Sign in

Amrita Srivathsan

@asrivathsan.bsky.social
228 followers 313 following 0 posts

Researcher at Museum für Naturkunde Berlin. Species interactions, nanopore sequencing

PostsRepliesMedia
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 14/08/2026
Five years back in Berlin #6: DNA barcodes reveal species, but vouchers let us study them. This means that we have to be able to find and retrieve the right specimens among thousands. Our open workflow keeps vouchers safe, searchable & organized. Preprint: doi.org/10.64898/202...
0186
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 13/08/2026
Five years back in Berlin #5: The neglected elephants of animal diversity: millions of unknown species create a taxonomic bottleneck. Triage option: 1: Target neglected taxa dominating biomonitoring samples 2: Make sure common species are described first tinyurl.com/435dsz9t tinyurl.com/3tb3da7b
085
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 12/08/2026
Five years back in Berlin #4c: Too many species, too little time Step 3: 3D imaging. KIT colleagues built 2 tools for us: the Levitator makes dead insects fly; DS-360° images wet specimens from all sides. Levitator www.degruyterbrill.com/document/doi... DS-360° ieeexplore.ieee.org/abstract/doc...
092
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 11/08/2026
Five years back in Berlin and 10 years of nanopore barcoding for everyone, everywhere. From ~10% read errors to live barcoding on a laptop. Now with additional use of DNA barcodes to turn images into AI training data for small insects. Too many species and too little time. doi.org/10.1111/cla....
01610
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 09/08/2026
Five years back in Berlin #4a: Finding the small and mighty Most species are <5 mm. But small ≠ unimportant: ants outweigh all wild birds + mammals and spiders eat as much prey as humans meat/fish: ~400–800 Mt per /lyear. Meet EntoSieve for size sorting onlinelibrary.wiley.com/doi/10.1111/...
02713
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 07/08/2026
Five years back in Berlin #4: Too many species, too little time. ~90% of species remain unknown. So we need methods that scale: robotics, nanopore barcodes & AI. The four DiversityScanners in the video image, measure, classify and sort insects, freeing taxonomists to focus on discovery.
0113
Reposted by Amrita Srivathsan
Daniel Bolnick @danielbolnick.bsky.social · 07/07/2026
Hari Sridhar hs a nice bew paper on the role of natural history in ecology and evolution www.journals.uchicago.edu/doi/10.1086/...
journals.uchicago.edu
Spark, Scaffold, Substrate: The Multiple Hidden Roles of Natural History in Ecology and Evolutionary Biology | The American Naturalist: Vol 0, No 0
AbstractOver the last 30 years, as ecology and evolutionary biology (EEB) has become more theoretical, experimental, and data driven, there has been a growing worry that the space for natural history ...
14325
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 08/04/2026
Species descriptions should not be confined to "summary" PDFs only providing access to a fraction of the data underlying the conclusions. We here argue for "digitally native species" built around structured, specimen-linked, machine-actionable evidence from day one. rdcu.be/fcbwh
rdcu.be
Digitally native species are a necessary shift in taxonomic practice
Nature Reviews Biodiversity - Biodiversity science laments how little is known about the planet’s biodiversity, yet routinely discards much of the taxonomic evidence generated during species...
03117
Reposted by Amrita Srivathsan
David Eccles 🌻🇵🇸7x🩹🛡️ @gringene.org · 19/01/2026
Well... community post confirms it: ONT is getting rid of P2 Solo, their most cost-effective platform. By transitioning to P2i-only and "contact for quotes" purchase models, ONT is now in the realm of the sequencing companies that they initially claimed to be distancing themselves from.
365
Reposted by Amrita Srivathsan
Integrative Systematics @integsyst.bsky.social · 15/01/2026
An integrative taxonomic treatment of the Mycetophilidae of Singapore, describing 98 new species of fungus gnat Now also with a brand new cover, featuring Integricypta fergusondavie gen. et sp. nov. Free download: doi.org/10.18476/202... @rudolf-meier.bsky.social @derschwingfliegen.bsky.social
The cover of Vol. 8 (3), featuring an outline of the island of Singapore and the striking, newly-described fungus gnat Integricypta fergusondavie gen. et sp. nov.
