Sign in

Alexander Piper

@apiper.bsky.social
89 followers 212 following 8 posts

Biologist using genes 🧬 and computers 💻 to study evolution and spread of invasive Insect pests. Senior Research Scientist @ Agriculture Victoria. Adjunct Research Fellow @ LaTrobe University 🇦🇺

PostsRepliesMedia
Alexander Piper @apiper.bsky.social · 02/09/2026
New review paper (and first PhD publication!) from my student Lachlan Gretgrix. Check it out if youre interested in high-throughput insect monitoring, measurement, and management in agriculture and beyond academic.oup.com/jee/advance-...
academic.oup.com
Quantitative metabarcoding for invertebrate pest monitoring and management
Abstract. Invertebrate pests pose one of the most significant threats to global agriculture. Trap-based surveillance is widely used to monitor the presence
032
Reposted by Alexander Piper
Darrin T. Schultz @dts.bsky.social · 19/08/2026
Our new paper in Science Advances asks how animals' genomes have changed since their origin from a common ancestor over 600 million years ago, and what patterns in their DNA have arisen in the churn of speciation and extinction. www.science.org/doi/10.1126/...
Five-panel diagram explaining fusion-with-mixing in chromosome evolution. Red and blue represent two different ancestral chromosomes throughout.

A, Fusion-with-mixing: a red chromosome and a blue chromosome fuse into one half-red, half-blue bar. Down the page, successive rows show inversions, drawn as X-shaped crossings between rows, progressively interleaving the two colors until the bottom bar is finely striped. A widening gray wedge labeled Entropy runs alongside an arrow marked Time plus evolution, pointing down.

B, Independent regulation: two separate chromosomes, one red and one blue. In each, a regulatory element, drawn as an oval, acts by an arrow on a gene within its own chromosome only.

C, FWM and novel regulation: on a fused, mixed chromosome, a red gene and a blue gene now sit next to each other across an inversion breakpoint. Red and blue arrows show regulatory elements reaching across it to act on the other chromosome's gene.

D, Regulatory entanglement: an extensively mixed chromosome, finely striped. Below it, a row of alternating red and blue genes is linked by a dense web of crossing curved arrows, so many overlapping regulatory connections that unmixing the chromosome would break them.

