New study 🧬 Inbreeding depression is a concern in small populations, and evaluating its genomic proxies is important for #ConservationGenomics. In hihi, genome-wide homozygosity best predicts lifetime reproductive success, compared to genetic load and FROH. Publication: doi.org/10.1111/eva.... 1/3

Genome‐Wide Homozygosity Predicts Inbreeding Depression in the Hihi/Stitchbird (Notiomystis cincta) Better Than Realised Load

Population declines result in increasingly small populations, which often experience an increase in inbreeding. Inbreeding may be negatively associated with fitness traits like survival and reproduct...

doi.org

Whole-genome data from yellow-eyed penguins (hoiho) identify three lineages with high geographical and genomic divergence, and candidate gene variants associated with differential susceptibility to neonatal respiratory distress syndrome, according to a paper in Nature Ecology & Evolution. 🌍🧬🧪

Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome - Nature Ecology & Evolution

Whole-genome data from 249 yellow-eyed penguins (hoiho) identify three lineages with high geographical and genomic divergence, and candidate gene variants associated with differential susceptibility to neonatal respiratory distress syndrome.

go.nature.com

Now out in ME: dx.doi.org/10.1111/mec.... Empirical comparison of WGS and RADseq selection scans shows missed signals and false outliers in RADseq selection scans resulting from population specific allelic dropout @katarinastuart.bsky.social @lee-rollins.bsky.social @annasanture.bsky.social

Missing or Mis‐Telling the Story? Trade‐Offs for Restriction‐Site Associated Compared to Whole Genome Sequencing

Researchers must navigate several trade-offs when deciding which population sequencing method to use. The decision between reduced representation approaches and whole genome sequencing (WGS) impacts ...

dx.doi.org

New Zealand’s invasive starlings on the cover of Molecular Ecology! 🐦🧬 This collaborative project unpacks the invasion history of starlings in Aotearoa New Zealand, combining population genomics with historical records of human-mediated translocations. onlinelibrary.wiley.com/doi/10.1111/...

💡 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.

GitHub - vibaotram/simulation

Contribute to vibaotram/simulation development by creating an account on GitHub.

github.com

💥 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

Assessing Genotype Imputation Methods for Low‐Coverage Sequencing Data in Populations With Differing Relatedness and Inbreeding Levels

Low-coverage sequencing (LCS) followed by genotype imputation has become a cost-efficient approach for obtaining whole-genome SNPs. Several imputation methods for LCS data have been developed over th....

onlinelibrary.wiley.com

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!

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/...

High Imputation Accuracy Can Be Achieved Using a Small Reference Panel in a Natural Population With Low Genetic Diversity

Genotype imputation, the inference of missing genotypes using a reference set of population haplotypes, is a cost-effective tool for improving the quality and quantity of genetic datasets. Imputation...

onlinelibrary.wiley.com

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

In Research, Ignoring Female Birds Harms Scientific Understanding

A new study shows that ecological research often ignores or excludes data on female birds and behavior, resulting in erroneous assumptions on conservation.

audubon.org

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

Last of the Curlews: Part II

LINKED PAPER Global extinction of Slender-billed Curlew (Numenius tenuirostris). Buchanan, G. M., Chapple, B., Berryman, A. J., Crockford, N., Jansen, J. J. F. J., Bond, A. L. 2024. IBIS. DOI: 10.1111...

bou.org.uk

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...

A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta) - Heredity

Heredity - A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta)

doi.org

🎉 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/...