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Tris Dodge

@tododge.bsky.social
184 followers 189 following 31 posts

PhD candidate with Molly Schumer | structural variation, balancing selection, genome evolution | 🐟🦎🌻🧬👨‍💻 www.tododge.com

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Reposted by Tris Dodge
Kelsie Hunnicutt @kelsiehunnicutt.bsky.social · 25/09/2026
My News & Views is out now in @natecoevo.nature.com ! I cover an excellent study by Hosoki et al. on long-term monitoring of hybrid stickleback populations post-tsunami. 🌊🐟 (1/2) Read it here: rdcu.be/MW75PMTbgP1a
rdcu.be
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Lukas Schrader @shaggyschrader.bsky.social · 25/09/2026
1/ New paper: doi.org/10.1126/scia... 🐜🧬 Ants exploded into >15,000 species just after the dinosaur-killing asteroid hit Earth. We think we've found one catalyst behind that radiation: transposable elements. With @jannelrinke.bsky.social, @esthervandenbos.bsky.social & others not on here. 🧵1/11
A Pseudomyrmex ant walking casually on a drop of honey.
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Dmitri Petrov @petrovadmitri.bsky.social · 17/09/2026
We are searching for an Assistant Professor in Evolutionary Biology! Looking for colleagues asking fundamental questions relating to evolutionary processes and drivers of evolutionary patterns. If you think it is you, please do apply! And please repost. facultypositions.stanford.edu/jobs/assista...
facultypositions.stanford.edu
Assistant Professor in Evolutionary Biology - Stanford University, California, United States
The Department of Biology at Stanford University seeks applicants for a tenure-track Assistant Professor in Evolutionary Biology. A successful candidate will conduct research that asks fundamental que...
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Polina Novikova @pnovik.bsky.social · 16/09/2026
I am happy to present our work @liverworks.bsky.social @robinburns.bsky.social @alisondawnscott.bsky.social on centromeric repeat turnovers, of which we counted three in the Arabidopsis genus:
biorxiv.org
The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis
Centromeres are critical for accurate segregation of chromosomes and are often composed of megabases of tandemly arranged satellite repeats. Yet, despite their conserved function, the DNA sequence of ...
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Yun Deng @yundeng.bsky.social · 14/09/2026
I am excited to share that I will be joining the Baker Institute for Animal Health and College of Veterinary Medicine at Cornell University as an Assistant Professor next spring! I am grateful to my mentors and colleagues who have supported me throughout this journey.
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Tony Gamble @tonygamble.eurosky.social · 27/08/2026
New collaborative paper from the lab on gecko sex chromosome and genome evolution! 🧪🦎 www.science.org/doi/10.1126/...
science.org
Genomic predisposition is associated with the direction of sex chromosome evolution
Sex chromosome evolution is among the most dynamic genomic innovations in vertebrates, yet why some lineages evolve XY while others evolve ZW remains unclear. Using chromosome-level genomes from 19 ge...
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Nature @nature.com · 26/08/2026
Nature research paper: Long-read sequencing reveals pre-meiotic gene conversion in sperm go.nature.com/4zEnrnr
go.nature.com
Long-read sequencing reveals pre-meiotic gene conversion in sperm - Nature
Single-molecule long-read sequencing of human sperm reveals variation in recombination across donors and that a substantial fraction of non-crossover gene conversions arises before meiosis, distinct from PRDM9-driven recombination and associated with fragile sites.
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Ben Moran @ben-moran.bsky.social · 25/08/2026
Hybrid zones are increasingly common; to what extent are human impacts on the environment the cause? We used pop gen, water chemistry, GIS, and ecotoxicology to explore the causes of hybridization in swordtails. With @mollyschumer.bsky.social, now out in Current Biology! www.cell.com/current-biol...
cell.com
Increased rates of hybridization in swordtails are associated with water pollution
Anthropogenic disturbance can drive hybridization by altering pre-mating reproductive barriers. Moran et al. pair population genomic surveys with water chemistry and GIS data to show that human develo...
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Jonathan Pritchard @jkpritch.bsky.social · 09/08/2026
So, I've started a substack. I'll be writing about biology, but my first posts are about applying statistical methods to one of my hobbies: track fandom. In the first posts I describe the Pareto trade-off between a fast overall speed and finishing speed: jkpritchard.substack.com/p/greatest-1...
jkpritchard.substack.com
Greatest 1500m races? Fast times vs fast finishes, and the Pareto Frontier.
A statistical analysis of how overall race speed relates to finishing speed.