E, Emergence of entangled loci: a five-species phylogeny. A red and a blue chromosome fuse at an ancestral node, and helical icons on later branches mark continued mixing. Colored boxes mark four new red-blue regulatory interactions arising after inversions. Species A keeps its two chromosomes separate. In species B through E, the two earliest interactions, cyan boxes 1 and 2, are present in every descendant lineage, while later ones, yellow 3 and magenta 4, appear in fewer.
315055
Reposted by Alexander Piper
Tim Linksvayer @tlinksvayer.bsky.social · 05/08/2026
The signal was driven by a single lineage: the aculeate Hymenoptera (stinging wasps, bees, ants). Outside that lineage, haplodiploid insects did not evolve eusociality faster than diploids. The apparent association between haplodiploidy and eusociality is not a general property across insects. 11/13
estimated transition rates to eusociality when accounting for a lineage specific rate in aculeate haplodiploids.
1153
Reposted by Alexander Piper
Aimee McKinnon @aimeeemac.bsky.social · 02/05/2026
We're #hiring a post doc Research #Scientist to contribute to our exciting new RNAi #biopesticides project! Note the VISA requirements and follow the instructions to apply! 🧪🧫🧬🔬🪲🐛 www.seek.com.au/job/91780432...
seek.com.au
Research Scientist - RNAi Job in Bundoora, Melbourne VIC - SEEK
Research Scientist developing RNA‑based biopesticides, applying dsRNA and RNAi to protect horticultural crops through innovative molecular science.
052
Reposted by Alexander Piper
Ashar Malik @proteinmechanic.bsky.social · 22/10/2025
Announcing @official-smbe.bsky.social Australasian Protein Structural Phylogenetics Meeting in Brisbane Feb 15-18, 2026. FREE registration. Join for exciting talks & workshops at the interface of protein structure, function & evolution. biosig.lab.uq.edu.au/strphy26/ #StrPhy26 @strphy.bsky.social
biosig.lab.uq.edu.au
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
062
Reposted by Alexander Piper
Zamin Iqbal @zaminiqbal.bsky.social · 09/09/2025
Just spotted this paper saying their tree search/genetic algorithm writes better bioinformatics software than SOTA. Does batch correction of scRNAseq, and covid hospitalisation estim. Noth outside my wheelhouse. Does anyone have expertise and energy to look at it? arxiv.org/abs/2509.06503
arxiv.org
An AI system to help scientists write expert-level empirical software
The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert...
3124
Reposted by Alexander Piper
Maxim Greenberg @maxvcg.bsky.social · 03/09/2025
🚨 🐜 is there a Bluesky starter pack for researchers who don’t study ants but who get lightheaded every time there’s an awesome ant paper? CC @mariusw.bsky.social @jrichardalbert.bsky.social www.nature.com/articles/s41...
nature.com
One mother for two species via obligate cross-species cloning in ants - Nature
In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...
1014032
Reposted by Alexander Piper
EvolDir @evoldir.bsky.social · 19/08/2025
Postdoc position available in insect genetics at USDA-ARS, Hilo, HI. Focus on functional genomics in tephritid pests. Applications via Zintellect until filled. More info: www.zintellect.com/Opportunity/Deta… #postdoc
zintellect.com
Zintellect - U.S. Department of Agriculture (USDA) - USDA-ARS Postdoctoral Fellowship in Insect Genetics and Molecular Biology - USDA-ARS-PWA-2025-0071
Zintellect - U.S. Department of Agriculture (USDA) - USDA-ARS Postdoctoral Fellowship in Insect Genetics and Molecular Biology - USDA-ARS-PWA-2025-0071
033
Reposted by Alexander Piper
The Tattooed Professor @schwessinger.bsky.social · 03/08/2025
Our first wheat stripe rust Avr effector story. It is a short one that points to suppressors in this pathosystem while we could not link this Avr effector to a described R gene. www.biorxiv.org/content/10.1...
biorxiv.org
A conserved stripe rust effector elicits variable resistance responses in wheat
Plant resistance (R) and pathogen avirulence (Avr) gene interactions are central to pathogen recognition and disease resistance in crops. However, functional characterisation of Avr effectors in Pucci...
01711
Reposted by Alexander Piper
PLOS Biology @plosbiology.org · 29/05/2025
Commercial isothermal fluorimeters are pricey & unsuitable for field work, limiting their use in low-resource settings. @jenny-molloy.bsky.social &co develop an #open-source, #low-cost, portable isothermal #fluorimeter designed for various biotech applications @plosbiology.org 🧪 plos.io/3FA7Fmn
The shows an exploded view of the qByte device in the foreground, alongside a smartphone displaying output data app, with a fully assembled unit in the background. qByte is an open-source, 8-tube isothermal fluorimeter developed to address these barriers by offering a cost-effective (∼$60), yet production-ready solution. Its compact form factor, along with compatibility with smartphones and laptops for data readout, makes it well-suited for both laboratory and field use.
2105
Reposted by Alexander Piper
Philipp Bayer @philippbayer.bsky.social · 23/05/2025
Excited to announce that we're collaborating with Citizens of the Sea! www.citizensofthesea.org/news/citizen... It's an amazing citizen science effort to equip ocean cruisers, racers, commercial vessels with #eDNA collection devices. So much data from so many vessels and locations!
