Ziv E. Lieberman

Ziv E. Lieberman

@formicula.bsky.social

ants. emmets. mires 🞚 systematics🞚evolutionary morphology & anatomy🞚 paleoentomology🞚biogeography🞚3D imaging PhD candidate at UC Davis || views & statements my own {they|them} ☄

179 followers183 following118 posts

Ziv E. Lieberman
@formicula.bsky.social

Please, journal websites, I do not want to have your AI chatbot as a pop up window before I can read the article. I do not want it as a sidebar that can't be minimized. I don't want it as a button that can't be dismissed. Please let me just read the fucking paperrrrraaasdfasdfnasdf

Ziv E. Lieberman reposted

Miles Zhang | 张远濛
@ymilesz.bsky.social

Your regular reminder to not publish or review for MDPI, what is this hot garbage of a figure. Drosophila and Nasonia are mixed up, and the photo of B. kinseyi is MY PHOTO of Eupelmus parasitoid that I reared out of B. kinseyi gall, instead of the inducer. Thanks for lifting and not crediting me?

Ziv E. Lieberman reposted

Albert Ch. Soewongsono
@albertchristian.bsky.social

A new preprint w/ @landismj.bsky.social that I’m excited to share! We develop a theoretical framework linking evolutionary scenarios to mathematical constraints on parameters that produce given stationary frequencies in state-dependent speciation-extinction models. We call these “rulesets.” #EvoBio

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social

On the mapping between evolutionary scenarios and governing rules in state-dependent speciation-extinction models https://www.biorxiv.org/content/10.64898/2026.09.24.754193v1

Ziv E. Lieberman reposted

Dominik Kusy
@dominik-kusy.bsky.social

New preprint: a phylogenomic tree of Elateriformia (fireflies, click, jewel, soldier beetles and relatives). 195 taxa, 31 of 34 families, up to ~4,200 genes. The group goes back ~285 Mya, and soft bodies and neotenic females evolved independently at least 15 times. www.biorxiv.org/content/10.6...

Ziv E. Lieberman
@formicula.bsky.social

A very nicely stated and demonstrated reiteration of some principles which we should all recognize, but often don't get enough attention, consistency, or precision in discussion. These lineages still deserve study - but we should be temperate about premises and conclusions.

Joseph W. BRRRAAAIIINNNSSS@josephwb.bsky.social

Early-diverging lineages provide little information about ancestors academic.oup.com/sysbio/advan... From @phylieu.bsky.social @sinkingdiatom.bsky.social @omearabrian.bsky.social

academic.oup.comEarly-diverging lineages provide little information about ancestorsAbstract. Large phylogenetic trees are often unbalanced near the root, with a species-depauperate lineage sister to a far more species-rich clade. The spec

Ziv E. Lieberman reposted

Andy Farke
@andyfarke.bsky.social

Student Collections Study Award for Natural History Museum of Los Angeles County - next cycle of applications due October 1. Details at their website: nhm.org/student-coll... - the Alf Museum is also close by, so it's a good visit us, too, once you are in the area!

nhm.orgStudent Collections Study AwardThe NHM Collections Study Awards provide funding for undergraduate and graduate students to visit and study the collections of the Natural History Museum of Los Angeles County, the La Brea Tar Pits & ...
Ziv E. Lieberman
@formicula.bsky.social

Much of this could also be said for other areas of fundamental research like taxonomy and descriptive morphology, which have been referred to as 'non-scientific' to to their exploratory nature.

Andy Farke@andyfarke.bsky.social

Your big data is only a big data set because a whole bunch of people did the insignificant, unworthy of your time, not important enough to publish, effort to build & maintain collections over the years, which you then scooped up into your dataset for a proper "big picture" study. <6/n>

Ziv E. Lieberman reposted

Hoyaboya
@hoyaboya1.bsky.social

Dunn (2026-08, Casey W. Dunn) 「系統生物学」 Phylogenetic Biology doi.org/10.5281/zeno... dunnlab.org/phylogenetic... 動物系統学の大家，Dunn先生による系統学の新たな教科書です！オンライン版は無料公開されています！！ イェール大学の講義で使用されています！ New textbook on phylogenetics (available online for free)!