0125
Reposted by Amrita Srivathsan
Bjoern Rulik @zfmk.bsky.social · 14/01/2026
Delegation of @leibnizlib.bsky.social #Bonn visiting @mfnberlin.bsky.social the lab of @rudolf-meier.bsky.social sneaking in rapid #biodiversity methods... 😎
174
Reposted by Amrita Srivathsan
Integrative Systematics @integsyst.bsky.social · 01/01/2026
Happy New Fungus Gnats! 🥂🦟🦟 Prof. Dalton Amorim and co-authors name 98 new species of Mycetophilidae from Singapore in a monograph just published in @integsyst.bsky.social The paper can be downloaded for free from the following link: tinyurl.com/342cs43t Enjoy! @rudolf-meier.bsky.social
Neoempheria merlio Amorim & Oliveira sp. n. from Singapore
0218
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 31/10/2025
Halloween News: Meet a new vampire fly (Hippoboscidae) 🧛‍♂🪰 1 of 10 species found on citizen-reported bird carcasses in Singapore: Even dead birds can have productive afterlives! See host records, annotated images, pictorial keys & DNA diagnostics here: doi.org/10.1155/jzs/...
0185
Reposted by Amrita Srivathsan
Kamil Hupało @kamilhupalo.bsky.social · 20/05/2025
🚨 Thrilled and honoured to lead the chapter on using #eDNA for studying aquatic #parasites - a part of just-published book on #openaccess Aquatic Parasitology led by @berndsures.bsky.social & @nicojsmit.bsky.social with top parasitologists contributing! link.springer.com/book/10.1007... More ⬇️🧵
link.springer.com
Aquatic Parasitology: Ecological and Environmental Concepts and Implications of Marine and Freshwater Parasites
A unique open access collection on ecological and environmental parasitology in marine and freshwater. Covers climate change and parasite conservation.
1127
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 14/05/2025
The top 10 flying insect clades rule the skies—but defy the rules. Weak or inverted latitudinal diversity gradients leave biogeographers puzzled. Entomologists? Mildly amused. www.biorxiv.org/content/10.1...
19045
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 09/05/2025
🚫 Farewell to species descriptions with consensus barcodes. ✨ Hello to Diagnostic Molecular Combinations (DMCs) for your taxonomic research ✅ State-specific ✅ Contrastive ✅ Publication-ready Now even easier with the latest UITOTO, our updated user-friendly software; Preprint: doi.org/10.1101/2025...
0146
Reposted by Amrita Srivathsan
Allan McDevitt @shrewgod.bsky.social · 05/05/2025
A very up-to-date review led by the brilliant @hollybroadhurst.bsky.social on the applications of #eDNA and iDNA for monitoring terrestrial and semi-aquatic mammals! The beginnings, the milestones, where we're heading. Water, soil, air, the inverts, all here! onlinelibrary.wiley.com/doi/abs/10.1...
onlinelibrary.wiley.com
From Water to Land: A Review on the Applications of Environmental DNA and Invertebrate‐Derived DNA for Monitoring Terrestrial and Semi‐Aquatic Mammals
This review explores global applications of environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) for surveying terrestrial and semi-aquatic mammals. By providing a comprehensive overview of t...
03315
Reposted by Amrita Srivathsan
Dezene Huber 🍁 🌻 @dezene.me · 28/04/2025
Sill need to digest this new meta-review on insect decline. Taxonomic bias: lots of research on bee/ant/wasp decline (mainly on a limited range of pollinator taxa). A fair amount on beetles and butterflies/moths. Virtually none on other groups of insects. 🧪 🌎 🪲🪳 academic.oup.com/bioscience/a...
From the paper: "Figure 4.Taxonomic bias in the treatment of hypothesized drivers of insect declines from 106 articles containing taxon-specific hypotheses. (a) The distribution of hypotheses about broad classes of drivers of decline across insect taxonomic groups. (b) The distribution of higher resolution driver and outcome nodes across taxonomic groups. Each colored point shows a node in the network in figure 2 that was said to affect at least two different orders. The nodes are plotted in the taxonomic section where they are most frequently mentioned. Therefore, all taxon-specific nodes are most associated with Coleoptera, Hymenoptera, or Lepidoptera. The line length from the center indicates how biased a term is. The dashed lines indicate which nodes are mentioned about a given taxonomic group more than 50%, 70%, or 90% of the time. The nodes are colored the same way as in figures 1, 2, and 3 (see supplement for node labels). Insect icons were designed by Suyeon Jang."