citizensofthesea.org
Citizens of the Sea partners with Minderoo Foundation — Citizens of the Sea
Citizens of the Sea has been given a significant boost from Minderoo Oceanomics from Western Australia. “We are thrilled to welcome Minderoo to our family of supporters,” says Adele Fitzpatrick, Execu...
093
Reposted by Alexander Piper
Astrid Böhne @astridboehne.bsky.social · 21/05/2025
Happy to share this collaborative effort on recommendations for #genomics of #type specimens academic.oup.com/sysbio/advan...
academic.oup.com
Type genomics: a Framework for integrating Genomic Data into Biodiversity and Taxonomic research
01313
Reposted by Alexander Piper
Thomas L Schmidt @identitybydissent.bsky.social · 08/05/2025
Our new paper on the parallel evolution of insecticide resistance is online now at @elife.bsky.social doi.org/10.7554/eLif... Pest: the two spotted spider mite
052
Alexander Piper @apiper.bsky.social · 28/02/2025
Our group is recruiting 3 PhD students for insect IPM projects in Victoria, Australia 🦘 1- Exploring the genomic basis of virulence in grapevine phylloxera 🍇 2- Optimising sampling for surveillance and diagnostics of grain pests. 🌾 3- Investigating the use of biological control in almond IPM 🐞
110
Reposted by Alexander Piper
Keith Robison @omicsomics.bsky.social · 24/02/2025
Roche SBX preprint out www.biorxiv.org/content/10.1...
biorxiv.org
Sequencing by Expansion (SBX) — a novel, high-throughput single-molecule sequencing technology
Remarkable advances in high-throughput sequencing have enabled major biological discoveries and clinical applications, but achieving wider distribution and use depends critically on further improvemen...
03115
Reposted by Alexander Piper
Jason Munshi-South @urbanevol.bsky.social · 17/02/2025
Immediately assigning this new paper to my pop gen students! Waples publishes some real hits - "What is a population?" is another instant classic onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
The Idiot's Guide to Effective Population Size
This is a reference manual for the elegant, yet hideously complex concept of effective population size (Ne), inspired by a classic, self-published manual of automotive repair ‘for the compleat idiot’...
03014
Reposted by Alexander Piper
coregenomics.bsky.social @coregenomics.bsky.social · 14/02/2025
Hi everyone on Bluesky working in #genomics #NGS. Today is Valentines day. How many of you are more excited about Feb 20th?! Read my new post on Enseqlopedia Roche emerges from the Lazarus pit to take on Illumina enseqlopedia.com/2025/02/roch...
enseqlopedia.com
Roche emerges from the Lazarus pit
Is Roche going to "knock it out of the park" or "jump the shark"? Everyone I know is excited, even if many of them are sceptical, about the Feb 20th webinar and what we will learn about SBX. Alex Dick...
2106
Reposted by Alexander Piper
Brent Emerson @brentcemerson.bsky.social · 06/02/2025
Here are some thoughts and suggestions from me as to how barcoding (particularly of dark taxa at scale) and taxonomy might better come together. doi.org/10.1111/mec.... @biogeneurope.bsky.social
doi.org
Delimiting Species—Prospects and Challenges for DNA Barcoding
Discovering, describing and cataloguing global species diversity remains a fundamental challenge both for biodiversity research and for the management and conservation of biodiversity. Among animals,....
055
Reposted by Alexander Piper
Emi Tanaka @emitanaka.org · 02/01/2025
Want to use your #statistics, ML/AI or #bioinformatics skills to solve problems in #agriculture? We are seeking 3 postdocs (up to 3 years) to join at ANU Biological Data Science Institute as part of Analytics for 🇦🇺 Grains industry by 📅 19 Jan We now also have a (WIP) website! 🌐 anu-aagi.github.io
ANU-AAGI team featuring investigators: Eric Stone, Emi Tanaka, Alan Welsh and Francis Hui
11718
Reposted by Alexander Piper
Raoul Mazhar @cic3r0.bsky.social · 29/01/2025
If your partner complains about a lack of #intimacy: Platynothrus peltifer has gone 20 million years without #sex. With clever genome management (and no dates), this #mite cheats evolution like a pro. 🕷️ #Evolution #Science www.science.org/doi/10.1126/...
science.org
Chromosome-scale genome dynamics reveal signatures of independent haplotype evolution in the ancient asexual mite Platynothrus peltifer
Haplotype independence contributes to genome evolution under ancient asexuality.
064
Reposted by Alexander Piper
Rob Waterhouse @rmwaterhouse.bsky.social · 26/01/2025
#Mosquito #genome chromatin architecture #evolution - extremely long-ranged looping interactions, conserved for ~100 million years www.nature.com/articles/s41...
nature.com
Anopheles mosquitoes reveal new principles of 3D genome organization in insects - Nature Communications
Anopheles mosquitoes are vectors of human malaria, and better understanding of them has implications for public health. Here, the authors apply Hi-C, FISH, RNA-seq, and ChIP-seq techniques to comprehe...
062
Reposted by Alexander Piper
Pam Engelberts @pam-engelberts.bsky.social · 19/12/2024