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Adam Phillippy @aphillippy.bsky.social · 06/08/2026
For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]
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Jeff Groh @jeffgroh.bsky.social · 28/07/2026
Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...
pnas.org
Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS
In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...
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Quentin Bacquelé @quentinbacquele.bsky.social · 23/07/2026
1/ The world's songbirds sing in just 8 basic sounds. And where a bird lives decides which ones it uses. My first PhD paper is out now in @science.org (www.science.org/doi/10.1126/science.aee6239) Here is what we found:
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Joana Meier @joanameier.bsky.social · 23/07/2026
Very excited to share our new manuscript by Arif Maulana @arf-mln.bsky.social on 338 beetle genomes. It shows how beetle genomes have evolved and how this compares to fly and Lepidoptera genome evolution. It was a great pleasure to collaborate with @kamilsjaron.bsky.social and his team on this.
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Emília Santos @emiliapsantos.bsky.social · 14/07/2026
🎨 job alert 🐠 Come join us! We have two positions open! These are part of our @erc.europa.eu funded project on the mechanisms underpinning convergence of colour patterns in cichlid fishes! Closing date: 16th August. Postdoc: www.cam.ac.uk/jobs/researc... Technician: www.cam.ac.uk/jobs/researc...
static.klipy.com
Callipterus Cichlid Collecting Shell
ALT: Callipterus Cichlid Collecting Shell
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 29/06/2026
The evolution of structural variation across 500 million years of vertebrate evolution www.biorxiv.org/content/10.64898/20…
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Lyle Given @lagiven.bsky.social · 09/06/2026
Big thanks to @tododge.bsky.social and @mollyschumer.bsky.social for their invaluable mentorship!! I’ll also be presenting a poster on this work at PEQG this Thursday (8:30-10pm, PgmNr 284T)
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Molly Schumer @mollyschumer.bsky.social · 09/06/2026
Exciting new work from the lab led by @lagiven.bsky.social & co-advised by @tododge.bsky.social mapping pigmentation variation in the swordtail X. nezahualcoyotl! Spotting variation is linked to xmrk but embedded in complex genomic regions that Tris & Lyle tackled with UL nanopore: shorturl.at/Ljw1z
shorturl.at
Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtail Xiphophorus nezahualcoyotl
Sex-linked traits are widespread, but their genetic architecture has been challenging to characterize, due in part to the repetitive and structurally complex nature of sex chromosomes. In swordtails a...
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Tris Dodge @tododge.bsky.social · 09/06/2026
Excited to share new work on two sex-linked pigment traits in Xiphophorus! This project was led by undergrad @lagiven.bsky.social, who’s worked with me for the last 3(!) years. www.biorxiv.org/content/10.6...
biorxiv.org
Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtail Xiphophorus nezahualcoyotl
Sex-linked traits are widespread, but their genetic architecture has been challenging to characterize, due in part to the repetitive and structurally complex nature of sex chromosomes. In swordtails a...
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Joana L. Rocha @joanocha.bsky.social · 08/06/2026
We are excited to share our pan-pangenome paper! This is a long time coming work of my postdoc with the incredible @psudmant.bsky.social, and a stellar group of people! I hope you enjoy reading it! And I am excited to talk more more about it this week at #PEQG26!! www.biorxiv.org/content/10.6...
biorxiv.org
A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos
Complete, haplotype-resolved genome assemblies have provided unprecedented insight into the evolution of structurally complex, rapidly evolving regions of human genomes; however, population-scale pang...
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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.
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Tris Dodge @tododge.bsky.social · 19/05/2026
Thrilled to present my dissertation research at the Hamilton Symposium! We used approaches including GWAS, long-read sequencing, phylogenetic methods, and behavior experiments to uncover the genetic basis and evolutionary history of a shared polymorphism. Can’t wait to share what we’ve learned!
Picture of three diverged Xiphophorus species that display the false gravid spot, a sexual mimicry polymorphism that allows males to mimic females.
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Kelsie Hunnicutt @kelsiehunnicutt.bsky.social · 12/05/2026
Thrilled that our new review article on animal hybridization is now up on EcoEvoRxiv! 🎉 Working on this review with @mollyschumer.bsky.social was a blast, and it was such a wonderful opportunity to catch up on all the amazing work in animal hybridization over the last few years!