03411
Reposted by Amrita Srivathsan
Rod Page @rdmpage.bsky.social · 25/04/2025
I've started exploring how @boldsystems.bsky.social BINs change over time. How stable are identifications of specimens based on DNA barcoding? The record so far is 10 changes between 2016 and 2024(!) There seems to be quite a bit of "BIN bouncing" where barcodes hop back and forth between BINs.
271
Reposted by Amrita Srivathsan
Rupam Debnath @rupamd.bsky.social · 19/04/2025
Thrilled to share our globally pioneering research on DNA metabarcoding of spider egg sacs! A proud moment for Indian science - revealing novel host-parasitoid complexes and trophic networks. #DNAmetabarcoding #IndianScience #Biodiversity #Hymenoptera #Spider www.nature.com/articles/s41...
13511
Reposted by Amrita Srivathsan
Hasindu Gamaarachchi @hasindu2008.bsky.social · 19/04/2025
This new Hifiasm --ont option is amazing. It worked like a charm for us in the nanopore adaptive sampling based assembly paradigm we introduced in a preprint recently. www.biorxiv.org/content/10.1...
biorxiv.org
Adaptively integrated sequencing and assembly of near-complete genomes
Recent advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals, plants and other eukaryotes. However, there...
2166
Reposted by Amrita Srivathsan
Sebastien Calvignac-Spencer @scs22.bsky.social · 09/04/2025
We just succeeded in formally linking a specific rodent species - the otherwise charming fire-footed rope squirrel - to the onset of a mpox outbreak in a primate species - sooty mangabeys. Here Kai’s report on the preprint we released yesterday 1/2
1157
Reposted by Amrita Srivathsan
Ambrosio Torres G. @atorresgalvis.bsky.social · 04/04/2025
Happy to share this video about UITOTO, our user-friendly software designed to infer, test, and visualize reliable Diagnostic Molecular Combinations (DMCs)—essential for species descriptions in integrative taxonomy. 🔬 Preprint available at: www.biorxiv.org/content/10.1... bsky.app/profile/rudo...
biorxiv.org
UITOTO: a new software for molecular diagnoses in species descriptions
Millions of species remain undescribed, requiring molecular and morphological diagnoses. However, no efficient software reliably derives and tests —state-specific and contrastive— molecular diagnoses....
032
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 04/04/2025
UITOTO for taxonomy. Get your molecular diagnoses right without coding or breaking a sweat! Use state-specific, contrastive DMCs instead of fuzzy consensus barcodes! 🪰🦋🪱🦎🦀🐌🦉 doi.org/10.1101/2025...
0156
Reposted by Amrita Srivathsan
RES Publications @respublications.bsky.social · 26/03/2025
A new #RESEcolEnt paper investigates the influence of host species & seasonal interactions on bacterial community structure in fungus-growing #termites🍄 Read the article🔽 doi.org/10.1111/een.13424 @sheborg.bsky.social @robwilsonmncn.bsky.social @callomac.bsky.social
Graphical abstract of: Influence of host species and seasonal interactions on bacterial community structure in fungus-growing termites: Insights into symbiotic adaptation and ecological function
011
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 14/03/2025
🚨 EntoSieve is now published in Molecular Ecology Resources: Fast and accurate size-sorting of bulk insect samples! Perfect for boosting DNA megabarcoding & metabarcoding projects. 🧬🔬 DIY low-cost device, gentle on specimens and yet efficient 🦋🐞 here: onlinelibrary.wiley.com/doi/full/10....
2349
Reposted by Amrita Srivathsan
Scott P. Egan @scottpegan.bsky.social · 09/03/2025
Botanical parasitism of an insect by a parasitic plant: Current Biology www.cell.com/current-biol...
cell.com
Botanical parasitism of an insect by a parasitic plant
Egan et al. report the discovery of a new trophic interaction in nature whereby a parasitic plant attacks multiple species of insects that manipulate plant tissue when the two co-occur on a shared pri...
24325
Reposted by Amrita Srivathsan
Dr Simon Goodman @phoca-sapiens.bsky.social · 04/03/2025
Can #eDNA recover biotic interactions? Our new study says Yes sometimes! Co-occurrence network analyses with data for the Moray Firth marine ecosystem recovered subsets of known food web trophic links but methodological issues are still a challenge ⤵️ 🧪🧬🌍🐳🦭🐟 onlinelibrary.wiley.com/doi/10.1111/...
A scientific figure showing a species ecological interaction network derived from environmental DNA for a marine ecosystem. The trophic levels span zooplankton to whales and other large predators.
