When you're working with a mentee's draft manuscript, what kind of feedback should you give? To be both efficient and effective, we suggest suppressing some of your instincts... scientistseessquirre... 🧪
Preprint up now! With @ferrisifolius.bsky.social, we found positive selection on leaf shape plasticity across the altitudinal range of the cutleaf monkeyflower. This experiment was a HUGE personal undertaking. If you give it a read, I’d love to hear your thoughts!
www.biorxiv.org/content/10.6...
There are many days when I think that "less" is the single most powerful bioinformatics tool. Just look at your data.
NSF bio hour - NSF BIO lost 40% of its staff 😑
Some more context on my university’s proposal to discontinue offering a Philosophy degree.
scienceforeveryone.science/humanities-a... 🧪
A group of people standing in a field in front of some pretty tall poplar trees
This study was a huge collaborative effort, with contributions from many collaborators (only a few of whom are pictured here). Huge thanks to my coauthors along with everyone who did fieldwork, planted and took care of trees, and collected data!
Variation in predicted reaction norms in response to mean coldest month temperature (MCMT) across admixed Populus genotypes. The reaction norm of each genotype is shown as a separate line colored by species ancestry, with green indicating Populus trichocarpa and blue indicating Populus balsamifera. Predictions for the overall model (a, d) incorporate both yearly growth increment in centimeters (cm) and the probability of mortality; predictions for the conditional model (b, e) only predict growth, ignoring the probability of zeros arising from other processes including mortality; and predictions for the zero-inflated model (c, f) predict the probability of zeros arising from mortality. (a–c) Responses across the range of MCMT values at garden and home climates. Actual values of home climates (|) and garden climates (circle) used for model training are shown on the x-axis. (d, e) Responses based on distance from climate of origin (garden–home MCMT); positive values indicate a warmer climate and negative values indicate a colder climate. If genotypes perform best in environments similar to their home environment, growth should be highest and mortality should be lowest when the transfer distance is 0.
Maps showing the predicted shift in species ancestry in the Populus hybrid zone, based on genotype-specific responses to mean coldest month temperature (MCMT). In (a, b), the color of the base layer shows the species ancestry of the studied genotype which is predicted to have the highest fitness (as measured by growth and mortality) in that location under historic (a) and future climates (b). (c) The change in optimal species ancestry between future (b) and historic (a) climates, indicating regions where increased Populus trichocarpa ancestry is expected to be beneficial in green, and regions with no change in gray. As MCMT increases, we predict that genotypes with higher P. trichocarpa ancestry may be able to outcompete genotypes with higher Populus balsamifera ancestry in some portions of the P. balsamifera range, favoring a northeastern shift of the P. trichocarpa range and the hybrid zone and into historically colder, more continental regions. Regions with MCMT values outside of the range measured in the common gardens (−13.05°C to 10.85°C) are masked and colored white. Actual ancestry of collected genotypes is shown as circles. Species ranges are shown as dark blue and green outlines (Little, 1971). The same predictions are mapped across North America, including the common garden sites (Supporting Information Fig. S15).
Very happy to see our article comparing the responses of hybrid poplars in 17 common gardens, out now in @newphyt.bsky.social! We estimated reaction norms to predict how warming winters could change where different ancestries are favored.
nph.onlinelibrary.wiley.com/doi/10.1111/...
This just out from @mortonarboretum.bsky.social Rebekah Mohn: reference genome and read mapping method both affect phylogenetic inference & heterozygosity estimates across species.
Punchline? Use a closely related but not conspecific reference.
Open-access!
onlinelibrary.wiley.com/doi/10.1111/...
Sampling and common garden design.
Climate and hybridization shape #stomatal trait evolution in #Populus
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
by Zavala-Paez et al.
@WileyPlantSci @michellezavala.bsky.social @jillahamilton.bsky.social
It is official! DR. @michellezavala.bsky.social defended a very impressive dissertation today!! With friends, family, stomata cookies, and Ecuadorian Guinea pigs cheering her along! We understand so much more about the consequences of hybridization to the evolution of physiological traits!! #proudPI
A spider with long green and brown striped front legs hides behind the petals of a yellow flower
A black and white beetle trundles along the underside of a goldenrod stem
A slightly blurry iridescent green bee takes off from a yellow goldenrod, with blue sky behind
A yellow beetle with black spots sitting on a yellow goldenrod flower
Happy goldenrod season to all who celebrate (and bonus Coreopsis)
Bright green, newly formed leaves growing from a poplar stem in a field.
Hi #ESA2025! I'll be talking about phenology in a poplar hybrid zone at 3:45 this afternoon in the "Beyond Budburst–Connecting Phenological Transitions Among Tissues and Times in Woody Plants" session. Excited to hear some phenology talks!
I am thrilled to share this paper outlining some ideas I’ve been thinking about for a little while on a simple but powerful approach for predicting risk of inbreeding depression from long runs of homozygosity and non-ROH heterozygosity. 1/n @klohmueller.bsky.social doi.org/10.1016/j.tr...
