iiinova — where your digital self keeps evolving

Ellen Leffler @ellenleffler.bsky.social · 30/09/2026

My department at University of Utah is recruiting new faculty, with "Human" and "Genetics" broadly defined. It is a fantastic place to start a lab, with collaboration, creativity and conviviality encouraged. Applications due Oct 16. Please share and apply! utah.peopleadmin.com/postings/208...

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Ellen Leffler @ellenleffler.bsky.social · 30/09/2026

You can download the dataset (datadryad.org/dataset/doi:...), search it on our Rshiny app (lefflerlab.chpc.utah.edu/erc_plasmodi...), and *hopefully soon* find it on plasmoDB. Please also feel free to reach out with any questions including on interpretation!

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Ellen Leffler @ellenleffler.bsky.social · 30/09/2026

We uncover and functionally validate a new connection between a relatively uncharacterized protein (PF3D7_0811600, aka MAP1) and the RhopH complex. We hope others will look up their Plasmodium proteins of interest and it can help prioritize and discover new interactions!

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Ellen Leffler @ellenleffler.bsky.social · 30/09/2026

There are lots of Plasmodium genes with no annotation, no known function, and/or no close ortholog in other model species. Evolutionary rate covariation gives another clue to help infer functional connections between proteins and integrate with candidates from molecular screens.

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Ellen Leffler @ellenleffler.bsky.social · 30/09/2026

Functionally related proteins tend to show similar shifts in evolutionary constraint over a phylogeny, captured as a correlation in relative evolutionary rates. In Plasmodium, we calculated ERC between every pair of proteins and show that known pathways and complexes tend to have high ERC.

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Ellen Leffler @ellenleffler.bsky.social · 10/07/2026

This would be a good fit for someone coming out of undergrad with a biology background and basic bioinformatics skills they want to build on by applying to some interesting host-parasite genomic/transcriptomic data.

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Ellen Leffler @ellenleffler.bsky.social · 10/07/2026

Job opening: I'm looking for a lab tech primarily supporting ongoing projects and running computational analyses for the lab. Apply here and reach out with questions! utah.peopleadmin.com/postings/205...

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Reposted by Ellen Leffler

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 03/05/2026

A deserved highlight from World Malaria Day on the fantastic host parasite conflict research from @ellenleffler.bsky.social's lab!

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Reposted by Ellen Leffler

James Gagnon @james-gagnon.bsky.social · 29/04/2026

Applications due tomorrow!

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

Nonetheless, it is protective against this infection and so could have contributed to a historically lower P. vivax prevalence in the southern Arabian peninsula than nearby countries with lower Duffy null allele frequency. 11/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

Duffy negativity is associated with neutropenia and potentially other phenotypes and so we question whether P. vivax malaria is truly the driving selective pressure across such different environmental contexts... 10/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

Finally, we reflected on the multiple, consistent findings of strong selection for this allele in different African-admixed populations that others have reported (e.g., Cape Verde, Madagascar, Pakistan, Sudan). 9/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

We think this makes sense – as soon as the Duffy negative allele was introduced, it appears to have spread. We did not see any signal of enrichment for African ancestry surrounding loci that have been associated with protection from P. falciparum malaria. 8/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

Oman has a long history of interaction with East Africa, and we inferred a two-pulse model of admixture, 5 and 59 generations ago. The haplotypes surrounding the Duffy negative allele are short – much more consistent with an older introduction. 7/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

Mostly this was due to the same RBC-specific enhancer mutation that is common across Africa, and the locus had a strong increase in local African ancestry to 78% (vs. 11% genome-wide). We also found a null frameshift allele that contributes to Duffy negativity specifically in the Middle East. 6/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

With funding from the Omani Research Council (and later NIH to my group), we performed paired blood group serology and whole genome sequencing. Indeed, we confirmed that absence of Duffy antigen was very common, with 87/100 lacking this important receptor for P. vivax on their RBCs. 5/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

We wondered how admixture and selective pressure from malaria played a role. Some blood group alleles are associated with protection from P. vivax malaria, others with P. falciparum malaria, both of which have been present in Oman (though it is now malaria-free). 4/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

Arwa noted that in her studies of blood group antigens in Oman, some had more similar frequencies to African populations and some to European populations. 3/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

We report analyses of whole genome sequence data from 100 Omani blood donors. This project stemmed from a conversation with Dr. Arwa Al-Riyami, a hematologist at Sultan Qaboos University in Muscat, at the International Society for Blood Transfusion meeting in Toronto in 2018. 2/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