Ziv E. Lieberman
@formicula.bsky.social

Paleontology people! Is there a term for 'rock fossils' which is inclusive of adpression, compression, and impression fossils? I have not found one, and I am looking for a way to refer to these fossil in contrast to amber fossils, which is agnostic to the specific preservation.

Ziv E. Lieberman reposted

Priscilla Lau
@prilau.bsky.social

Our paper (also, my first first-author paper) is now available in MEE early view! In this study, we introduced a state-dependent Ornstein-Uhlenbeck model we implemented in RevBayes to test adaptive hypotheses in macroevolution. (1/3) besjournals.onlinelibrary.wiley.com/doi/10.1111/...

besjournals.onlinelibrary.wiley.comAn efficient Bayesian phylogenetic approach for joint inference of continuous and discrete trait evolution under a state‐dependent Ornstein–Uhlenbeck modelMacroevolutionary adaptation of a continuous trait to different discrete states across species can be modelled using a phylogenetic state-dependent Ornstein–Uhlenbeck (OU) process. Existing infere...

Ziv E. Lieberman reposted

Jeffrey Ross-Ibarra
@jrossibarra.bsky.social

UC Davis will no longer pay the difference so that GRFP recipients earn the same as other students. So mid-PhD students will lose nearly 25% of salary & new students will make less than their peers. Apply for the GRFP, it’s a wonderful help to your career. Just don’t come here if you get one.

Ziv E. Lieberman reposted

Daniel Kronauer
@danielkronauer.bsky.social

New paper from the lab on the molecular regulation of parenting in ants. Spearheaded by postdocs Alex Paul and @tomaskay.bsky.social

Tomas Kay@tomaskay.bsky.social

In an article published today, we show that ancient feeding-related neuropeptides have been repurposed to control brood care in clonal raider ants. Photo: Bart Zijlstra, UNIL /1

Ziv E. Lieberman
@formicula.bsky.social

Doing a lil reread of some history of ant taxonomists and, um, hm. "...Wheeler felt guilty about having temporarily expelled Creighton from the Bussey." - Buhs 2000 J. Hist. Biol.

Ziv E. Lieberman reposted

Ted McCormick
@tedmccormick.bsky.social

Uninterested in leading a pile-on but no, AI does not “have access” to everything ever published. Not archival material, obviously, but not secondary material either. Nor across times nor languages. AI is not human knowledge personified. It’s exactly not that, in fact. It’s not even a search engine.

Ziv E. Lieberman reposted

Hoyaboya
@hoyaboya1.bsky.social

Lozano et al. (2026-05, Journal of Molecular Evolution) (open access) Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection doi.org/10.1007/s002...

doi.orgConcatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection - Journal of Molecular EvolutionPhylogenetic conflict—particularly hidden gene-tree discordance generated by incomplete lineage sorting (ILS)—is pervasive in multilocus and phylogenomic datasets, yet its consequences for nucleotide substitution model selection remain poorly understood. Modern molecular studies increasingly collect and concatenate large sets of independent loci sampled across distant and often poorly characterized regions of the genome, creating significant potential for heterogeneity when analyzed in combination. Here, we examine whether intra-alignment genealogical conflict can influence standard model selection procedures to favor parameter-rich substitution models even when sequences evolve under a simple substitution process. Through a series of in silico case studies, we simulated sequence evolution under the simplest rate-homogeneous Jukes–Cantor (JC69) model and generated concatenated alignments as mosaics of multiple loci, each evolving on its own gene tree drawn under the multispecies coalescent. Conflict was increased by manipulating conditions expected to elevate ILS and gene-tree heterogeneity and embedding progressively more hidden genealogies within alignments while holding total alignment length constant. Despite all data being generated under JC69, model selection frequently favored more complex models, with varying sensitivity depending on the number of taxa, the expected amount of conflict, and the specific selection criterion applied. A dominant pattern was frequent inclusion of among-site rate variation parameters (+ G4 and/or + I), and under extreme conflict, model selection increasingly favored richer substitution models (e.g., SYM, GTR). Broadly, our results showed that hidden conflict can manifest as substitutional and rate heterogeneity, driving selection procedures to compensate with additional parameters in concatenated analyses under high conflict. Broadly, our study contributes to a greater understanding and appreciation of the challenges in modeling molecular evolution in the era of multilocus phylogenetics.
Ziv E. Lieberman
@formicula.bsky.social

I've been wanting to see a study like this for a long time...good stuff!

