💡 Bonus: Open Snakemake pipelines for both simulation and imputation are provided:
- github.com/vibaotram/si...
- github.com/vibaotram/im...

Feel free to test and optimize imputation strategies for your own datasets before committing to large-scale LCS projects.

💥 Downstream impact:
- PopGen analyses (relatedness, population structure) were congruent with imputation accuracy and depend on genetic relatedness.
- Inbreeding coefficient estimates were more sensitive to imputation.
- Demographic analysis on imputed data showed similar results across the tools.

🔑 Choosing your imputation tool:
- All tools worked well in highly related populations.
- Accuracy varied in populations with low relatedness, but GLIMPSE2 & QUILT2 generally outperformed the other tools.
- STITCH is useful when no reference panel exists but results in some missing data.

👩🏻‍💻 We tested 5️⃣ imputation methods (GLIMPSE2, GeneImp, QUILT2, STITCH, Beagle5.4), simulated realistic populations with different genetic structures, and applied the methods to data from 283 wild hihi (stitchbird) 🧬.

We explored that in this new study in Molecular Ecology Resources 🔎

onlinelibrary.wiley.com/doi/10.1111/...

@vbtram.bsky.social
@huizhentan.bsky.social
@katarinastuart.bsky.social
@annasanture.bsky.social

Low-coverage sequencing (LCS) + genotype imputation is a cost-effective approach to genotype hundreds of samples at a full-genome level. But how do different imputation tools perform across populations with varying relatedness and inbreeding?

Excited to say my poster on our recent work on the humpback song of the Cook Islands placed second at the University’s faculty of science postgraduate poster competition! 🐋 🎶

Fabulous presentation to Forest & Bird Youth Auckland by @huizhentan.bsky.social on conservation management and genetic research for hihi, a taonga (precious) threatened bird species in Aotearoa New Zealand. VIP treatment for a very special bird!

Thank you to my amazing supervisor @annasanture.bsky.social and awesome team of co-authors: @katarinastuart.bsky.social, @vbtram.bsky.social, Annabel Whibley, Sarah Bailey, @pbrekke.bsky.social #WomenInSTEM

We found that heterozygosity estimates and the site frequency spectrum using imputed genotypes were more sensitive to filtering and SNP density. Runs of homozygosity (ROH) using #RZooRoH were relatively robust, perhaps because imputed genotype likelihoods were used as input.

We used Beagle v5.4 to test various imputation parameters and input data structures. We achieved mean r² > 0.95 in most tests except at very low target SNP densities and reference panel sizes. Surprisingly, adding a #linkagemap (Tan et al., 2024) didn’t improve accuracy!

Genomic imputation can boost dataset quality and benefit research on wild populations. In hihi, we found high #imputation accuracies despite a small reference panel of high-fecundity individuals. Imputation improves downstream #ConservationGenomics analyses. onlinelibrary.wiley.com/doi/10.1111/...

The magic number ✨ 11,131 ✨ A unified global bird checklist: www.avilist.org/checklist/v2... Congratulations Frank and colleagues!

Legit there’s nothing less dignified than weighing a baby parrot (regent parrot bum in a keep cup)🪶

Abstract submission and registration for🧬GSA’s 2025 conference🧬is now open!
The conference will be held at Waipapa Taumata Rau - The University of Auckland in Aotearoa - New Zealand 🥝 from 7-10 July 2025.

🚩Important dates
Abstracts due- April 7
Early bird registration ends- May 11

www.gsa-2025.com

The first paper of your PhD is always so exciting! 🤩 An all-#Galbatross effort, "A focus on females can improve science and conservation!" See press release (www.audubon.org/news/researc...) and the study here: onlinelibrary.wiley.com/doi/10.1111/...! #FemaleBirds #FemaleBirdDay

Genetic diversity has declined within two-thirds of more than 600 species over the past three decades, according to research published in Nature. The findings highlight the need for conservation efforts to prevent genetic diversity loss. https://go.nature.com/42EpVo5 🧪

"when the last individual of a race of living beings breathes no more, another heaven and another earth must pass before such a one can be again" Last of the Curlews: Part II bou.org.uk/blog-berryma... via
@alexjb497

That’s a wrap for the first chapter of the PhD! Very stoked also to see another illustration of mine in print (Fig. 1). A biiiiig thank you to my supervisor, Anna Santure, for her dedicated guidance and support, and to my co-authors for their helpful insights.

Linkage map construction from large SNP panels is efficient. Future comparative analyses can elucidate broad patterns in heterochiasmy – although systematic differences in results across programs should be accounted for. Our map also improved our genome assembly! #linkagemap

We found that male hihi recombine more. Heterochiasmy in the hihi is relatively high and seem to be driven by micro-chromosomes. Enrichment of genes in regions of extreme heterochiasmy suggests that it could have functional implications. #heterochiasmy #birds #hihi #stitchbird

Recombination has a major role in evolution. Sex-differences in recombination (yes!!) – heterochiasmy – are common but not well understood. Our new paper in @HeredityJournal examines heterochiasmy in the hihi/stitchbird using a high-density linkage map.🧬 doi.org/10.1038/s414...

🎉 NEW PAPER IN PNAS 🎉

We estimated the proportion of species that have gone extinct in Singapore, including those that went extinct before we had a chance to discover them.

www.pnas.org/doi/10.1073/...