Our latest preprint on using machine learning to infer WGDs in Ks plots is now up at biorxiv! Check it out below!
Mike Barker
Assoc Prof & Assoc Department Head at UofA EEB in Tucson studying #PlantEvolution, #Botany, #Polyploidy, #Chromosomes, #Biodiversity, #Pteridophytes, #Xanthisma, and #Brassica. Enjoys #Boxing and #Whisky. #firstgen #iamabotanist. Views are my own. He/Him
@MikeBarker #fedi22
Mike Barker boosted:
SLEDGe: Inference of ancient whole genome duplications using machine learning https://www.biorxiv.org/content/10.1101/2024.01.17.574559v1?med=mas
Mike Barker boosted:
A new preprint from the lab testing aspects of a hypothesis that lower chromosome numbers may result from selection to reduce independently assorting incompatibilities. In short, we do not find evidence to support the hypothesis in our analyses. Great work led by PhD student Geoff Finch!
Post-zygotic reproductive isolation is not correlated with chromosome number in plants
Mike Barker boosted:
A new preprint from the lab on the distribution of ancient whole-genome duplications across the angiosperm phylogeny. Great work led by PhD student Michael McKibben! We used a variety of methods and different species trees to infer and place WGDs across the phylogeny. Overall, similar results to our past work, but species tree had a large impact on WGD inferences. Check it out here:
Mike Barker boosted:
Nice paper by my colleague "How many species are there on Earth? Progress and problems" by John J. Wiens #biodiversity #ecology #biosphere https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002388
A new preprint from the lab testing aspects of a hypothesis that lower chromosome numbers may result from selection to reduce independently assorting incompatibilities. In short, we do not find evidence to support the hypothesis in our analyses. Great work led by PhD student Geoff Finch!
Post-zygotic reproductive isolation is not correlated with chromosome number in plants
A new preprint from the lab on the distribution of ancient whole-genome duplications across the angiosperm phylogeny. Great work led by PhD student Michael McKibben! We used a variety of methods and different species trees to infer and place WGDs across the phylogeny. Overall, similar results to our past work, but species tree had a large impact on WGD inferences. Check it out here:
Mike Barker boosted:
Post-zygotic reproductive isolation is not correlated with chromosome number in plants. https://www.biorxiv.org/content/10.1101/2024.01.05.573914v1?med=mas
Mike Barker boosted:
Species Tree Topology Impacts the Inference of Ancient Whole-Genome Duplications Across the Angiosperm Phylogeny https://www.biorxiv.org/content/10.1101/2024.01.04.574202v1?med=mas
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Mike Barker boosted:
Shrinkage-based Random Local Clocks with Scalable Inference https://doi.org/10.1093/molbev/msad242 #science #evolution #biology #genome #evolgen_paper
Mike Barker boosted:
Interesting study of the performance of phylogenetic models for gene expression evolution, although they seem to have only investigated single-optimum OU models, which IMO limits conclusions on datasets with orthologs and paralogs. (Indeed they find poor performance for our 2016 dataset testing the ortholog conjucture.)
https://www.biorxiv.org/content/10.1101/2023.02.09.527893v2
#phylogeny #GeneExpression #MolecularEvolution #bioinformatics #phylogenetics
Mike Barker boosted:
The UC Davis Center for Population Biology postdoctoral fellowship is now being advertised. This is a great opportunity to come join our wonderful community of Evolution & Ecology here at Davis. Please RT.
Mike Barker boosted:
We're looking to hire a program manager for our postbac research program STEGG-INTERACT. We're interested in hiring a recent BS/MS bio grad.
Reach out to me at the email on the website if interested.
https://uh.edu/nsm/biology-biochemistry/news-events/stegg-interact/
Mike Barker boosted:
Karyotype instability varies by species and genotype combination in allohexaploid Brassica https://www.biorxiv.org/content/10.1101/2023.09.22.559010v1?med=mas
Mike Barker boosted:
V2 of my preprint with PhD student Kim Verity is now online: https://www.biorxiv.org/content/10.1101/2023.07.17.549219v2
tldr: If you want to assess the shape (e.g. balance, diversity) of a rooted tree then generally you're better off using our new indices than Sackin's index, phylogenetic entropy, etc.
The article is long mainly because we provide lots of examples. I plan soon to write a shorter #mathonco blog post explaining why these indices are better than prior approaches. Meanwhile, here's a poster.
Mike Barker boosted:
The Ka /Ks and πa /πs Ratios under Different Models of Gametophytic and Sporophytic Selection https://doi.org/10.1093/gbe/evad151 #science #evolution #biology #genome #evolgen_paper
Mike Barker boosted:
Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species https://doi.org/10.1093/gbe/evad149 #science #evolution #biology #genome #evolgen_paper
Mike Barker boosted:
📃 🎤 Opinion piece published:
'Understanding natural selection and similarity: Convergent, parallel and repeated evolution'
🧵 - I was frustrated by the different definitions regarding parallel/convergent evolution. Every colleague I asked had a different definition.
So I delved on the literature and tried to understand (and disentangle) this mess. I found that there are five frameworks to define par/conv evolution.
Mike Barker boosted:
Excited to share our new #research #preprint on Determinants of Plant Species Richness along Elevational Gradients
Check it out ResearchSquare 👇
https://researchsquare.com/article/rs-3352045/latest
Access the #Reproducible draft with all data and #RStats code 👇
https://github.com/kumar-a/richness-determinants
Any comments, #feedback, or suggestions are welcome!
#SpeciesRichness #ElevationalGradient #PlantEcology #Himalayas #ResearchPreprint #FeedbackWelcome
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