Sign in

Pia Schwarz

@pfschwarz.bsky.social
332 followers 499 following 14 posts

PhD candidate @ Coughlan Lab @yale_eeb | evolutionary genetics & population genomics, speciation & plant immunity 🌸🧬|@UBBiology 🎓'22| former D1 student-athlete 🎾 | 🇩🇪

PostsRepliesMedia
Reposted by Pia Schwarz
Botanical Society of America @botsocamerica.bsky.social · 14/09/2026
🌿 Congratulations to Dr. Jenn Coughlan (Yale University), recipient of the 2026 BSA Emerging Leader Award! We're honored to recognize them as a rising star in our community. 👏 Learn more at www.botany.org (click Awards). #BSA2026AwardsBlitz #IamaBotanist #PlantPeopleFTW
A portrait of Jennifer Coughlan wearing dark-framed glasses and a navy shirt patterned with cranes, pineapples, and blue flowers, smiling in front of a sunlit brick wall. The text reads: "Botanical Society of America 2026 Emerging Leader Award, Jennifer Coughlan, Yale University." A QR code and the text "Learn more about the Emerging Leader Award here!" appear at the bottom, along with the Botanical Society of America logo. The graphic has a border of pale green agave leaves.
49224
Reposted by Pia Schwarz
Dan MacGuigan @dmacguig.bsky.social · 08/09/2026
New paper in Systematic Biology! We show how micro-synteny can help resolve a tricky fish #phylogenetic problem where traditional sequence-based analyses fall short. Genomes archive evolutionary history in more than just their basepairs. doi.org/10.1093/sysb... #fish #genomics #evolution
35026
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 02/08/2026
So proud of this manuscript- lead by the fantastic @henryarenas.bsky.social with two undergraduates (Cage Cochran and Quinn Evans) each doing a Herculean effort during their honors theses, and Hongfei Chen helping out tremendously with lab work. www.biorxiv.org/content/10.6...
biorxiv.org
Maintenance of phenotypic divergence in two sympatric monkeyflowers with weak reproductive isolation
Sympatric species often exhibit permeable reproductive barriers, yet many of them coexist as phenotypically distinct entities. One way to account for this apparent paradox is that selection on loci th...
27328
Reposted by Pia Schwarz
Dan MacGuigan @dmacguig.bsky.social · 02/07/2026
Working with mitogenomes for eDNA, phylogenetics, etc, but not sure what's available on GenBank? Maybe your study group has weird mitogenome features? Come explore with with my new GenBankMitoReview tool! github.com/dmacguigan/G... #DNA #bioinformatics #eDNA #GenBank
097
Reposted by Pia Schwarz
Takuji Usui | 薄井拓路 @usuitakuji.bsky.social · 03/07/2026
I am incredibly thrilled to announce that I will be starting as an Assistant Prof at Yale EEB in January 2027!! 🎉🎊 Stay tuned for student and postdoc openings, and please feel free to reach out to me if you are interested in eco-evo, range dynamics, species interactions, and global change! 🌐🌱🦠🧬
1412628
Reposted by Pia Schwarz
Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 04/07/2026
I talked about this at PEQG a few weeks ago. In addition to github.com/RILAB/argprep (preps your genome assemblies for SINGER), argtest github.com/RILAB/argtest does some QC to clean up an ARG estimated with SINGER.
unfolded sis before (left) and after (right) argtest. still an imperfect fit, but a much better fit to intermediate frequency polymorphismsbefore (left) and after (right) running argtest simulated (y) and observed (x) diversity from the ARG. argtest removed a bunch of outliers where there was much higher diversity than expected (lower right corner, lefthand plot)screenshot of part of the html summary of argtest showing parameter choices, how much of the ARG is retained, and how each sample faredcomparison of derived mutation count per individual before (left) and after (right) running argtest. on the right the overall mutation rate is still off by a bit, but the real data tracks the expectation from the ARG much better
13115
Reposted by Pia Schwarz
Heng Li @lh3lh3.bsky.social · 16/06/2026
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
1193109
Reposted by Pia Schwarz
Leibniz IPK @leibnizipk.bsky.social · 16/06/2026
A team led by the @leibnizipk.bsky.social and @fz-juelich.de has developed an AI-model that predicts where regulatory proteins bind to plant DNA in order to switch genes on and off. The study has been published in "Nature Communications". ➡️Paper: tinyurl.com/mryxendn ➡️PR: tinyurl.com/37kpbpzh
New deep learning models predict how complex DNA-protein interactions turn plant genes on and off, revealing how genetic variations help wild species and crops adapt to environmental stress.