24418
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 07/03/2025
Species- versus specimen-level congruence between DNA barcodes and morphology. Species-level dominates papers but specimen-level matters more for sample evaluation. Read more in "Illuminating Entomological Dark Matter with DNA Barcodes..." in Ann Rev Ent: www.annualreviews.org/content/jour...
02414
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 21/02/2025
Dark Taxonomy: From unknown to ready for biomonitoring in 5 steps. By describing 120 species, most species of fungus gnats routinely caught in Malaise traps in Singapore now have names. Bees, butterflies and birds, make room for your new friends. Read here: onlinelibrary.wiley.com/doi/10.1111/...
16122
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 08/02/2025
Malaise Trap Polka Dots vs. Biodiversity Smudge: Similar latitudinal data deficiency gradients for DNA barcodes and all data. Read more in "Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics" Ann. Rev. Entomol.: doi.org/10.1146/annu...
02410
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 07/02/2025
"Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics" Who uses insect DNA barcodes for which taxa? The usual suspects dominate... Now in Annual Review of Entomology: doi.org/10.1146/annu...
04014
Reposted by Amrita Srivathsan
Laura Finnegan @lfinnegal.bsky.social · 30/01/2025
New paper!! Led by Suzanne Stevenson 🧪 www.facetsjournal.com/doi/10.1139/...
facetsjournal.com
Winter diet of five sympatric ungulates in west-central Alberta, Canada—inference from DNA metabarcoding of fecal pellets
Diet is one of the determinants of ungulate ecology. However, there have been few studies of the diet of sympatric ungulates in western Canada. We used DNA metabarcoding of fecal samples to evaluate t...
075
Reposted by Amrita Srivathsan
Francois Keck @francoiskeck.bsky.social · 28/01/2025
144,000 biological interactions extracted from 84,000 publications—in just a few hours using GPT4o. 🚀 The potential applications seem endless. Check out our preprint: doi.org/10.1101/2025... With @florianaltermatt.bsky.social
A reconstructed graph of species interactions using LLMs
3175
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 21/01/2025
Episode 3 (imaging): Don't just sort. Also image! No money for a robot? Try the Entomoscope! 🦟🔬 DIY microscope for imaging tiny insects in ethanol: 3D-print case, order parts, assemble, image! 📸Perfect for entomologists www.youtube.com/watch?v=VEoZ... ieeexplore.ieee.org/document/104...
youtube.com
DIY Photomicroscope
YouTube video by Integrative Biodiversity Discovery
0245
Reposted by Amrita Srivathsan
Dr Kylie Soanes @drkyliesoanes.bsky.social · 27/01/2025
A nifty little summary of our #roadecology evdience synthesis: how well do wildlife crossing structures help animals across roads? 🚗🐨🦡🦌 transportecology.info/research/eff...
transportecology.info
How well do wildlife crossing structures help animals across roads? — Transport Ecology
Wildlife crossing structures seem like a simple and attractive solution to help animals across roads. But how well do they actually work? This latest global research summary tried to find out.&nbsp;
22911
Reposted by Amrita Srivathsan
Jamie Wood @larusnz.bsky.social · 27/01/2025
smithsonianmag.com
Fossilized Poop Reveals How Extinct, Flightless Birds Helped Spread New Zealand's Colorful Fungi
The upland moa was likely drawn to the fungi because of their resemblance to berries, scientists say, allowing the creature to fill a role typically played by mammals
0135
Reposted by Amrita Srivathsan
Sara Mendes @sarammendes.bsky.social · 03/12/2024
🔥 New paper out 🔥 Seed dispersers help plants tracking climate change on mountains! Animals are dispersing plant species to higher elevations... but over half of the plants arriving at higher elevations were exotic. 🦎🐦💩🌿 @newphyt.bsky.social 🧪🍁🌐🌏 nph.onlinelibrary.wiley.com/doi/full/10....
nph.onlinelibrary.wiley.com
Climb forest, climb: diverse disperser communities are key to assist plants tracking climate change on altitudinal gradients
Climate change is forcing species to shift their distribution ranges. Animal seed dispersers might be particularly important in assisting plants tracking suitable climates to higher elevations. Howe.....
