Registration is now open for the next edition of the #RADseq data analysis using Stacks course with @naiarare.bsky.social Tereza and Natalia!
🔗 www.physalia-courses.org/courses-work...
🔗 www.physalia-courses.org/courses-work...
RAD-seq data analysis
ONLINE, 27-31 October 2025 To foster international participation, this course will be held online
www.physalia-courses.org
April 7, 2025 at 10:05 AM
Registration is now open for the next edition of the #RADseq data analysis using Stacks course with @naiarare.bsky.social Tereza and Natalia!
🔗 www.physalia-courses.org/courses-work...
🔗 www.physalia-courses.org/courses-work...
Catching up on the #genetics literature? Did you read the debate on RADseq from 2017? "Breaking RAD: An evaluation of the utility of restriction site‐associated DNA sequencing for genome scans of adaptation" and related comments...
May 22, 2025 at 11:05 PM
Catching up on the #genetics literature? Did you read the debate on RADseq from 2017? "Breaking RAD: An evaluation of the utility of restriction site‐associated DNA sequencing for genome scans of adaptation" and related comments...
Abby Perkins @acperkins.bsky.social untangles how the Philippine bulbul (Hypsipetes) complex are represented across their region. Using RADseq data, we can see how genetic data can challenge previous assumptions about closely (or so we thought) related subspecies. #AOS25
August 12, 2025 at 9:28 PM
Abby Perkins @acperkins.bsky.social untangles how the Philippine bulbul (Hypsipetes) complex are represented across their region. Using RADseq data, we can see how genetic data can challenge previous assumptions about closely (or so we thought) related subspecies. #AOS25
Repeat prelim announcement- plan to hire a bioinformatician for processing & analyzing RADseq data & performing simulations of microsat vs. sequence data for conservation genetics. Formal ad in Feb, hiring March to June ish. 18 to 24 months funding. DM me and RT pls! #phdchat
May 22, 2025 at 12:17 AM
Repeat prelim announcement- plan to hire a bioinformatician for processing & analyzing RADseq data & performing simulations of microsat vs. sequence data for conservation genetics. Formal ad in Feb, hiring March to June ish. 18 to 24 months funding. DM me and RT pls! #phdchat
ICYMI: A brief comment and review of RADseq. Published in its final form and #OpenAccess <a href="http://onlinelibrary.wiley.com/doi/10.1111/mec.12965/full" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://onlinelibrary.wiley.com/doi/10.1111/mec.12965/full
November 17, 2024 at 4:38 AM
ICYMI: A brief comment and review of RADseq. Published in its final form and #OpenAccess <a href="http://onlinelibrary.wiley.com/doi/10.1111/mec.12965/full" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://onlinelibrary.wiley.com/doi/10.1111/mec.12965/full
Do you know of any examples of population structure identified with whole genome data but not with microsats or RADseq-type methods?
December 9, 2024 at 10:09 PM
Do you know of any examples of population structure identified with whole genome data but not with microsats or RADseq-type methods?
2nd UK RAD Sequencing Meeting: wrap-up #RADseq http://ff.im/-q208d
November 25, 2024 at 10:58 AM
2nd UK RAD Sequencing Meeting: wrap-up #RADseq http://ff.im/-q208d
Cool! Blair et al. showed genomiphied samples have 98% concordance & no bias compared to nonamplified samples in RADseq #Evol2014 @je_light
November 17, 2024 at 5:01 AM
Cool! Blair et al. showed genomiphied samples have 98% concordance & no bias compared to nonamplified samples in RADseq #Evol2014 @je_light
📢 We have a new study out in Taxon, exploring phylogenetic relationships in the tribe Barlerieae of #Acanthaceae using RADseq data, laying the groundwork for a revised classification of this fascinating group of ca. 500 tropical species. Led by Robert Comito. onlinelibrary.wiley.com/doi/full/10....
April 18, 2025 at 10:28 AM
📢 We have a new study out in Taxon, exploring phylogenetic relationships in the tribe Barlerieae of #Acanthaceae using RADseq data, laying the groundwork for a revised classification of this fascinating group of ca. 500 tropical species. Led by Robert Comito. onlinelibrary.wiley.com/doi/full/10....
