Tris Dodge

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.

07.10.2025 02:31 — 👍 30    🔁 13    💬 3    📌 0

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

30.09.2025 02:19 — 👍 75    🔁 27    💬 0    📌 0

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.

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...

04.09.2025 17:32 — 👍 42    🔁 19    💬 2    📌 0

Postdoctoral Scholar – Genomics, Aging, Somatic Mutation, Structural Variation, Evolution , Cancer – Integrative Biology University of California, Berkeley is hiring. Apply now!

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

13.08.2025 04:22 — 👍 54    🔁 55    💬 0    📌 1

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!

21.07.2025 16:38 — 👍 15    🔁 8    💬 0    📌 0

Xiphophorus fish species displaying a false gravid spot

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

21.07.2025 15:28 — 👍 15    🔁 4    💬 0    📌 0

Graphical overview of the biological foundations of the proposed approach.

Application of SCINKD to identify XY chromosomes in the Christmas island skink

Application of SCINKD to identify previously unannotated sex chromosomes in the Lesser electric ray.

🚨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

11.07.2025 12:44 — 👍 45    🔁 24    💬 0    📌 1

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.

01.07.2025 14:51 — 👍 0    🔁 0    💬 0    📌 0

📣📣📣 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...

01.07.2025 13:22 — 👍 40    🔁 12    💬 0    📌 1

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...

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...

01.05.2025 13:15 — 👍 59    🔁 25    💬 2    📌 2

We’ve had success with this hybrid approach, but preliminarily >40x ONT UL alone also seems to get us near T2T. Genome is 720mb. Didn’t collect HiC for this individual and scaffolded to an existing reference

19.04.2025 16:28 — 👍 2    🔁 0    💬 0    📌 0

Black are gaps (contig breaks) and red are telomeres!

19.04.2025 15:03 — 👍 1    🔁 0    💬 1    📌 0

Already seeing big improvements by combining PacBio and ONT Ultralong reads!

19.04.2025 14:19 — 👍 17    🔁 2    💬 1    📌 1

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!

14.04.2025 02:53 — 👍 156    🔁 76    💬 12    📌 8

A phylogeny of the 7 ape genomes that have now been completed from "T2T", with Homer Simpson representing mankind.

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...

09.04.2025 21:31 — 👍 156    🔁 77    💬 5    📌 3

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.

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/...

10.03.2025 16:22 — 👍 5    🔁 5    💬 0    📌 0

zebrafish pigment cells

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/...

18.02.2025 20:59 — 👍 22    🔁 10    💬 1    📌 1

A century of theories of balancing selection Traits that affect organismal fitness are often very genetically variable. This genetic variation is vital for populations to adapt to their environments, but it is also surprising given that nature (...

Finally ready to see the world! Theories of balancing selection - past, present and future: www.biorxiv.org/content/10.1... A true collaborative effort that brought together theoreticians and empiricists, models, data, and fresh perspectives on how balancing selection can shape genetic variation.

14.02.2025 16:49 — 👍 29    🔁 15    💬 2    📌 1

Rising temperatures are not slowing #mosquitoes down... A new study coauthored by Stanford's Lisa Couper and @stanfordwoods.bsky.social Erin Mordecai finds that mosquitoes -- and the diseases they carry -- can adapt to hotter temperatures. Read the study: bit.ly/3PqTNw8

07.01.2025 22:58 — 👍 6    🔁 7    💬 0    📌 2

Science magazine front cover. Picture of a walnut in its opened shell. The text reads "All about timing. Mating type evolution in walnuts and pecans"

graphical abstract: "In Juglans (top left) and Carya, two morphs show complementary temporal separation between male and female flowering (heterodichogamy). Mating types are controlled by two nonhomologous single-locus mechanisms that arose in the common ancestor of each genus, respectively. (Bottom left) Simplified schematic of a putative functional regulatory element at the Juglans locus. (Bottom right) Strong genotypic correlations across the Carya locus indicate a lack of recombination between two colinear haplotypes with similar gene content."

Congrats to @jeffgroh.bsky.social et al on publication of "Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories"

www.science.org/doi/10.1126/...

02.01.2025 21:49 — 👍 189    🔁 70    💬 3    📌 2

Moved here recently and figured I should shamelessly promote our recent paper for my very first post.

16.11.2024 17:01 — 👍 30    🔁 6    💬 0    📌 0