A world map showing the distribution of species studied in hybridization research
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Scott V. Edwards @scottvedwards.bsky.social · 22/04/2026
Ver excited to share my just-published Darwin Review with @lh3lh3.bsky.social on population-scale long-read sequencing! royalsocietypublishing.org/rspb/article...
royalsocietypublishing.org
Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics
Abstract. Population-scale long-read DNA sequencing (PLRS) is rapidly reshaping our understanding of genomic variation in humans and non-model species. In
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Dr. Brendan "Doesn't-go-to-Ravenholm" Pinto @drpintothe2nd.bsky.social · 04/04/2026
Happy to announce the alpha release of the SCINKD3! SCINKD3 is an extension of SCINKD streamlines the use of WGS data from multiple individuals to identify sex chromosomes. In testing, its shown to be robust in many cases with as few as 4 individuals. github.com/DrPintoThe2n...
github.com
GitHub - DrPintoThe2nd/SCINKD3: development repo of SCINKD (v3)
development repo of SCINKD (v3). Contribute to DrPintoThe2nd/SCINKD3 development by creating an account on GitHub.
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Heng Li @lh3lh3.bsky.social · 23/03/2026
Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.
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Megan Dennis @mydennis.bsky.social · 17/03/2026
Excited so share our newest study using a single-library HiFi-CiFi approach to generate chromosome-scale diploid assemblies of two vole genomes, identifying putative drivers of divergent pair-bonding behavior, namely a prairie-vole-specific duplication of Avpr1a gene, led by @mabuelanin.bsky.social
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James Hemker @jahemker.bsky.social · 11/03/2026
Proud that this work is now published! We hope it helps orient future #Nanopore long-read sequencing studies hunting for structural variants Also really happy to share eight new high-coverage (>100x) long-read read pools and assemblies with the #Drosophila community! doi.org/10.1093/g3jo...
doi.org
Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore
Abstract. The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of popul
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Mitchell R. Vollger @mrvollger.bsky.social · 12/01/2026
I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt: employment.utah.edu/salt-lake-ci...
employment.utah.edu
Jobs | University of Utah
Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...
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Victoria B. Grant @victoriabgrant.bsky.social · 11/01/2026
Excited to join PAG this year! Tomorrow (01/11) I will be sharing my work on black-footed cat genomics! Stop by the "Wildlife Genomics" session @ 8:55 am in Pacific F-G to learn about Africa's smallest cat
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Gabe Preising @gpreising.bsky.social · 10/01/2026
I'll be presenting my work tomorrow morning at #PAG33! Stop by Pacific C (Comparative Genomics - Animals) @9:16am to learn about structural variation of swordtail Y-chromosomes and alternative reproductive tactics.
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Tris Dodge @tododge.bsky.social · 09/01/2026
Excited to present at #PAG33 on the dynamic evolution of a balanced polymorphism. We've uncovered unexpected patterns using long-read sequencing and other fun methods. Talk: Saturday @8:40am in Pacific C (Comparative Genomics - Animals) Poster: Monday @10-11:30am in Golden State Ballroom (P216)
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Glennis Logsdon @glennislogsdon.bsky.social · 16/12/2025
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
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Filip Ruzicka @filipruzicka.bsky.social · 14/11/2025
Modestly, we decided to review a century's worth of theories of balancing selection :) onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
A century of theories of balancing selection
Traits that affect organismal fitness are often highly genetically variable. This genetic variation is vital for populations to adapt to their environments, but it is also surprising given that natur...
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Tris Dodge @tododge.bsky.social · 12/11/2025
Beautiful work by @nadiahaghani.bsky.social and @mollyschumer.bsky.social on perhaps the most charismatic coloration trait in swordtails and platys!
A Xiphophorus evelynae male with the iridescent "sparkle" trait
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Megan Dennis @mydennis.bsky.social · 07/10/2025
Happy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.
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Heng Li @lh3lh3.bsky.social · 30/09/2025
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
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Rachel Moran @rachelmoran.bsky.social · 04/09/2025
First pop gen paper from our lab! We find repeated evolutionary turn over of sex chromosomes in darters contributes to reproductive isolation. Turnover may be an escape hatch to resolve mitonuclear conflict & neo sex chromosomes evolved via a rare recessive mutation. www.biorxiv.org/content/10.1...
Top left: Results of genome-wide association study (GWAS) for sex in E. caeruleum, E. radiosum, and E. spectabile showing sex chromosome turnover has occurred repeatedly. Top right: Phylogeny showing sex chromosome turnover in darters and non-darter percids. Chromosome 9 is the putative ancestral sex chromosome, shared by Perca flavescens and multiple members of the orangethroat darter complex (e.g., E. spectabile, E. pulchellum). Bottom: Schematic depicting repeated turnover of sex chromosomes as a mechanism to resolve mitonuclear conflict and promote speciation.
