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Our latest MS by Lucas Czech & Yunru Peng+GrENE-net collaborators! This methods paper--protocols and new C++ pool popgen tool--is a prelude to a global🌱experiment to climate adaptation from re-sequencing populations over 5 years! grene-net.org Pls feedback! 🧵

w/ collaborators @spence_jeffrey_ Patricia Lang Tati Bellagio Hildebrandt, Fritchi, Schwab Beth Rowan @PlantEvolution, Scheepens, Vasseur, GrENE-net

First, we describe protocols in detail for Pool-sequencing of direct pools of #Arabidopsis flowers, set up in the lab by Yunru Peng (during the pandemic!, thanks friends Patricia Lang Beth Rowan @MollySchumer )

We started simple: testing pools of 2 flowers for our Pool-seq approach, and verified that we recovered ~50% and we could statistically model the noise

We then tested whether this would correctly recover a variety of different allele frequencies with combinations from 5 to 100 flowers of different genotypes. We need to sequence over 40X or 50X, but it works!

Then we tested this in the field: several replicates of diverse populations resequenced 2 generations after sowing, and we discovered signals of pronounced allelic frequency evolution (in many regions in the genome, but our "positive control" FLC gene showed high Fst)

Because we needed speed for all the upcoming GrENE-net data, programmer postdoc Lucas Czech though he could do better than common softwares 😛 Lucas created the C++ tool grenedalf: github.com/lczech/greneda… reimplementing pool-seq popgen methods of PoPoolation and more!

.. upcoming preprint w/ a full in-detail description of Lucas Czech's grenedalf, with additional unbiased methods for Fst and diversity estimates thanks to collab @spence_jeffrey_ (looking @ DrosEU Paul Schmidt👀 friends for feedback) (under construction) github.com/lczech/greneda…

With this, we are ready to analyze GrENE-net's 2500 samples in over 30 locations of the world and 3 years #Arabidopsis ☀️🌱🌧!

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Excited to share our new paper out today in Royal Society Publishing on the importance of understanding the interplay between individual and ecosystem-level adaptations doi.org/10.1098/rstb.2… Summer Vance 🌞 Brendan Cornwell Megan Ruffley, PhD Tati Bellagio Moi Expósito-Alonso (#MOILAB) Steve Palumbi Elizabeth Hadly

Our paper "Genetic diversity loss in the Anthropocene" is out in Science Magazine! We study how genetic diversity is lost by habitat loss to help define UN Biodiversity #Sustainable targets science.org/doi/10.1126/sc… @CarnegieScience Carnegie Plants Carnegie Ecology Stanford University

We won. ❤️✊

Yo no hablo de economía, porque no sé de economía. Pero sé de ciencia. Y de cómo la ciencia y la tecnología están en la base del desarrollo, incluso (y sobre todo) en Argentina.