Alessio Capobianco@acapomorphic.bsky.social

My new paper with @gdarlim.bsky.social and @hoehna.bsky.social is now out in Proceedings B! We set out to compare two different approaches to time-calibrate a molecular phylogeny: traditional node calibrations, and unresolved FBD... @royalsocietypublishing.org doi.org/10.1098/rspb...

doi.orgHow to date a molecular phylogeny: comparison of effective priors between node calibration and fossilized birth–deathAbstract. Time-calibrating a phylogenetic tree is a fundamental step in phylogenetic inference, as it allows the study of macroevolutionary processes such

Ziv E. Lieberman reposted

Thibault Latrille
@phylogenetrips.bsky.social

Should we measure trait evolution in unit of time or in unit of substitutions? Our new paper in @evolletters.bsky.social looks at this from a theoretical perspective. #Evolution #Phylogenetics DOI: doi.org/10.1093/evle... 🧵 thread below 🧵

doi.orgPhylograms better fit neutrally evolving traits than chronogramsMany species are characterized by trait differences between each other. For example, the brain size of different primate and human lineages varies. The que

Ziv E. Lieberman reposted

Alex Wild
@alexwild.bsky.social

I would have bet actual money that the dark rover ant, Brachymyrmex patagonicus, was supercolonial. This is a relatively recent arrival to Texas, and it's one of our most common ants now, getting into everything, in huge numbers. And I would have been very wrong.

onlinelibrary.wiley.comThe underdog invader: Breeding system and colony genetic structure of the dark rover ant (Brachymyrmex patagonicus Mayr)Almost all invasive ant species studied so far form supercolonies, a dense network of interconnected nests comprising numerous queens, without aggression toward non-nestmates. Here, we show that most...

Ziv E. Lieberman reposted

Joseph W. BRRRAAAIIINNNSSS
@josephwb.bsky.social

The paper: Statistical and Structural Bias in Birth-Death Models by @phylieu.bsky.social & @omearabrian.bsky.social link.springer.com/article/10.1...

link.springer.comStatistical and Structural Bias in Birth-Death Models - Bulletin of Mathematical BiologyAccurate estimation of speciation ( $$\lambda $$ λ ) and extinction ( $$\mu $$ μ ) rates from phylogenetic trees is central to studies of diversification, yet it remains unclear whether commonly used ...
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Ziv E. Lieberman
@formicula.bsky.social

Looking for perspectives! Background: For some time I've been cooking up a document which provides etymologies for all genus-group names of ants, plus historical and sociocultural commentary. The direct inspiration is Wheeler&Wheeler's 'Myrmecological Orthoepy & Onomatology". [continued]

View full thread
Ziv E. Lieberman
@formicula.bsky.social

One obvious thing is to add this information to AntCat, which I do plan to do, but I want to maintain the additional discussion and other short chapters. Right now, I'm considering just maintaining a website while possibly self-publishing a small run of books. A site can be updated...

Ziv E. Lieberman
@formicula.bsky.social

...as new names are established and would be a companion to any publication. I would love to have some physical copies too, though. It's a passion project, so not really needed for my citation record, but ofc it wouldn't hurt :P Any thoughts about avenues for developing this work are appreciated!

Ziv E. Lieberman
@formicula.bsky.social

Looking for perspectives! Background: For some time I've been cooking up a document which provides etymologies for all genus-group names of ants, plus historical and sociocultural commentary. The direct inspiration is Wheeler&Wheeler's 'Myrmecological Orthoepy & Onomatology". [continued]

Ziv E. Lieberman
@formicula.bsky.social

I'm struggling to find a suitable outlet for publishing this work. It's not right for linguistics publishers or entomology journals. I've considered things like History of Science...It's also hampered by being very long and highly-formatted, though I could hypothetically compromise on the latter...

Ziv E. Lieberman
@formicula.bsky.social

What's your favorite tool for extracting mitogenomes from whole-genome sequences? Since the last time I tried this, the options have proliferated. Any recommendations would be great!