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Peter Sudmant @psudmant.bsky.social · 13/08/2025
The Sudmant lab at UC Berkeley is seeking a postdoc to work on a fully funded NIH project to understand differences in DNA repair and somatic mutation across the primate tree of life. Please spread widely to those who may be interested aprecruit.berkeley.edu/JPF05052
aprecruit.berkeley.edu
Postdoctoral Scholar – Genomics, Aging, Somatic Mutation, Structural Variation, Evolution , Cancer – Integrative Biology
University of California, Berkeley is hiring. Apply now!
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Molly Schumer @mollyschumer.bsky.social · 21/07/2025
If you're attending #SMBE2025 check out graduate student @tododge.bsky.social 's talk at 11:30 am tomorrow (8:30 pacific time tonight if you're watching remotely). It's a wild ride with lots of complex structural variation, balancing selection, and introgression!
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Tris Dodge @tododge.bsky.social · 21/07/2025
Excited to talk about balancing selection, hybridization, and independent evolution at the #SMBE2025 hybridization & introgression symposium! Symposium 14: Day 3, Room 2 @ 11:30am Beijing Time
Xiphophorus fish species displaying a false gravid spot
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Melissa Wilson @sexchrlab.bsky.social · 11/07/2025
🚨Preprint🚨 Sex chromosome identification & genome curation from a single individual with SCINKD www.biorxiv.org/content/10.1... Incredible work led by @drpintothe2nd.bsky.social in collaboration w/ @drsimonegable.bsky.social @stuartvnielsen.bsky.social @tonygamble.bsky.social SE Keating & CH Smith
Graphical overview of the biological foundations of the proposed approach. Application of SCINKD to identify XY chromosomes in the Christmas island skinkApplication of SCINKD to identify previously unannotated sex chromosomes in the Lesser electric ray.
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Tris Dodge @tododge.bsky.social · 01/07/2025
Please share with early career researchers interested in pursuing a PhD! Our goal is to make the application process more transparent with info sessions and 1:1 mentorship.
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Judith Mank @judithmank.bsky.social · 01/07/2025
📣📣📣 So pleased to see @vdbijl.bsky.social's stunning analysis of the inheritance and genetics of guppy color diversity out today @natecoevo.nature.com! Deep learning reveals the complex genetic architecture of male guppy colouration. www.nature.com/articles/s41...
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Ben Moran @ben-moran.bsky.social · 01/05/2025
1/9 Excited to share the preprint for the second half of my PhD with @mollyschumer.bsky.social: Connecting human environmental impacts to hybridization in swordtail fish through genomics, GIS, water chemistry, and histology. Thread below! #SciSky www.biorxiv.org/content/10.1...
biorxiv.org
Increased rates of hybridization in swordtail fish are associated with water pollution
Biodiversity loss can occur when disturbance compromises the reproductive barriers between species, causing them to collapse into a single population through hybridization. Recent research has documen...
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Tris Dodge @tododge.bsky.social · 19/04/2025
Already seeing big improvements by combining PacBio and ONT Ultralong reads!
Two plots of swordtail genome assemblies generated with PacBio HiFi only and HiFi plus ONT UL data. Black dots represent dots and red dots represent telomeres. The HiFi-only assembly has multiple gaps per chromosome, while the HiFi plus ONT UL assembly has only 2 gaps and is missing only 3 telomeres
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Arnaud Martin @evolvwing.bsky.social · 14/04/2025
Awesome new paper by @lucalivraghi.bsky.social et al. doi.org/10.1016/j.cu... in @currentbiology.bsky.social on the evo-devo of a butterfly color variation enjoy the show!
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Adam Phillippy @aphillippy.bsky.social · 09/04/2025
A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...
A phylogeny of the 7 ape genomes that have now been completed from "T2T", with Homer Simpson representing mankind.
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 10/03/2025
Call for Papers! Special Issue: Functional and Adaptive Effects of Genomic Structural Variation in @heredityjournal.bsky.social 📅 Submission Deadline Extended: 1st April 2025 Guest Editors: @ellenleffler.bsky.social, @mydennis.bsky.social, Omer Gokcumen, and myself www.nature.com/collections/...
nature.com
Special Issue: Functional and Adaptive Effects of Genomic Structural Variation
See more information on the new Heredity special issue on functional and adaptive effects of genomic structural variation.
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Parichy Lab | Dave Parichy @dparichy.bsky.social · 18/02/2025
New NIH funded research from our group now out. We are interested in development and evolution of cell types and adult phenotypes. In this paper, postdoc Dylan Huang and collaborators asked how a pigmentary ornament of bright white cells develops on the fin of zebrafish. www.pnas.org/doi/10.1073/...
zebrafish pigment cells
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