0128
Pia Schwarz @pfschwarz.bsky.social · 16/06/2026
Just got back from an incredible week at #PEQG2026 packed with learning, great science, and exciting conversations!🌱 I had the opportunity to present my ongoing research on a #pangenomic perspective on #NLR gene diversity in #Mimulus. Grateful for the inspiring talks, workshops, and conversations!
120
Reposted by Pia Schwarz
Science Magazine @science.org · 28/05/2026
Researchers have identified superparamagnetic macrophages in the livers of rock pigeons to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation. scim.ag/4nTQ3nq
How animals sense Earth’s magnetic field is one of biology’s enduring mysteries. Researchers have now identified superparamagnetic macrophages in the livers of rock pigeons (Columba livia) to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation.

Photo: Andreas Teichmann/laif/Redux
12519196
Reposted by Pia Schwarz
Amrei Bahr @amreibahr.bsky.social · 29/05/2026
5 Jahre #IchBinHanna. Alle sind sich inzwischen einig, dass sich grundlegend was ändern muss. Zig konstruktive Vorschläge. Und dann das: Der neue Referentenentwurf fürs #WissZeitVG ist 1 Witz. Und zwar 1 ganz schlechter. Meine Einordnung ⬇️ #IchBinHanna @drkeichhorn.bsky.social @kubon.bsky.social
628298
Reposted by Pia Schwarz
John Lovell @jotlovell.bsky.social · 19/05/2026
We are often asked whether pangenomes are worth the hassle. The files can be large and methods to explore them are much more challenging than linear references. Earlier this week, we preprinted a clear example of how and why pan-genome graphs are so important for trait discovery.
13423
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 10/03/2026
I am SO THRILLED to share our first fully-lab lab paper!!!!!! Led by @hybridzones.bsky.social & @hagarsoliman.bsky.social, w/ a major assist from @pfschwarz.bsky.social!!!!!!!!!!!!! Read more below, if you're curious (you should be- it's AWESOME!!!!!!!) link: www.sciencedirect.com/science/arti...
sciencedirect.com
Introgression and parental conflict shape repeated occurrences of postzygotic isolation in Mimulus
Postzygotic reproductive isolation is often thought to accumulate as a byproduct of neutral divergence. Yet it frequently evolves rapidly, in line wit…
1017366
Reposted by Pia Schwarz
Amrei Bahr @amreibahr.bsky.social · 20/02/2026
Gestern hab ich bekannt gegeben, dass ich spätestens 2028 aus der Wissenschaft aussteigen werd — darüber schreibt @evamurasov.bsky.social nun im @tagesspiegel.de. Zig Kommentare & Nachrichten zeigen mir: Sehr viele Wissenschaftler_innen hadern. Bedingungen müssen dringend besser werden! #IchBinHanna
tagesspiegel.de
#IchbinHanna-Gründerin schmeißt hin: Amrei Bahr wurde Juniorprofessorin – und verlässt die Wissenschaft
Mit ihrem Einsatz für bessere Arbeitsbedingungen an Unis wurde Amrei Bahr bekannt und löste eine Bewegung aus, die das Wissenschaftssystem ändern will. Jetzt gab die Juniorprofessorin ihren Ausstieg a...
31581150
Reposted by Pia Schwarz
Trevor Krabbenhoft @fishgenomes.bsky.social · 10/02/2026
Biological invasions present an interesting paradox: often little genetic variation is accompanied by dramatic ecological success. Led by PhD student Chris Osborne, we evaluated genetic diversity in a classic invader, brown treesnake on Guam. www.biorxiv.org/content/10.6... Photo: Pavel Kirilliov
Brown treesnake photo and karyogram of a haplotype phased genome assembly.