Excited to share GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities. @sjmcilroy.bsky.social, @benjwoodcroft.bsky.social, @jamesvolmer.bsky.social doi.org/10.21203/rs.... 🧵1/6
doi.org
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities
Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditional FISH has several limitations, including ​​limited p...
42316
Reposted by Alexander Piper
Melanie D. @melulater.bsky.social · 04/01/2025
Biosecurity urges people to report Oriental fruit fly findings - fruit fly found in Papatoetoe. Here's hoping our Biosecurity services can handle this effectively after all the cuts in 2024. www.rnz.co.nz/news/nationa...
rnz.co.nz
Biosecurity urges people to report Oriental fruit fly findings
Controls have now been imposed on the movement of fruit and vegetables in Papatoetoe, Auckland, where an Oriental fruit fly was found yesterday.
32312
Reposted by Alexander Piper
bioRxiv Genomics @biorxiv-genomic.bsky.social · 22/12/2024
The use of iconPCR for 16S library preparation improves data quality and workflow www.biorxiv.org/content/10.1101/202…
041
Reposted by Alexander Piper
Xavier Dallaire @xdallaire.bsky.social · 16/12/2024
New #phylogeography preprint is out, just in time for the holidays! Here we explore glacial lineages, mito-nuclear discordance and local ancestry tract detection using low-coverage WGS (2X), all in Arctic Char of course! 🐟🏔️ @jeansebmoore.bsky.social @michaelmhansen.bsky.social #PopGen
Local ancestry inferred through local PCA. Fig. 5 on the manuscript : Representative case of a low-recombining diverged putative haploblock corresponding to a local PCA outlier region (win8) on LG9 (NC_036849.1). a) Position of the MDS outlier region (red) on the linkage group (above) and standardized PC1 coordinates in PCAs for successive non-overlapping 100-SNP windows inside and around the outlier region (below). Each sample is represented by a line colored according to their haplogroup inferred from panel b). b). PCA for SNPs in the outlier region where the three major clusters found on PC1 are attributed to the 2 homozygotes (AA, blue, left; BB, yellow, right) and their heterozygote (AB, green, middle). Intermediate genotypes (A0, light blue; 0B, light green) were assigned to individuals outside of the cluster distributions. The histogram (above) represents the density of individuals along the first axis of the PCA. c) Proportion of inferred haplogroups for the win8 haploblock across sampling sites.
0347
Reposted by Alexander Piper
Simon Fisher @profsimonfisher.bsky.social · 05/12/2024
In a @currentbiology.bsky.social paper earlier this year, led by @laurawesseldijk.bsky.social, we analysed Beethoven’s genome with a polygenic index related to musicality, as a way to communicate limits of genetic predictions at the individual level & the complexity of links between DNA & behaviour:
cell.com
Notes from Beethoven’s genome
Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven with population-based datasets used to quantify musical achievement.
1217377
Reposted by Alexander Piper
Conrad Hackett @conradhackett.bsky.social · 05/12/2024
Over the last century, milk productivity by the average U.S. dairy cow has risen 6-fold! Full story worksinprogress.co/issue/how-bi... 🧪
Charts shows that the average US dairy cow yields growing amounts of milk. At the same time, the number of dairy cows in the US has been declining.
46514
Reposted by Alexander Piper
Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience
211156
Reposted by Alexander Piper
Mark Pallen @mjpallen.bsky.social · 03/12/2024
Letter sent in to the Editor of the Guardian on brain microbiome nonsense.
2134691
Reposted by Alexander Piper
The Tattooed Professor @schwessinger.bsky.social · 01/12/2024
Our latest contribution to understanding plant pathogenic fungi better led by UQ. Intragenomic variants of a putative effector drive early-stage infection in a broad host-range rust fungus www.biorxiv.org/content/10.1...
biorxiv.org
Intragenomic variants of a putative effector drive early-stage infection in a broad host-range rust fungus
Rust fungi are pathogens that impact plants of environmental, agricultural, cultural, and economic importance. Their mechanisms of pathogenicity are not well-understood but are likely governed by effe...
02110
Reposted by Alexander Piper
Darren Obbard @darrenobbard.bsky.social · 27/11/2024
#PhD Advert: Please share! Are you looking for a PhD studentship in comparative- or population-genomics, using 300+ species of #Drosophila and 1000+ genomes of #melanogaster? #Entomology #Genomics #PopGen #Phylogenetics
Diverse species of Drosophilidae
3145113
Reposted by Alexander Piper
Rob Lanfear @roblanfear.bsky.social · 26/11/2024
If you had a really nice looking alignment of about thirty 100kb virus genomes and you wanted to find recombination breakpoints, what software/methods would you use? All suggestions, snark, links to papers etc. welcome. Trying to navigate a new field... Please repost! 🧪
184331
Alexander Piper @apiper.bsky.social · 18/11/2024
My PhD student Lachlan Gretgrix gave his first conference talk on improving quantification of #metabarcoding assays for agroecosystem monitoring! Presenting experiments using unique molecular identifiers to reduce amplification bias
120