Annie G West

SPAAM Newsletter #7 Hello from the SPAAM Steering Committee!

Dear SPAAM Community members,
We are excited to share with you the latest SPAAM Newsletter!
Inside, you’ll find:
- updates on events and workshops
- funding/research opportunities
- latest publications
We hope you enjoy this edition!
www.spaam-community.org/assets/media...

New kākāpō paper out! PhD student Natalie Ayriss has done fabulous work analysing RNA-seq data of cloacal swabs obtained from adult and juvenile kākāpō to explore the virome and antibiotic resistance in the microbiome of t...

anniegwest.wixsite.com/anniegwest/p...

The oral microbiome of King Richard III of England Metagenomic investigation of archaeological dental calculus has provided insights into the changing oral health, disease, and diet of past human societies, but little is known about the oral microbiot...

Great News!

The Ricardians are one step closer to recreating Richard III’s unique brand of halitosis!

🏺

www.biorxiv.org/content/10.1...

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...

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/...

Ancient host-associated microbes obtained from mammoth remains Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we a…

What can a million-year-old mammoth teach us about microbes? 🦠 From pathogens to commensals, this new study reconstructs the oldest known host-associated microbial DNA. #MetagenomicsMonday #SPAAM #aDNA
doi.org/10.1016/j.ce...

The Earth Hologenome Initiative: Data Release 1 AbstractBackground. The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from

📣Another publication from our amazing researchers and colleagues: The Earth Hologenome Initiative: Data Release 1

@ehologenome.bsky.social 🦠💡

Find it in
@gigascience.bsky.social
👇

and how this aligned with other MAGs obtained for these genera worldwide :)

As both lineages were initially described and isolated from freshwater environments, this natural population represented a great opportunity to explore the underlying genetic mechanisms that facilitated Aquiluna's transition and adaptation to the brackish (salty) estuarine environment...

The background behind this particular paper is that we found clear niche differentiation of two Actinomycetota sister lineages (Aquiluna and Rhodoluna) across the saline divide of the Waiwera River estuary...

New publication! One of the seminal projects from my Genomics Aotearoa Postdoc position with Associate Professor Kim Handley is now published online at ISMEJ Communications. The background behind this particular paper is that we found clear niche differentiation of two Actinomycetota sister lineages (Aquiluna and Rhodoluna) across the saline divide of the Waiwera River estuary. As both lineages were initially described and isolated from freshwater environments, this natural population represented a great opportu

One of the seminal projects from my Genomics Aotearoa Postdoc position with Associate Professor Kim Handley is now published online at @isme-microbes.bsky.social Communications!! 🥳🦠 "Salinity-driven niche differentiation within the aquatic Luna-1 subcluster"

In the thick of the 2025 @femsmicro.org Postdoc Summer School in Ohrid, meeting amazing colleagues and ready for a week of solid learning

ESEB2025 Barcelona This was my very first ESEB conference, and as a microbial ecologist I was thoroughly impressed with the breadth of research and fields showcased this year! The Guschanksi group was (almost) out in fu...

Trying to get better at updating my new website, so here is the latest blog post! #eseb2025
anniegwest.wixsite.com/anniegwest/p...

Relatable #eseb2025

#eseb2025

If you're interested in bears, metagenomics, or struggling to understand a kiwi accent, come sit in on my @eseb2025.bsky.social ESEB Barcelona talk Monday morning at 11:30 in room 116 :D

Thoroughly enjoying the @eventswcs.bsky.social K-mers for Biodiversity workshop this week, complete with extensive k-mer history, hands-on practical exercises, showcasing the latest software, and meeting people from all over the world. What a blast! (pun intended...)

Two rangers doing a health check on a kākāpō at night. Credit: Petrus Hedman.

Our team on Te Kākahu/Chalky Island have recaptured male #kakapo Te Awa, who's been missing for 6 years having dropped his transmitter. He was in great condition and it's good to have track of him again with a possible breeding season next year. 📷: Petrus Hedman #conservation #parrots #birds

Working in animal #aDNA? Present your research at our first AaRConference!

PopGen Seminar Series Summer Term 2025 04.03.25 – Lutz Becks (Univ. of Konstanz, DE)
The evolutionary dynamics of novel endosymbiosis. 11.03.25 – Ilkka Kronholm (Univ. of Jyväskylä, FI)
How chromatin structure influences genetic and epigenetic variation. 18.03.25 – Katja Hoedjes (Vrije Univ. Amsterdam, NL)
Understanding functional impact of genetic variation on complex traits at a single nucleotide resolution. 25.03.25 – Sophie Armitage (Freie Univ. of Berlin, DE)
Evolutionary ecology of host-pathogen interactions. 01.04.25 – Matthew Rockman (New York Univ., US)
Developmental evolution is a population-genetics problem. 08.04.25 – Wen-Juan Ma (Vrije Univ. Brussels, BE)
The evolution of sex chromosomes and sex determination in frogs. 15.04.25 – Almorò Scarpa (Vetmeduni, AT)
Two centuries of transposable element invasions in Drosophila melanogaster 22.04.25 – Julia Kreiner (Univ. of Chicago, US)
The mode and tempo of genomic adaptation to contemporary agriculture. 29.04.25 – Martin Kaltenpoth (Max Planck Inst. for Chemical Ecology, DE)
Microbial symbionts as sources of evolutionary innovations in beetles. 06.05.25 – Luisa Pallares (Friedrich Miescher Laboratory, DE)
Phenotypic robustness across the genotype-phenotype map, from genes to environment and back. 13.05.25 – Diana Rennison (Univ. of Calif., San Diego, US)
Understanding the predictability of evolutionary trajectories using threespine stickleback.

20.05.25 – Filipa Sousa (Univ. of Vienna, AT)
Bioenergetics Evolution: The link between Earth’s and Life’s history. 27.05.25 – Yun Song (Univ. of California, Berkeley, US)
Learning and applying complex probability distributions over biological sequences. 03.06.25 – April Wei (Cornell Univ., US)
Enabling efficient analysis of biobank-scale data with genotype representation graphs. ALT TEXT OUT OF SPACE, GO TO https://www.popgen-vienna.at/news/seminars/

The PopGen Vienna Seminar series schedule is ready for the next term (Mar-Jun). It's jam-packed with fantastic speakers in #evolution, #genetics, #genomics, #popgen, and more! Details and streaming link signup can be found on our website www.popgen-vienna.at/news/seminars/

3-y postdoc position in (meta)Genomics of Population Declines elxw.fa.em3.oraclecloud.com/hcmUI/Candid.... If you have experience with low-coverage genomic data, care about biodiversity loss, want to understand host-microbiomes interactions, this post is for you! #museomics #ancientDNA #mammals