On my way to Switzerland to teach at B@G! I'm leading a full day workshop on RADseq bioinformatics. Not sure I have ever talked that much.
November 17, 2024 at 4:37 AM
On my way to Switzerland to teach at B@G! I'm leading a full day workshop on RADseq bioinformatics. Not sure I have ever talked that much.
Happy to release Stacks v2.67 today. This release updates process_radtags to make it easier to use SRA data and to filter poly-G (error) runs coming from Nextseq/Novaseq machines + bugfixes. We also added a genotype depth filter to populations #RADseq
catchenlab.life.illinois.edu/stacks/
catchenlab.life.illinois.edu/stacks/
Stacks
catchenlab.life.illinois.edu
July 18, 2024 at 5:50 PM
Happy to release Stacks v2.67 today. This release updates process_radtags to make it easier to use SRA data and to filter poly-G (error) runs coming from Nextseq/Novaseq machines + bugfixes. We also added a genotype depth filter to populations #RADseq
catchenlab.life.illinois.edu/stacks/
catchenlab.life.illinois.edu/stacks/
We studied RADseq markers across two hybrid zones and found that, although geographic clines tended to be narrow, markers in regions supporting putative 'introgressed' topologies followed wider clines. This supports that contemporary gene flow indeed contributes to gene-tree heterogeneity. (8/10)
May 14, 2025 at 3:12 PM
We studied RADseq markers across two hybrid zones and found that, although geographic clines tended to be narrow, markers in regions supporting putative 'introgressed' topologies followed wider clines. This supports that contemporary gene flow indeed contributes to gene-tree heterogeneity. (8/10)
More disagreement between demographic inferences based on #microsatellites vs those based on #RADseq: http://onlinelibrary.wiley.com/doi/10.1111/mec.12636/abstract?deniedAccessCustomisedMessage=&userIsAuthenticated=false @EEPuckett
May 24, 2025 at 2:11 AM
More disagreement between demographic inferences based on #microsatellites vs those based on #RADseq: http://onlinelibrary.wiley.com/doi/10.1111/mec.12636/abstract?deniedAccessCustomisedMessage=&userIsAuthenticated=false @EEPuckett
Resolving phylogenetic relationships within the Trichophyton mentagrophytes complex: a RADseq genomic approach challenges status of "terbinafine-resistant" Trichophyton indotineae as distinct species http://biorxiv.org/cgi/content/short/2024.12.03.626654v1
December 5, 2024 at 12:39 AM
Resolving phylogenetic relationships within the Trichophyton mentagrophytes complex: a RADseq genomic approach challenges status of "terbinafine-resistant" Trichophyton indotineae as distinct species http://biorxiv.org/cgi/content/short/2024.12.03.626654v1
My new paper with Liz Zimmer, @jlandisbotany.bsky.social, and @fernway.bsky.social on polyploid speciation is out in Annals of Botany! In it, we use phased RADseq data and whole chloroplast sequences to probe recurrent origins of Isoetes appalachiana. academic.oup.com/aob/advance-...
Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a ‘diploids-first’...
AbstractBackground and Aims. Allopolyploidy is an important driver of diversification and a key contributor to genetic novelty across the tree of life. However,
academic.oup.com
December 4, 2023 at 7:09 PM
My new paper with Liz Zimmer, @jlandisbotany.bsky.social, and @fernway.bsky.social on polyploid speciation is out in Annals of Botany! In it, we use phased RADseq data and whole chloroplast sequences to probe recurrent origins of Isoetes appalachiana. academic.oup.com/aob/advance-...
