Phylogenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Phylogenomics</span></a> <a href="https://mstdn.science/tags/Biology25" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Biology25</span></a></p>
Annals of Botany<p>🔬📚The study provides a clearer evolutionary framework for Kalanchoe, but more work is needed to refine its classification. (8/8)</p><p>👉 <a href="https://doi.org/n5ck" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/n5ck</span><span class="invisible"></span></a></p><p><a href="https://botany.social/tags/AoBpapers" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>AoBpapers</span></a> <a href="https://botany.social/tags/Botany" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Botany</span></a> <a href="https://botany.social/tags/Phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Phylogenetics</span></a> <a href="https://botany.social/tags/Kalanchoe" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Kalanchoe</span></a></p>
grimmiges<p><span class="h-card" translate="no"><a href="https://mastodon.social/@planetaryecologist" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>planetaryecologist</span></a></span> <br>For everyone willing to go down the rabbit hole of concepts for non-trivial <a href="https://ecoevo.social/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a>; here's the links for the pics (and more)</p><p>Who published the first phylogenetic tree? <br><a href="https://phylonetworks.blogspot.com/2012/08/who-published-first-phylogenetic-tree.html" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">phylonetworks.blogspot.com/201</span><span class="invisible">2/08/who-published-first-phylogenetic-tree.html</span></a></p><p>The dilemma of evolutionary networks and Darwinian trees<br><a href="https://phylonetworks.blogspot.com/2014/01/the-dilemma-of-evolutionary-networks.html" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">phylonetworks.blogspot.com/201</span><span class="invisible">4/01/the-dilemma-of-evolutionary-networks.html</span></a></p><p>Clades, cladograms, cladistics, and why networks are inevitable<br><a href="https://phylonetworks.blogspot.com/2017/10/clades-cladograms-cladistics-and-why.html" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">phylonetworks.blogspot.com/201</span><span class="invisible">7/10/clades-cladograms-cladistics-and-why.html</span></a></p>
juli g pausas<p>Let's see the magic of <span class="h-card" translate="no"><a href="https://mastodon.social/@Mastodon" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>Mastodon</span></a></span> </p><p>Is there a way to plot a dated phylogeny with a log-scale time axis? If possible, using R </p><p><a href="https://fediscience.org/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a> <a href="https://fediscience.org/tags/phylo" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylo</span></a> <a href="https://fediscience.org/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rstats</span></a> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/rstats" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>rstats</span></a></span> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/ecology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>ecology</span></a></span> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/plants" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>plants</span></a></span> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/botany" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>botany</span></a></span> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/plantscience" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>plantscience</span></a></span> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/nature" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>nature</span></a></span> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/biodiversity" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>biodiversity</span></a></span> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/evolution" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>evolution</span></a></span></p>
Planetary Ecologist<p>Sister group (Evolutionary biology 🧬)</p><p>In phylogenetics, a sister group or sister taxon, also called an adelphotaxon, comprises the closest relative of another given unit in an evolutionary tree.</p><p><a href="https://en.wikipedia.org/wiki/Sister_group" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">en.wikipedia.org/wiki/Sister_g</span><span class="invisible">roup</span></a></p><p><a href="https://mastodon.social/tags/SisterGroup" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SisterGroup</span></a> <a href="https://mastodon.social/tags/Taxa" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Taxa</span></a> <a href="https://mastodon.social/tags/Phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Phylogenetics</span></a> <a href="https://mastodon.social/tags/EvolutionaryBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>EvolutionaryBiology</span></a> <a href="https://mastodon.social/tags/BiologicalClassification" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>BiologicalClassification</span></a></p>
CellBioNews<p><a href="https://scientificnetwork.de/tags/Computational" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Computational</span></a> tool streamlines <a href="https://scientificnetwork.de/tags/genetic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>genetic</span></a> analysis for <a href="https://scientificnetwork.de/tags/evolutionary" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>evolutionary</span></a> biologists </p><p><a href="https://scientificnetwork.de/tags/PsiPartition" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PsiPartition</span></a> <a href="https://scientificnetwork.de/tags/genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>genomics</span></a> <a href="https://scientificnetwork.de/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a> <a href="https://scientificnetwork.de/tags/Bayesian" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bayesian</span></a> </p><p> <a href="https://phys.org/news/2025-01-tool-genetic-analysis-evolutionary-biologists.html" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">phys.org/news/2025-01-tool-gen</span><span class="invisible">etic-analysis-evolutionary-biologists.html</span></a></p>
The Inquisitive Biologist<p>New review: How is the living world organized and classified? Encyclopaedic in scope yet compelling to read, the deeply researched Kingdoms, Empires, &amp; Domains is an 851-page behemoth that surveys 26 centuries of our changing understanding. </p><p><a href="https://inquisitivebiologist.com/2025/01/17/book-review-kingdoms-empires-domains-the-history-of-high-level-biological-classification/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">inquisitivebiologist.com/2025/</span><span class="invisible">01/17/book-review-kingdoms-empires-domains-the-history-of-high-level-biological-classification/</span></a></p><p><a href="https://scicomm.xyz/tags/Books" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Books</span></a> <a href="https://scicomm.xyz/tags/BookReview" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>BookReview</span></a> <a href="https://scicomm.xyz/tags/Bookstodon" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bookstodon</span></a> <a href="https://scicomm.xyz/tags/Scicomm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Scicomm</span></a> <a href="https://scicomm.xyz/tags/Classification" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Classification</span></a> <a href="https://scicomm.xyz/tags/Genetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Genetics</span></a> <a href="https://scicomm.xyz/tags/HistoryOfScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HistoryOfScience</span></a> <a href="https://scicomm.xyz/tags/ScienceHistory" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ScienceHistory</span></a> <a href="https://scicomm.xyz/tags/HistSci" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HistSci</span></a> <a href="https://scicomm.xyz/tags/Microbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Microbiology</span></a> <a href="https://scicomm.xyz/tags/Phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Phylogenetics</span></a> <a href="https://scicomm.xyz/tags/ScalaNaturae" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ScalaNaturae</span></a> <a href="https://scicomm.xyz/tags/Taxonomy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Taxonomy</span></a> <a href="https://scicomm.xyz/tags/Zoophyta" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Zoophyta</span></a> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/bookstodon" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>bookstodon</span></a></span></p>
