Laramie (Smith) Aközbek
@laramiemckenna.bsky.social
Comparative & Evolutionary Genomics in Myricaceae + Fagaceae, Sex Chromosomes, and Centromeres — PhD Candidate in the Harkess Lab || #NSFGRFP fellow || B.S. in Plant Bio from @uga_plantbio || 🐞
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
tidyverse.org
The Harkess Lab at the HudsonAlpha is representing at Evolution 2025! Come check out the variety of posters and talks from our group, including Dr. Philip Bentz, myself, Caroline Bendickson and Lauren Womack, as well as visiting scholars Erin Howard and Edison Rea Sancho.
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇
I'm excited to share our new preprint on the molecular evolution of heterodichogamy in two wingnut genera of Juglandaceae. Heterodichogamy features two morphs synchronously alternating male and female flowering phases in time to generate disassortative mating. doi.org/10.1101/2025...
For International Women's Day, let's pay homage to the great plant anatomist Katherine Esau. In her long career, she transformed our understanding of plant structure through her research and her very important books. She is my academic grandmother, advisor of my advisor.
REVIEW: 'Evolution of light-dependent functions of GIGANTEA' - Alena Patnaik et al., doi.org/10.1093/jxb/... 🧪 #plantscience
Telomeric transposons are pervasive in linear bacterial genomes | Science www.science.org/doi/10.1126/...
Telomeric transposons are pervasive in linear bacterial genomes
Eukaryotes have linear DNA and their telomeres are hotspots for transposons, which in some cases took over telomere maintenance. Here we identify several families of independently evolved telomeric tr...
science.org
The most recent lecture I gave on Oak Origins at The Morton Arboretum was really nicely recorded and is available for free online. This is the fullest and cleanest version of the lecture I've given to date, with some new info. I hope you enjoy it. Feel free to share. vimeo.com/1057955943
Oak Origins
On February 15, 2025, The Morton Arboretum hosted a lecture in honor of the release of Dr. Andrew Hipp's book Oak Origins: From Acorns to Species and the…
vimeo.com
Conservation genomics study of island oak by @alaynamead.bsky.social investigates conserving existing diversity, ecosystems, or species across its range. Finding: Climate change likely makes conservation of existing populations inadequate. Transplant preadapted genotypes. doi.org/10.1111/eva....
In our new work, we show that an improved long-read genome, use of both diploid & haploid assemblies, and considering the layer specificity of somatic mutations, one can discover more mutations, but still within the range of expectations. 2/2 #plantscience www.biorxiv.org/content/10.1...
What is a Differentially Expressed Gene? www.biorxiv.org/content/10....
What is a Differentially Expressed Gene?
The concept of ‘Differentially Expressed Genes’ (DEGs) is central to RNA-Seq studies, yet their identification suffers from reproducibility issues. This is largely a consequence of the inherent biological and technical variation that cannot be captured with small numbers of replicates. When thresholds for p-values and log2 fold changes are introduced, this variability can propagate an incomplete description of the data, leading to differing interpretations. Here, we compare traditional binary DEG classification with a rank-based method, grounded in Bayesian statistics, using a published yeast dataset comprising over 40 replicates. This analysis reveals how the choice of thresholds and number of replicates results in discrepancies between studies and potentially interesting genes being overlooked. Furthermore, by comparing wild-type with wild-type samples, we show how variability in gene expression can be mistaken for differential expression. Evaluating current practices for navigating
biorxiv.org
Structural analyses of gibberellin-mediated DELLA protein degradation https://www.biorxiv.org/content/10.1101/2025.02.08.637281v1
Octo-squid-nautiloid sex chromosomes! www.sciencedirect.com/science/arti...
Cephalopod sex determination and its ancient evolutionary origin
Octopuses, squids, and cuttlefishes—the coleoid cephalopods—are a remarkable branch in the tree of life whose members exhibit a repertoire of sophisti…
sciencedirect.com
I think some people hear “grants” and think that without them, scientists and government workers just have less stuff to play with at work. But grants fund salaries for students, academics, researchers, and people who work in all areas of public service. “Pausing” grants means people don’t eat.