ありがとうございます…！
RADseq→ipyRADです。
引き継ぎの研究なのですが、とにもかくにもこの辺りの解析など始めて日が浅く、よくわからないことだらけでして…。ありがたいです。
SpilitTree，ちょっと調べてみます。PGDSpiderは他の解析をするときに変換で使っているので、その辺りは問題ないと思います。Treemixも面倒なんですね。理解しておくに越したことはないと思うのでちょっと触れてみようかなと思います。とりあえず触っておけば後々何らかの役に立つ気はするので……
RADseq→ipyRADです。
引き継ぎの研究なのですが、とにもかくにもこの辺りの解析など始めて日が浅く、よくわからないことだらけでして…。ありがたいです。
SpilitTree，ちょっと調べてみます。PGDSpiderは他の解析をするときに変換で使っているので、その辺りは問題ないと思います。Treemixも面倒なんですね。理解しておくに越したことはないと思うのでちょっと触れてみようかなと思います。とりあえず触っておけば後々何らかの役に立つ気はするので……
May 3, 2025 at 1:01 PM
ありがとうございます…！
RADseq→ipyRADです。
引き継ぎの研究なのですが、とにもかくにもこの辺りの解析など始めて日が浅く、よくわからないことだらけでして…。ありがたいです。
SpilitTree，ちょっと調べてみます。PGDSpiderは他の解析をするときに変換で使っているので、その辺りは問題ないと思います。Treemixも面倒なんですね。理解しておくに越したことはないと思うのでちょっと触れてみようかなと思います。とりあえず触っておけば後々何らかの役に立つ気はするので……
RADseq→ipyRADです。
引き継ぎの研究なのですが、とにもかくにもこの辺りの解析など始めて日が浅く、よくわからないことだらけでして…。ありがたいです。
SpilitTree，ちょっと調べてみます。PGDSpiderは他の解析をするときに変換で使っているので、その辺りは問題ないと思います。Treemixも面倒なんですね。理解しておくに越したことはないと思うのでちょっと触れてみようかなと思います。とりあえず触っておけば後々何らかの役に立つ気はするので……
RADseq is a great and powerful tool for population genomics, but no one variety is better than the rest! <a href="http://onlinelibrary.wiley.com/doi/10.1111/mec.12965/abstract" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://onlinelibrary.wiley.com/doi/10.1111/mec.12965/abstract
November 17, 2024 at 5:01 AM
RADseq is a great and powerful tool for population genomics, but no one variety is better than the rest! <a href="http://onlinelibrary.wiley.com/doi/10.1111/mec.12965/abstract" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://onlinelibrary.wiley.com/doi/10.1111/mec.12965/abstract
What can RADseq tell us about sex-biased dispersal in sharks?
<a href="http://goo.gl/ARz4gg" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://goo.gl/ARz4gg
#dDocent #RADseq #genomics
<a href="http://goo.gl/ARz4gg" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://goo.gl/ARz4gg
#dDocent #RADseq #genomics
Goo.gl is sunsetting
goo.gl
November 17, 2024 at 4:00 AM
What can RADseq tell us about sex-biased dispersal in sharks?
<a href="http://goo.gl/ARz4gg" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://goo.gl/ARz4gg
#dDocent #RADseq #genomics
<a href="http://goo.gl/ARz4gg" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://goo.gl/ARz4gg
#dDocent #RADseq #genomics
Molly Garrett, Lisette Waits, et al. derived a #GTSeq panel for genotyping low quality tissue from the ESA-listed northern Idaho Ground Squirrel throughout it's extant range. They were able to recover population assignments and diversity stats similar to #RADSeq data, useful for monitoring #consgen
Development and validation of a GT‐seq panel for genetic monitoring in a threatened species using minimally invasive sampling
Here, we develop, optimize, and validate a GT-seq panel for the federally threatened northern Idaho ground squirrel (Urocitellus brunneus) to provide a standardized approach for future genetic monito...
onlinelibrary.wiley.com
February 2, 2025 at 3:38 PM
Kudos to this outstanding team of instructors
@TerezaManousaki, @naiarare.bsky.social and
@NataliaDA10, who have guided us through the intricate world of #RADseq data analysis. Their expertise has empowered our group of attendees, leaving them better equipped to navigate their own data.
@TerezaManousaki, @naiarare.bsky.social and
@NataliaDA10, who have guided us through the intricate world of #RADseq data analysis. Their expertise has empowered our group of attendees, leaving them better equipped to navigate their own data.
November 3, 2023 at 2:16 PM
Kudos to this outstanding team of instructors
@TerezaManousaki, @naiarare.bsky.social and
@NataliaDA10, who have guided us through the intricate world of #RADseq data analysis. Their expertise has empowered our group of attendees, leaving them better equipped to navigate their own data.
@TerezaManousaki, @naiarare.bsky.social and
@NataliaDA10, who have guided us through the intricate world of #RADseq data analysis. Their expertise has empowered our group of attendees, leaving them better equipped to navigate their own data.