Ziv E. Lieberman reposted

Neil Tsutsui
@neiltsutsui.bsky.social

Job alert! Post-doc position available in the Tsutsui lab at UC Berkeley. I'm specifically looking for someone optimize and scale RNA interference for invasive ant control and eradication. Happy to take questions at ntsutsui@berkeley.edu. Spread the word! aprecruit.berkeley.edu/JPF05325

aprecruit.berkeley.eduPostdoctoral Scholar – Insect Molecular Biology – ESPM (Organisms & the Environment) - Tsutsui LabUniversity of California, Berkeley is hiring. Apply now!

Ziv E. Lieberman reposted

Daniel Kronauer
@danielkronauer.bsky.social

Ants are experts at telling nestmates from foreigners via subtle differences in odor profiles. In this new paper, we explore the conditions under which ants develop and maintain tolerance to foreigners. Turns out the ant recognition system is surprisingly plastic. www.cell.com/current-biol...

cell.comTolerance toward foreigners in ants requires chronic exposure for establishment but only sporadic exposure for maintenanceBailly et al. show that ants learn to tolerate genetically distinct non-nestmates through prolonged exposure. Once established, this tolerance persists with occasional re-encounters with ants of the s...

Ziv E. Lieberman reposted

Kate Laskowski
@katelaskowski.bsky.social

Couldn't sum it up better than this: "I've realized now that writing *is* how I think best: often, my thoughts only crystallize once I try to put words on the page and then revise those words repeatedly." If you outsource your writing, you outsource your thinking. And then what is even the point?

gavin jones@ecologyofgavin.bsky.social

In a sea of opinions about the role of LLMs in academics I offer my own. Apart from being harmful, exploitive plagiarism machines, LLMs rob us of the opportunity to experience the gift of friction in writing, which changes how we think. We must not give away that gift. doi.org/10.1002/fee....

doi.orgThinking like a mountain in the age of AIClick on the article title to read more.

Ziv E. Lieberman reposted

𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
@basantakhakurel.bsky.social

Our new paper 'A covarion model for phylogenetic estimation using discrete morphological datasets,' is out in SysBio! We introduce the "covariomorph" model in RevBayes to capture character and lineage specific rates of morphological traits. 🔗 doi.org/10.1093/sysb...

doi.orgA covarion model for phylogenetic estimation using discrete morphological datasetsAbstract. The rate of evolution of a single morphological character is not homogeneous across the phylogeny and this rate heterogeneity varies between morp

Ziv E. Lieberman reposted

Jill Oberski, PhD
@jilloberski.bsky.social

Hey bsky! I’d like to share some cool work I recently coauthored that integrates entomology, paleontology, and German cultural history. 🔶🐜⚡️ We discovered a fossil ant in the amber collection of Johann Wolfgang von Goethe! Read on for a delightful story of #museomics and #collectomics. >> 1/

Ziv E. Lieberman reposted

invertebrate
@crevicedwelling.bsky.social

reading about organisms that aren’t your specialty is like margins of the quorbus eplungulate, ploobular processes bent posteriorly towards the foobulum define term “eplungulate” - lacking plungae. synonym: thubulous

Ziv E. Lieberman reposted

Mark A. Hanson
@hansonmark.bsky.social

We've got ISSUES. Literally. We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do? arxiv.org/abs/2601.07563 A 🧵 1/n

Ziv E. Lieberman
@formicula.bsky.social

Another responses to the recent sponge/ctenophore paper in Science. . .also worth a read!

Casey Dunn@caseywdunn.bsky.social

Our eLetter github.com/caseywdunn/s... responding to a recent Science paper was just posted. The paper found more genes with consistent support for sponge-sister than ctenophore-sister. We found several technical issues that, when corrected, reverse the conclusions and recover ctenophore-sister.

Ziv E. Lieberman reposted

Nathan Whelan
@nathan-whelan.bsky.social

I posted an eLetter to the recent Science paper claiming strong evidence for sponges as the sister group to all other animals. The eLetter can be found under the original article. www.science.org/doi/10.1126/...

science.orgIntegrative phylogenomics positions sponges at the root of the animal treeDetermining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru...