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

2024-01-19

Our latest preprint on using machine learning to infer WGDs in Ks plots is now up at biorxiv! Check it out below!

biorxiv.org/content/10.1101/20

#WGD #polyploidy #machinelearning #genomes #evolution

Mike Barker boosted:

SLEDGe: Inference of ancient whole genome duplications using machine learning biorxiv.org/content/10.1101/20

Mike Barker boosted:
2024-01-10

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

biorxiv.org/content/10.1101/20

#chromosome #WGD #plantevolution #speciation

Plots of expected relationships between the crossability index (y-axis) and chromosome number (negative relationship), median Ks of most recent WGD (positive relationship), and fraction of paleologs in a genome (negative relationship). These relationships were evaluated in the manuscript.
Mike Barker boosted:
2024-01-08

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:

biorxiv.org/content/10.1101/20

#WGD #polyploidy #phylogeny #angiosperms

Bar chart of the number of WGD from tip to root in the angisperm phylogeny for each species in the analysis. Overall, there was an average of 3.5 WGDs inferred the ancestry of each angiosperm species. The x-axis ranges from 1 to 8 WGDs with a peak of nearly 130 species having 3 rounds of WGD in their ancestry.
Mike Barker boosted:
Brian J. Enquistbjenquist
2024-01-08

Nice paper by my colleague "How many species are there on Earth? Progress and problems" by John J. Wiens journals.plos.org/plosbiology/

2024-01-08

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

biorxiv.org/content/10.1101/20

#chromosome #WGD #plantevolution #speciation

Plots of expected relationships between the crossability index (y-axis) and chromosome number (negative relationship), median Ks of most recent WGD (positive relationship), and fraction of paleologs in a genome (negative relationship). These relationships were evaluated in the manuscript.
2024-01-08

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:

biorxiv.org/content/10.1101/20

#WGD #polyploidy #phylogeny #angiosperms

Bar chart of the number of WGD from tip to root in the angisperm phylogeny for each species in the analysis. Overall, there was an average of 3.5 WGDs inferred the ancestry of each angiosperm species. The x-axis ranges from 1 to 8 WGDs with a peak of nearly 130 species having 3 rounds of WGD in their ancestry.
Mike Barker boosted:

Post-zygotic reproductive isolation is not correlated with chromosome number in plants. biorxiv.org/content/10.1101/20

Mike Barker boosted:

Species Tree Topology Impacts the Inference of Ancient Whole-Genome Duplications Across the Angiosperm Phylogeny biorxiv.org/content/10.1101/20

Mike Barker boosted:
2024-01-04
Mike Barker boosted:
Molecular Biology & Evolutionmolbioevol@ecoevo.social
2023-12-08

Shrinkage-based Random Local Clocks with Scalable Inference doi.org/10.1093/molbev/msad242 #science #evolution #biology #genome #evolgen_paper

Mike Barker boosted:
Marc Robinson-Rechavimarcrr@ecoevo.social
2023-10-31

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.)
biorxiv.org/content/10.1101/20
#phylogeny #GeneExpression #MolecularEvolution #bioinformatics #phylogenetics

Mike Barker boosted:
2023-09-23

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.

cpb.sf.ucdavis.edu/cpb-postdoc

Mike Barker boosted:
2023-09-23

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.

uh.edu/nsm/biology-biochemistr

Mike Barker boosted:

Karyotype instability varies by species and genotype combination in allohexaploid Brassica biorxiv.org/content/10.1101/20

Mike Barker boosted:
2023-09-22

V2 of my preprint with PhD student Kim Verity is now online: biorxiv.org/content/10.1101/20

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.

Academic poster title: A new system of rooted-tree indices

Authors: Kim Verity, Veselin Manojlovi¢, Robert Noble

Intro: The comparison and categorization of tree diagrams is fundamental to large parts of biology and other fields. Current indices have important flaws that complicate their interpretation and limit their scope. Here we introduce a unified system of indices with no such shortcomings, thus solving important practical problems.
Mike Barker boosted:
2023-09-21

The Ka /Ks and πa /πs Ratios under Different Models of Gametophytic and Sporophytic Selection doi.org/10.1093/gbe/evad151 #science #evolution #biology #genome #evolgen_paper

Mike Barker boosted:
2023-09-21

Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species doi.org/10.1093/gbe/evad149 #science #evolution #biology #genome #evolgen_paper

Study corals in Kāne‘ohe Bay, Oʻahu, Hawaiʻi. Colonies of (A) M. capitata, the rice coral, and (B) P. acuta, the lace coral. Images taken by D. Bhattacharya. (C) Aerial image of Kāne‘ohe Bay (modified from https://dlnr.hawaii.gov/) with the six reefs where the coral samples were collected highlighted using colored circles and labels. The color of the circles surrounding the collection sites corresponds to the colors used in all subsequent main text and supplementary figures. The legend for distance in meters is shown at the bottom of the image.
Mike Barker boosted:
2023-09-21

📃 🎤 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.

onlinelibrary.wiley.com/doi/fu

Mike Barker boosted:
Abhishek Kumarakumar@ecoevo.social
2023-09-21

Excited to share our new #research #preprint on Determinants of Plant Species Richness along Elevational Gradients

Check it out ResearchSquare 👇
researchsquare.com/article/rs-

Access the #Reproducible draft with all data and #RStats code 👇
github.com/kumar-a/richness-de

Any comments, #feedback, or suggestions are welcome!

#SpeciesRichness #ElevationalGradient #PlantEcology #Himalayas #ResearchPreprint #FeedbackWelcome

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