So pleased to share that our paper (led by Paige Haffener and in collaboration with @drriyamia.bsky.social) on genomic variation in Oman is now published in AJHG! www.cell.com/ajhg/fulltex... 1/n

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Ellen Leffler @ellenleffler.bsky.social · 24/03/2026

We've launched a department Trainee Emergency Fund, to help support EVERYONE BELONGING IN SCIENCE by meeting urgent financial needs of students and postdocs. Every gift will be matched, up to $1,000, by Nels Elde. Click to see a message from Aaron Quinlan and to donate! www.givecampus.com/s/w46xg1

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Reposted by Ellen Leffler

AmLarracuente @amlarracuente.bsky.social · 29/10/2025

Come be our colleague! The University of Rochester is hiring a TT Assistant Professor in evolutionary genetics and genomics: apply.interfolio.com/173431.

apply.interfolio.com

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

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Ellen Leffler @ellenleffler.bsky.social · 18/06/2025

Thanks to a constructive peer review, the published paper in PLoS Pathogens is stronger than the preprint, so thanks to the editor and reviewers!

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Ellen Leffler @ellenleffler.bsky.social · 18/06/2025

We also identify genes with high SNP density, including genes in the Hep1 and Hep2 gene families, which are unique to Hepatocystis. This might suggest they are under selection for immune evasion, despite Hepatocystis lacking blood stage replication.

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Ellen Leffler @ellenleffler.bsky.social · 18/06/2025

This gave us low-coverage whole-genome sequencing data for Hepatocystis from baboons and five species of Chlorocebus monkeys-- and so a first look at genetic variation and population structure genome-wide. There is support for substructure by host species, which was not as clear from mtDNA only.

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Ellen Leffler @ellenleffler.bsky.social · 18/06/2025

Congrats to the lab! We were parasites of parasite data, and recovered DNA sequences from Hepatocystis (a close relative of human malaria parasites) from 37 wild non-human primates originally sequenced to look at the host genome, whose blood happened to be sampled while infected. shorturl.at/KluV8

shorturl.at

Phylogenetics and genomic variation of Hepatocystis isolated from shotgun sequencing of wild primate hosts

Author summary Non-human primates are hosts to many species of Plasmodium, the parasites that cause malaria, and a closely related group of parasites called Hepatocystis. However, due to restrictions ...

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Ellen Leffler @ellenleffler.bsky.social · 18/06/2025

Thanks to a constructive peer review, the published paper in PLoS Pathogens is stronger than the preprint, so thanks to the editor and reviewers!

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Ellen Leffler @ellenleffler.bsky.social · 18/06/2025

We also identify genes with high SNP density, including genes in the Hep1 and Hep2 gene familiels, which are unique to Hepatocystis. This might suggest they are under selection for immune evasion, despite Hepatocystis lacking blood stage replication

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Ellen Leffler @ellenleffler.bsky.social · 18/06/2025

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Ellen Leffler @ellenleffler.bsky.social · 28/04/2025

Postdocs: Human Genetics at Utah will be hosting our annual Rising Stars in Genetics and Genomics Symposium in Sept. Apply here: shorturl.at/wBMg2 There will be sessions on developmental, evolutionary and disease genetics. A chance be invited to SLC to network here and with peers! Please share.

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Reposted by Ellen Leffler

Na Cai @caina89.bsky.social · 05/12/2024

Quantgen GRC (16-21 Feb 2025) updates: we are now 75% subscribed! Deadline: 19 Jan 2025 BUT: We will pick talks from submitted abstracts 16 Dec and aim to send decisions before Xmas. So submit your abstracts now (even if not perfect - editable after submission)! www.grc.org/quantitative...

grc.org

2025 Quantitative Genetics and Genomics Conference GRC

The 2025 Gordon Research Conference on Quantitative Genetics and Genomics will be held in Lucca (Barga), Lucca Italy. Apply today to reserve your spot.

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Ellen Leffler @ellenleffler.bsky.social · 06/12/2023

Recently learned about preLights -- and happy to support Alejandra (postdoc in the lab) as a contributor to highlight and generate discussion around preprints in evolutionary biology! t.co/oaiz287N4a

t.co

A direct experimental test of Ohno’s hypothesis - preLights

An experimental system to test hypotheses on the evolution of gene duplication. Was S. Ohno right?

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