16932
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 20/01/2025
Episode 3 (imaging): Don't just sort. Also image! Meet “DiversityScanner”, the robot that images, measures, identifies, and moves specimens into microplates; a good companion of “MinION barcodes by everyone, for everyone (see episode 2). tinyurl.com/mwx5k5s7 onlinelibrary.wiley.com/doi/full/10....
tinyurl.com
DiversityScanner: Robotic discovery of small invertebrates with machine learning methods
Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.
0216
Reposted by Amrita Srivathsan
Julie Lockwood @lockwoodlab.bsky.social · 24/01/2025
The Rutgers eDNA lab developed a novel method to collect #eDNA from tree surfaces that we call the 'roller method'. A game-changer for monitoring terrestrial forest biodiversity (insects, vertebrates). Here is a short methods video if you want to try it. www.youtube.com/watch?v=2306...
youtube.com
Terrestrial Environmental DNA (eDNA) Sampling Method: Roller Aggregation
YouTube video by Rutgers eDNA Lab
2289
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 23/01/2025
Episode 3 (imaging): Don't just sort. Also image, from multiple perspectives! Insect levitation with ultrasound: capturing 360° views to automate measurements and create 3D models. More here: www.techrxiv.org/users/813834...
34020
Reposted by Amrita Srivathsan
Benjamin Guinet @benjaminguinet.bsky.social · 22/01/2025
Our latest study uncovers a viral domestication event from ~75 million years ago, where viral genes enable parasitoid wasps to protect their eggs they lay within dipteran hosts! 🐝->🥚+🦠->🪰☠️ ->🐝🦠 Read more: royalsocietypublishing.org/doi/10.1098/... #paleovirology #parasitoid #evolution
0165
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 16/01/2025
Episode 1 (taxon triage): Identify the biggest knowledge gaps (in insects): Same 20 insect families contribute >50% of species and specimens in Malaise samples; regardless of continent, climate, or habitat. Most are neglected dark taxa. www.youtube.com/watch?v=PUMa... www.nature.com/articles/s41...
youtube.com
Top 20 most dominant flying insect families
YouTube video by Integrative Biodiversity Discovery
0224
Reposted by Amrita Srivathsan
Dr. Andrea Wishart @wishartae.bsky.social · 21/01/2025
Last year, my fantastic co-author @bioinfocus.bsky.social and I published this note observing squirrels foraging insect galls in the Yukon: www.canadianfieldnaturalist.ca/index.php/cf... #SquirrelAppreciationDay
canadianfieldnaturalist.ca
Red Squirrel (<i>Tamiasciurus hudsonicus</i>) feeding on Balsam Poplar (<i>Populus balsamifera</i>) galls induced by aphids | The Canadian Field-Naturalist
155
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 16/01/2025
Episode 2 (sorting triage): From bulk samples to putative species without going bankrupt: cheap MinION barcodes obtained with user-friendly software ONTbarcoder. Now also in real-time: onlinelibrary.wiley.com/doi/full/10.... bmcbiol.biomedcentral.com/articles/1 www.youtube.com/watch?v=nFl8...
onlinelibrary.wiley.com
ONTbarcoder 2.0: rapid species discovery and identification with real‐time barcoding facilitated by Oxford Nanopore R10.4
Most arthropod species are undescribed and hidden in specimen-rich samples that are difficult to sort to species using morphological characters. For such samples, sorting to putative species with DNA...
0192
Reposted by Amrita Srivathsan
anthrofuentes.bsky.social @anthrofuentes.bsky.social · 18/01/2025
Great essay "Rethinking Deterrence as a Continuum of Care" by @dialecticprimates.bsky.social www.anthropology-news.org/articles/ret...
anthropology-news.org
Rethinking Deterrence as a Continuum of Care - Anthropology News
Pseudonyms have been issued for ethnographic interlocutors, monkeys, and locations.  In Polyphony, an urban neighborhood in Penang, Malaysia, a woman
074
Reposted by Amrita Srivathsan
Michael Baym @baym.lol · 17/01/2025
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after
11304122
Reposted by Amrita Srivathsan
Rudolf Meier @rudolf-meier.bsky.social · 16/01/2025
Switching from X to Bluesky: Good opportunity to review my 3 years in Berlin at the Center for Integrative Biodiversity Discovery: We fight taxon neglect in biodiversity research through scientific discovery, a giant exercise in triaging given how little we know. scholar.google.com/citations?hl...
scholar.google.com
Center for Integrative Biodiversity Discovery
‪Museum für Naturkunde‬ - ‪‪Cited by 5,039‬‬
0445