White House pauses all federal grants, sparking confusion
The Trump administration has put a hold on all federal financial grants and loans, affecting tens of billions of dollars in payments.
washingtonpost.com
How are others helping their mentees during this time? My own career has been so positively impacted by NSF funding and DEI initiatives, so this news — along with everything else — is devastating. 😢 I’m trying to figure out the best ways to support our undergrads during these uncertain times…
Christina Areizaga Barbieri, Ph.D.@cabarbieri.bsky.social · 2y agoI’m an NSF panel reviewer that was scheduled to meet today. Just got notice that all NSF panels were canceled today. I reviewed some innovative proposals in support of students. Devastating if these scholars don’t get to do this work. For the love of science & students I hope this is just a delay.💔
The maintenance of genetic polymorphism underlying sexually antagonistic traits doi.org/10.1093/evle... Now in @evolletters.bsky.social by Ewan Flintham et al.
The maintenance of genetic polymorphism underlying sexually antagonistic traits
Abstract. Selection often favors different trait values in males and females, leading to genetic conflicts between the sexes when traits have a shared gene
doi.org
Having a color-blind colleague is a good reminder that we need to be more careful when designing figures for scientific publication 🧪 My lab has found this page especially useful for selecting color palettes, used in combination with different symbols: thenode.biologists.com/data-visuali...
Color blind friendly palettes for data visualizations with categories
A discussion of color blind friendly palettes for labeling unique catergories in data visualization.
thenode.biologists.com
Centromere evolution isn't a sudden switch! Our study shows centromere transitions are a step-by-step process driven by a combination of drift and selection. Discover how the kinetochore interface shapes this gradual change in our new preprint 🥳 doi.org/10.1101/2025.01.16.633479 🧵(1/8)
Also great talks in this session from Paige Ellestad (@jennifermandel.bsky.social’s lab) on comparative genomics across the Asterales and @zach-meharg.bsky.social (Harkess lab) on Dahlia genomics/cultivation!
Hey #PAG32, don’t miss the Compositae session this morning at 10:30am! @reidselby.bsky.social will be presenting new work on capitulum development and lettuce genomics 🥬🌻
If you’re at #PAG32 be sure to come check out @brannanrose.bsky.social’s talk on Jamesianthus and Bidens genomics in the Plant Reproduction section!! Starts at 1:30pm
NEW: 2024 has just been confirmed as the warmest year on record, and the first to breach the 1.5C threshold. We used a ridgeline (Joy Division inspired) chart to visualise daily temperature anomalies since 1940. 2024 clearly stands out with 100% of its days above 1.3C and 75% above 1.5C.
Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social
A phylogenetic approach to comparative genomics
Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...
rdcu.be
Are you headed to #PAG32 and interested in plant reproduction? 🌼 Come check out my talk in the “Sex Chromosomes and Sex Determination” session on Saturday! I’ll be talking about ancient ZW sex chromosomes, the impact of polyploidy on sexual system evolution, “leaky” dioecy, and much more.
Who else is heading to #PAG32 this weekend? If we haven’t met before, I’d love to connect! ☺️
How cool!
Vikram Shivakumar@vikramshivakumar.bsky.social · 2y agoExcited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.
Paper #2 - we generated 10 new chr-level genomes for hornworts covering all families and most genera. Also the first look into their U/V sex chromosomes! 3/4 www.nature.com/articles/s41...
Pan-phylum genomes of hornworts reveal conserved autosomes but dynamic accessory and sex chromosomes - Nature Plants
This study presents 11 new hornwort (Anthocerotophyta) genomes that clarify the structure and evolution of sex and accessory chromosomes in bryophytes and shed new light on the early evolution of land...
nature.com
