#ddRADseq
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prosanta.bsky.social
"Phylogenomic species delimitation of studfishes (Fundulidae: Fundulus): evidence for cryptic species in agreement with the central highlands vicariance hypothesis"

Fast et al. 2025 Zootaxa

Describe two new Fundulus species from the Tennessee River and Ouachita Highlands!
The Central Highlands ecoregion of the eastern United States represents a hotspot of freshwater biodiversity, with replicated patterns of vicariant speciation east and west of the Mississippi River. Previous phylogeographic investigation of the studfishes (Fundulus subgenus Fundulus) revealed evidence for vicariant speciation in the Central Highlands, but data were limited to a small number of gene sequences generated with Sanger sequencing. We used double digest restriction-site associated DNA sequencing (ddRADseq) to improve resolution of phylogeographic patterns and better characterize population genetic variation. Our sample design included individuals from the Fundulus catenatus species group (F. catenatus, F. bifax, and F. stellifer) and two outgroup taxa (F. julisia and F. rathbuni). Phylogenetic analyses support a monophyletic F. catenatus complex and a sister relationship with Mobile Basin studfishes (F. bifax and F. stellifer). Population genomics and species delimitation tests provide evidence for three species-level subdivisions of F. catenatus. We describe F. catenatus as limited to the Tennessee River and its drainages, F. caddo sp. nov., in the Ouachita Highlands, and F. cryptocatenatus sp. nov., occupying the remainder of the range. Modally, F. catenatus was characterized by fewer left pectoral rays (16 vs. 17). Fundulus caddo sp. nov. had modally fewer anal rays (15 vs. 16) and lateral scale rows (13 vs. 14). Fundulus cryptocatenatus sp. nov. was characterized by modally higher dorsal rays (15 vs. 14) and fewer caudal rays (16 vs. 17). The geographic distribution is likely the result of multiple pre-Pleistocene vicariance events congruent with the Central Highlands Vicariance Hypothesis as well as separate, possibly subsequent, dispersal events. Overall, results of this study corroborate previous evidence for a complex biogeographic history of taxa endemic to rivers of the Central Highlands ecoregion. The improved resolution of genomic variation amo…
March 14, 2025 at 11:11 PM
auroraobrien.bsky.social
Back to sequencing parasite DNA today after spending the last three weeks at Newcastle University learning ddRADseq - a next-generation technique that uses two enzymes to cut and sequence targeted genome regions to study genetic variation.

I had a great time networking & learning new lab skills! 👩🏻‍🔬
A photo of Eppendorf's in a magnetic rack. Eppendorf's contain UK common frog DNA and Serapure beads to concentrate DNA samples. A photo of a presentation about UK adders. A photo of a TapeStation. A photo of Newcastle University.
November 11, 2024 at 12:19 PM
jillwegrzyn.bsky.social
Poster by Ava Fritz and @Jeremy__Bennett @uconneeb - ddRADSeq on #EAB lingering green #ash populations from @usfs_nrs @treebreederKoch #PAG2020 #PAGXXVIII
November 13, 2024 at 6:13 PM
nicolegrimason.bsky.social
Recently spent 3 weeks at Newcastle University using ddRADseq as part of my PhD research 🧬🥼🐸
November 21, 2024 at 9:02 AM
natforsdick.bsky.social
Tista Ghosh uses ddRADseq to investigate dispersal potential of Ficus elastica, a culturally important tree in India where the roots are used to create bridges. Topography and wind speed influence population structuring due to dispersal ability. #consgen #ICCB2025
June 16, 2025 at 11:10 PM
danielbolnick.bsky.social
We have a QTL mapping cross we are about to start genotyping, and are debating:
a) ddRADseq to generate SNP markers,
or,
b) shotgut low coverage whole genome sequencing with haplotype imputation
Would love to hear where other groups stand on these alternatives...
July 14, 2025 at 6:12 PM
mstange.bsky.social
We are happy to host Dr. Jorge Gutierrez Rodriguez from Universidad Nacional Autónoma de México for our @leibnizlib.bsky.social MEEGene seminar on 28. January 2025 @ 15h CET. “Using genomic tools (ddRADseq) to study speciation processes”. To join, drop us an email: meegene@leibniz-lib.de
January 22, 2025 at 8:54 AM
natforsdick.bsky.social
Tista Ghosh uses ddRADseq to investigate dispersal potential of Ficus elastica, a culturally important tree in India where the roots are used to create bridges. Topography and wind speed influence population structuring due to dispersal ability. #consgen #ICCB2025
June 16, 2025 at 11:02 PM
simonmaddock.bsky.social
Led by my wonderful PhD student Rémi Martin, we look at approaches for recovery of DNA from buccal swabs in #frogs and provide recommendations. We used swabs to obtain data for Sanger, microsats, ddRADseq, and low-coverage whole genome seq.

Open Access onlinelibrary.wiley.com/doi/10.1002/...

🐍🧪
Flow chart for recommended swabs Box plot representing DNA concentration from different swabs and preservation methods A picture of all swab types used.
September 13, 2024 at 9:06 AM
timboeh.bsky.social
🌵 Our full taxonomic & phylogenomic revision of Austrocactus is out!
17 species (5 new!), 3 sections, 2 subgenera—and one prickly path through Patagonia.

ddRADseq meets cactus chaos, published in #Taxon

➡️ doi.org/10.1002/tax....

#Cactaceae #Systematics #ddRADseq #Taxonomy #newspecies
April 17, 2025 at 3:32 PM