1167
Pia Schwarz @pfschwarz.bsky.social · 09/02/2026
@stressedbranch.bsky.social
020
Reposted by Pia Schwarz
John Lovell @jotlovell.bsky.social · 06/02/2026
We’re excited to share the Pan-genomes Doorstep Meeting @ #PEQG26! Join this 3-hour workshop on evolutionary applications of pangenomics, covering construction, analysis, phylogenetics, annotation & graph QC. Register separately or as an add-on to PEQG: genetics-gsa.org/peqg-2026/do...
genetics-gsa.org
Pan-genomes Meeting - 2026 Population, Evolutionary, and Quantitative Genetics Conference
Visit our website to learn more.
01210
Reposted by Pia Schwarz
John Lovell @jotlovell.bsky.social · 30/01/2026
This article is now published! academic.oup.com/nargab/artic... We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.
academic.oup.com
Evolutionary and methodological considerations when interpreting gene presence–absence variation in pangenomes
Abstract. While graph-based pangenomes have become a standard and interoperable foundation for comparisons across multiple reference genomes, integrating p
22417
Reposted by Pia Schwarz
Dr. K. Lotterhos @drk-lo.bsky.social · 03/02/2026
Slim 5 can now simulate genomes with multiple chromosomes like autosomes, sex chromosomes, mitochondria and chloroplast dna academic.oup.com/mbe/article/...
academic.oup.com
SLiM 5: Eco-evolutionary Simulations Across Multiple Chromosomes and Full Genomes
Abstract. Evolutionary simulations of multiple chromosomes, even up to the scale of full-genome simulations, are becoming increasingly important in populat
09333
Pia Schwarz @pfschwarz.bsky.social · 26/12/2025
I am very excited to share our new paper with my amazing co-authors and mentors @dmacguig.bsky.social @fishgenomes.bsky.social @tjnear.bsky.social . We investigate a secondary contact zone in #darters. track.smtpsendmail.com/9032119/c?p=...
track.smtpsendmail.com
Mosaic tri-lineage secondary contact shapes diverse genomic outcomes in darters
Abstract. Speciation does not always lead to complete reproductive isolation, which can result in hybrid zones with gene flow. In freshwater fishes, second
11411
Pia Schwarz @pfschwarz.bsky.social · 25/09/2025
Go read our new pre-print!
072
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 25/09/2025
At the same time, Dr. Megan Frayer was finding that these two species have a ✨sorted✨ history of gene flow, including introgression of a large chromosomal inversion that has been previously implicated in hybrid seed inviability
media.tenor.com
a woman is holding a piece of paper with the words what the what written on it
ALT: a woman is holding a piece of paper with the words what the what written on it
131
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 25/09/2025
but here's where things get spicy: in her rotation project, Pia showed that the genetic basis of hybrid seed inviability is in fact SHARED between two such incidences involving two different (and phylogenetically distinct) species.
media.tenor.com
a man in a red jacket is eating popcorn with the words oh this is getting spicy below him
ALT: a man in a red jacket is eating popcorn with the words oh this is getting spicy below him
111
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 25/09/2025
She followed up with super awesome embryo rescues to show that these incidences of hybrid seed inviability arise in the endosperm, & that hybrid seeds show parent-of-origin biased growth effects, following some predictions that hybrid seed inviability may be evolving via parental conflict
111
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 25/09/2025
Then Hagar stepped up to the plate: she showed that RI follows a geographic rather than phylogenetic pattern: populations that are closer together have the same patterns of crossing. Importantly, these patterns TRANSCEND SPECIES BOUNDARIES, creating a complex landscape of hybrid seed inviability.
media.tenor.com
a man in a tie is sitting at a desk with his mouth open
ALT: a man in a tie is sitting at a desk with his mouth open
131
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 25/09/2025
This is work that I first started as a postdoc: I was befuddled about why we saw hybrid seed inviability evolve so many dang times in such a short period of time in monkey flowers, so I started just doing a ton of crosses.... like truly an unhinged amount...
media.tenor.com
a woman is looking at a triangle with a mathematical equation written on it .
ALT: a woman is looking at a triangle with a mathematical equation written on it .