Annals of Botany<p>🌐 Understanding the evolution of orchids is essential for uncovering the secrets behind their incredible diversification and ecological success across the globe. (8/8)<br>👉 <a href="https://doi.org/nzqf" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/nzqf</span><span class="invisible"></span></a></p><p><a href="https://botany.social/tags/OrchidEvolution" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OrchidEvolution</span></a> <a href="https://botany.social/tags/PlantScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PlantScience</span></a> <a href="https://botany.social/tags/Botany" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Botany</span></a> <a href="https://botany.social/tags/Orchids" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Orchids</span></a> <a href="https://botany.social/tags/Phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Phylogenetics</span></a> <a href="https://botany.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Genomics</span></a> <a href="https://botany.social/tags/Ecology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Ecology</span></a> <a href="https://botany.social/tags/PlantDiversification" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PlantDiversification</span></a></p>
grimmiges<p>Our new <a href="https://ecoevo.social/tags/preprint" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>preprint</span></a> is out<br>Cardoni et al. Pruning the tree: Comparing OTUs and ASVs for processing HTS 5S-IGS data<br><a href="https://doi.org/10.22541/au.173437938.80481043/v1" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.22541/au.173437938.</span><span class="invisible">80481043/v1</span></a></p><p>Organising 100k of reads per studied sample (5S <a href="https://ecoevo.social/tags/rDNA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rDNA</span></a> intergenic spacers) into a handier amount of tips (~100) for <a href="https://ecoevo.social/tags/phylogenetic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetic</span></a> inferences and assessing <a href="https://ecoevo.social/tags/biodiversity" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>biodiversity</span></a> </p><p><a href="https://ecoevo.social/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a> <a href="https://ecoevo.social/tags/taxonomy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>taxonomy</span></a> <a href="https://ecoevo.social/tags/genetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>genetics</span></a> <a href="https://ecoevo.social/tags/NGS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>NGS</span></a></p>
grimmiges<p>Our new dataset is out, paper coming soon (hopefully 😅)</p><p>Pruning the tree: Comparing OTUs and ASVs for processing HTS 5S-IGS data<br><a href="https://doi.org/10.6084/m9.figshare.28000349" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.6084/m9.figshare.28</span><span class="invisible">000349</span></a></p><p>Testing two pipelines for bulk DNA sorting: MOTHUR, we used so far to sort our plethora of spacer variants<br>(Piredda et al. 2021 <a href="http://dx.doi.org/10.1111/1755-0998.13264" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">http://</span><span class="ellipsis">dx.doi.org/10.1111/1755-0998.1</span><span class="invisible">3264</span></a> |Cardoni et al. 2022 <a href="http://dx.doi.org/10.1111/tpj.15601" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">http://</span><span class="">dx.doi.org/10.1111/tpj.15601</span><span class="invisible"></span></a> | Denk et al. 2024 <a href="http://dx.doi.org/10.3372/wi.54.54301" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">http://</span><span class="">dx.doi.org/10.3372/wi.54.54301</span><span class="invisible"></span></a>) vs. DADA2</p><p>Spoiler and summary: less tips, more fun</p><p><a href="https://ecoevo.social/tags/beech" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>beech</span></a> <a href="https://ecoevo.social/tags/nrDNA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nrDNA</span></a> <a href="https://ecoevo.social/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a></p>
J of Systematics and Evolution<p>In this study of the <a href="https://mstdn.science/tags/biogeographic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>biogeographic</span></a> history and distribution of the <a href="https://mstdn.science/tags/ginseng" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ginseng</span></a> genus, Zheng et al. find that <a href="https://mstdn.science/tags/Panax" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Panax</span></a> originated outside the <a href="https://mstdn.science/tags/Himalayan" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Himalayan</span></a>-Hengduan Mountains but diversified there after colonization.<br><a href="https://doi.org/10.1111/jse.13138" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/10.1111/jse.13138</span><span class="invisible"></span></a> <br>@WileyEcolEvol<br> <a href="https://mstdn.science/tags/evolution" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>evolution</span></a> <a href="https://mstdn.science/tags/JSE" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>JSE</span></a> <a href="https://mstdn.science/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a> <a href="https://mstdn.science/tags/botany" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>botany</span></a></p>
EverydayHuman(I0)<p><span class="h-card" translate="no"><a href="https://ecoevo.social/@EVDHmn" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>EVDHmn</span></a></span> <span class="h-card" translate="no"><a href="https://a.gup.pe/u/academicchatter" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>academicchatter</span></a></span> <br><span class="h-card" translate="no"><a href="https://mander.xyz/c/academia" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>academia</span></a></span> <br><a href="https://infosec.exchange/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a></p>
Chase W. Nelson 倪誠志<p>“There's a maximum likelihood that I'm doing phylogenetics wrong,” he writes elsewhere. | xkcd by Randall Munroe, shared by Meredith Yeager. <a href="https://fediscience.org/tags/evolution" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>evolution</span></a> <a href="https://fediscience.org/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>phylogenetics</span></a> <a href="https://xkcd.com/3010/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">xkcd.com/3010/</span><span class="invisible"></span></a></p>