Very excited to have our study come out looking at multiple plant mosaic hybrid zones and their implications for hybrids to act as "sutures" of species ranges. We use genomic data to project shifts into future climates and discuss impacts on conservation/management.
www.pnas.org/doi/10.1073/...
Super sad to be missing out on #Botany2025, but Hamilton Lab is represented by @sammymuraguri.bsky.social - be sure to drop by his poster to learn about the genomic architecture of adaptive introgression across repeated contact zones between two sister Poplar species #PopUpPoplars
Winter is great, thunderstorms in spring are great, leaves changing colors in fall is great. Californians insulate themselves from the beauty and changes of the seasons in search of a mythical “perfect weather”. It’s perverse Utopianism and a weakness of the spirit
One week to go!!! So excited to host our colleagues next week in the Happy Valley of Pennsylvania! Over 150 registrants from around the world!! If you’re interested in coming but unable to join in person - email me to learn about virtual options forestgeneticsconference2025.com #forestgenetics2025
Based on some quick math, this alone could fund the NSF Plant Genome Research Program for ~4 years; the NSF Postdoctoral Research Fellowship in Biology, which was totally axed in the NSF budget request, for ~9 years; and ~ half the total NSF GRFP budget
ADMIXTURE analysis. Admixture plots for (a) K = 5 and (b) K = 6, partitioned by species (leaf silhouettes; from left to right, Q. macrocarpa, Q. alba, Q. bicolor, Q. stellata, Q. muehlenbergii). (c) Plot of cross-validation error as a function of K, from K = 2 to K = 8. (d) Heatmap of pairwise FST scores between ancestral clusters inferred in the K = 6 ADMIXTURE run.
Our new study out in Molecular Ecology, led by 3 early-career scientists, uses hyb-seq on rangewide field collections to document introgression, species differentiation, and phylogeograhy of bur oak (Quercus macrocarpa) & relatives. Great work by a large team over many yrs!
doi.org/10.1111/mec....
Progressive Pride Flag made in 2022 by Dr. Justin Luong from photos taken by Justin Luong of California Native Plants. #Pride #Pride2025 ##CaliforniaNativePlants
Happy Pride from California Native Plants!
Super excited for the first manuscript #NSFFunded led by the very talented
@alaynamead.bsky.social
from our #PopUpPoplar common gardens spanning 17 environments across the US that examined fitness variation and predicted range shifts for hybrids to new environments www.biorxiv.org/content/10.1...
Constantia, Lassen County, CA
🗺39.9228, -120.0034 🧭216° ⛰5604 ft
https://ops.alertcalifornia.org/cam-console/1635
A map of the US showing how most people aren't talking about climate change. Source: https://climatecommunication.yale.edu/visualizations-data/ycom-us/ The palette goes from dark red (100% of people in that state hear about climate change weekly), to a transition between pale orange and pale blue at 50%, to dark blue (people never hear climate change messages). In the U.S. no state is above 50%, so states with more frequent climate communication (Colorado, Massachusetts) are lighter than states with less (Oklahoma, West Virginia). This visually de-emphasizes those states.
One thing I’ve noticed as people move away from the rainbow palette is more use of divergent palettes for sequential data. That’s not *always* a bad idea, but often is. This example inadvertently de-emphasizes states (Colorado) where people hear about climate change more frequently.
#dataviz 📊
Excited by new #NSFFunded research from #PopUpPoplars led by @michellezavala.bsky.social that shows the importance of considering cytonuclear interactions to plant function
The role of cytonuclear interactions to plant adaptation across a Populus hybrid zone www.biorxiv.org/content/10.1...
The PLANTS program (funded by NSF) at @botsocamerica.bsky.social was a cornerstone of the conference each year, bringing together new-to-science scholars with more experienced mentors. It helped provide community, support, and connection to new scientists.
The grant was terminated last week.
happy to see our study on genetic parallelism of reproductive isolation in chickadee hybrid zones out in @evolletters.bsky.social—great work led by Georgy Semenov & Scott Taylor: doi.org/10.1093/evle...
With all the chaos, it was good to help put some trees in the ground today! 🌿💚
Digital painting of a sunset sky, a gradient of a deep blue to a bright orange, with long wisps of red and pink clouds sprawled across the sky.
We report: the first few days of May happened like a drawn-out sigh, a spill of warmth and light. Spring is now rolling out at full speed, and we remember now how hungry green can be, crawling onto pavements and walls and trees. The sunset seems a weak attempt at stopping it.
Upset about federal funding cuts in the US? Want some ideas of what to do? I wrote a long-ish blog post about it here
ecoevoevoeco.blogspot.com
summarizing things I learned meeting with Senate & House aides this week with the @aibsbiology.bsky.social Congressional Visits Day event.
