@sam-siwatlaali
PhD student at CPG @cpgsthlm.bsky.social and Swedish Museum of Natural History | Bioinformatics, metagenomics, bulkDNA, science outreach ๐ฒ๐ฝ๐ด๓ ง๓ ข๓ ณ๓ ฃ๓ ด๓ ฟ ADHDer views are my own
โญ Mรฉxico atraviesa un momento delicado, situaciรณn invisible para la estadรญstica
Una sombra se extiende, la sombra de la extorsiรณn, un mal practicado por las mafias para el que la autoridad no parece tener respuesta
๐๐ tinyurl.com/bd8fmhh8
Have a look at the paper, and visit insitulabs.org to learn more about the project and decentralised labs โค๏ธ
๐ ๐ to all coauthors. I feel very lucky to be part of such a fantastic project!
Using portable and low-cost sequencing in the field can help address biodiversity barcoding biases seen in many biodiverse regions, where local researchers often rely on foreign institutions to process their samples.
In this study, we generated over 1,800 publicly available barcodes for Amazonian vertebrate ๐ฆ and plant ๐ฟ taxa.
Of these, 30 mammal and 196 bird barcodes were the first ones for that species! ๐คฏ
This is work I was involved in when I moved to the field for some months a few years ago to help set up one of the field genetics labs in Peru with @fieldprojects.org @surroundscience.bsky.social
So excited to share a new paper Iโm coauthor on which has just come out in Scientific Data: โDecoding the Peruvian Amazon with in situ DNA barcoding of vertebrate and plant taxaโ
๐
www.nature.com/articles/s41...
Together with the growing number of genome reference assemblies and specialised bioinformatics tools being shared and developed, we believe our study shows how much potential metagenomics approaches hold for #BiodiversityMonitoring and #ConservationGenomics.
๐ฟ The metagenomic data also allowed us to taxonomically classify some of the "by-catch" plant DNA present in the samples, and explore potential plant-arthropod interactions.
๐ High coverage bulkDNA genomes were further explored by analysing their mitochondrial allele frequency distributions, which indicated the presence of several individuals with different haplotypes within the same sample.
We obtained #bulkDNA genomes from the samples and used them to calculate genome-wide heterozygosities and - by comparing their genomic profile to previously published genomes - confirm their geographic population of origin ๐.
In this study, we used a comprehensive, custom-built, terabyte-scale #Kraken2 database (also publicly available) to taxonomically classify all reads before mapping to selected references.
๐งฌ Through shotgun sequencing, metagenomics can help us go from a barcode to a full genome, and unlock insights like genetic diversity and population structure.
๐งฌ Metabarcoding is exceptionally good at detecting species, especially at low abundance, and it's widespread use means thousands of barcode species references are publicly available.
Our new study is out!
We analysed 40 Malaise trap samples collected across Sweden by the Insect Biome Atlas project using #metabarcoding and #metagenomics
onlinelibrary.wiley.com/doi/10.1002/...
@cpgsthlm.bsky.social @tvdvalk.bsky.social
So excited this is happening! See you next year in Stockholm! ๐
#VAbloggen: Why sign up to #Borrowaresearcher #Lรฅnaenforskare Read Phd-student @sam-siwatlaali.bsky.social #Naturhistoriskariksmuseet #Guestblog: vetenskapallmanhet.se/2025/02/in-t...
#Scicomm #outreach #forskom
Message from SMBE Leadership
Short blog I wrote about being a researcher in โLรฅna en forskareโ (borrow a researcher). Such a cool opportunity! #ForskarFredag
Halfway there!!
Had a fantastic post-seminar feedback discussion with @anitajnorman.bsky.social @indianadiez.bsky.social Francisco Almada and @tvdvalk.bsky.social
Thanks all! Hyped for whatโs next! ๐
At Stockholm University, we are now starting a 2-year Masterโs programme in Evolutionary Genomics!
Topics include population genetics, phylogenetics, molecular & genome evolution, DNA sequencing, bioinformatics, and palaeogenetics.
Please spread the word!
www.su.se/english/sear...
โช๏ธ Open postdoc position โช๏ธ ๐๐งฌ๐
I'm recruiting a postdoc to work with me on mapping the genomic legacy of the elephant ivory trade in Europe using ancient DNA.
Hosted by Lund University ๐ธ๐ช with Bengt Hansson
Please RT!
Info and apply here: lu.varbi.com/en/what:job/...
๐งฌ๐ญ๐ด๐ปJob Alert๐ป๐ด๐ญ๐งฌ
We are hiring 3 postdoctoral researchers in DeepTime Palaeogenomics!
All positions are for 2 years (extension possible), & are fully funded both in terms of employment and project costs.
Deadline: 2 Dec 2024
Please RT!
Apply:
www.su.se/english/abou...
Asked my fellow scientists if they had any props to lend to me for #ForskarFredag and I got so many cool things that Iโve had to move them around in a suitcase.
Now back to planning the talks for around 250 students across Sweden!
#ScienceCommunication
#LรฅnaEnForskare https://t.co/wIvsviy781
โผ๏ธJust one week left to submit your โidea for IDEAโ in 800 words or less ๐
Please RT!
Reach out if you have questions, weโre happy to help.
#Grants #Funding #DEI
@OfficialSMBE @SMBE_IDEA @SMBEmeetings https://t.co/3KBerpKRXF
Planning #forskarfredag talks for #lรฅnaenforskare week! Iโll be giving talks (in person and zoom) at 10 different schools in Sweden about life as a researcher at @CpgSthlm, collecting monkey ๐ฉ with @Field_Projects, and why DNA is so cool! ๐งฌ
So chuffed to be part of this. https://t.co/JeridrQ9N3
Llรฉvele llรฉvele!
Dos semanas mรกs para meter tu aplicaciรณn y recibir hasta 25 mil dรณlares para proyectos IDEA!
Revisa las bases en el link, retwittรฉanos y/o pasa la voz! Every little helps :) https://t.co/LBQyuvZyYa
Deadline extended!
We want to hear YOUR ideas for IDEA ๐
Initial submission is only 800 words or less ๐คฏ https://t.co/3KBerpKRXF
ยกLlรฉvele llรฉvele!
Apply now!
โฐ ๐จ #SMBE #Inclusion #Diversity #Equity #Access #Accessibility https://t.co/N5QKOrzIK0
Weโre so eager to know what ideas you may have that would benefit from SMBE funding, but we havenโt received ANY proposals yet ๐คฏ
Please share! ๐ https://t.co/sIPsgbJViL
Also big shout out to Pablo Esteban Uribe Herrera for his poster! Fantastic work and delivery! ๐ด I was very impressed when he mentioned this was his undergrad work! ๐คฏ ยกFelicidades! (I donโt have his tag so please tag him if you do!) @FSanchezQuinto #SMBE2024 https://t.co/li5jGfVTpe