121
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 25/09/2025
We're on a roll: Super proud of this paper lead by Dr. Megan Frayer & GS Hagar Soliman (with a major contrib from GS Pia Schwarz): Introgression and Parental Conflict Shape Repeated Occurrences of Postzygotic Isolation @hybridzones.bsky.social @hagarsoliman.bsky.social @pfschwarz.bsky.social
13314
Reposted by Pia Schwarz
Facundo Romani @fromani.bsky.social · 22/09/2025
Very important paper and resource. Bryophyte genomes expanded by one order of magnitude. www.nature.com/articles/s41...
nature.com
Bryophytes hold a larger gene family space than vascular plants - Nature Genetics
A super-pangenome analysis incorporating 123 newly sequenced bryophyte genomes reveals that bryophytes exhibit a larger number of unique and lineage-specific gene families than vascular plants.
29653
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 24/09/2025
This was a HUGE effort, taking years of diligent work. Hongfei was a true leader, and I'm really proud of this cool piece. We'd love any feedback y'all might have. www.biorxiv.org/content/10.1...
biorxiv.org
Unique genetic bases of repeated life-history divergence associated with high altitude adaptation in Mimulus perennials
Understanding evolutionary repeatability is a central question in biology, as it informs how predictably organisms respond to similar selection pressures. However, the extent to which phenotypic repea...
01513
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 24/09/2025
Lots of cool data to dig into, but the big take homes: Phenotypic evo is repeatable, but the genetic bases of these traits is largely not. Of the QTL we do find in more than one cross, QTL with large effect sizes or those implicated in more than one trait tend to pop up in more than one cross!!!!
172
Reposted by Pia Schwarz
Jenn Coughlan @jenncoughlan.bsky.social · 24/09/2025
Late to the party, but I'm so excited about the first paper from our lab: ✨Unique genetic bases of repeated life-history divergence associated with high altitude adaptation in Mimulus perennials ✨ This work was led by the ABSOLUTE ROCKSTAR Hongfei Chen!
15615
Reposted by Pia Schwarz
Casey Dunn @caseywdunn.bsky.social · 11/06/2025
I hope to take a PhD student in the coming application cycle. Please reach out if you are interested in joining our lab in EEB at Yale, especially if interested in working on the natural history/ phylogenetics/ morphology/ population biology/ development/ genomics of siphonophores. dunnlab.org
dunnlab.org
The Dunn Lab
Casey Dunn's laboratory in the Department of Ecology and Evolutionary Biology at Yale University.
04050
Reposted by Pia Schwarz
Moisés A. Bernal @evofish.bsky.social · 12/11/2024
New manuscript by graduate student @kmeaton.bsky.social. Along with UG students she found that Pinfish pops have similar max thermal tolerance despite experiencing different water temps. This can make southern pops more susceptible to #climatechange & #oceanwarming www.biorxiv.org/content/10.1...
3113
Reposted by Pia Schwarz
Trevor Krabbenhoft @fishgenomes.bsky.social · 16/08/2024
New paper on the timing and geological context of two co-evolving salmonid fish radiations (predator-prey system) driven by adaptation-to-depth in the Great Lakes: www.nature.com/articles/s42...
nature.com
Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum - Communications Biology
Laurentian Great Lakes fish diversification predates the Last Glacial Maximum and was likely driven by novel habitats and predator–prey dynamics.
1106
Pia Schwarz @pfschwarz.bsky.social · 02/08/2024
I had a great time presenting my undergraduate thesis at #Evolution2024 #Evol2024. Stay tuned for more, the manuscript is submitted!!!
020
Pia Schwarz @pfschwarz.bsky.social · 02/08/2024
In case you missed my talk at #Evolution2024 #Evol2024 on mosaic hybridization and secondary contact of three darter lineages with @fishgenomes.bsky.social, Tom Near and @dmacguig.bsky.social you can see it here (starting at 56:00) youtu.be/H-vue8TJsrA?...
youtu.be
July 30th - Hybridization I
00:00 - Ben Schultz 13:48 - Elizabeth Mandeville 27:54 - Sofia Mendes 41:58 - Katherine Drotos 55:57 - Pia Schwarz
072