GitHub - DrPintoThe2nd/SCINKD3: development repo of SCINKD (v3) development repo of SCINKD (v3). Contribute to DrPintoThe2nd/SCINKD3 development by creating an account on GitHub.

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...

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.

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

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...

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...

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

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.

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)

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...

Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism The false gravid spot is a sexual mimicry polymorphism that allows males to mimic females. Dodge et al. link the phenotype to structural variation that increases expression of the nearby kitlga gene. ...

Here are three Northern Swordtail genomes where we think LG21 is the sex chrom.

Xiphophorus birchmannni: www.cell.com/current-biol...

X. malinche: www.nature.com/articles/s41...

X. cortezi: journals.plos.org/plosbiology/...

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...

Modestly, we decided to review a century's worth of theories of balancing selection :) onlinelibrary.wiley.com/doi/10.1111/...

Beautiful work by @nadiahaghani.bsky.social and @mollyschumer.bsky.social on perhaps the most charismatic coloration trait in swordtails and platys!

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.

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

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...

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

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!

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

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

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.

📣📣📣 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...

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...

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

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

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

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!

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...

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/...

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/...