A Appendix 1: Meetings

A.1 11/02/2021 Sylvain’s Kick-off

NT, MH, & SS

Regina
- 1 LiDAR in 2016 (ONF, see Fig. 2.1 and Fig. @ref(fig:2.1))
- Possibility of clearing for drone
- Destructive sampling for tree rings? Coring individuals. Ask ONF.
- Higher trees. Maybe not older but at least implying more cell divisions regarding mutations.
Paracou
- 4 LiDAR campaigns from 2004 to 2015 (Fig. ??)
- Proximity, easier to follow phenology and collect flowers and fruits

Sextonia rubra:
- already sampled
- Paracou
Dicorynia:
- Paracou & Regina
- flowering time? Ask Natalia Norden and Jerome Chave for original data + Patrick Heuret for his shared article
- Suggestion: spot one already flowering before sampling
- Check the phenology at the herbarium
Eschwerilera sp:
- Parcou (small) and Regina (big)
Handoranthus sp:
- published genosegmenmes (to read) but high variation
- Regina
- Need to be collected for flux cytometry
Caryocar sp:
- Paracou (big)
- many lianas
- no self shading?

Regina
- beginning of march
- wood samples
- drone
- dry leaves of Handoranthus sp for flux cytometry from our favorite individuals and two other potential candidates
- Sample (Big shot) Eschweilera sp for identification and gene pool attribution with Myriam’s SSRseq experiment (results in spring)
Paracou
- Dycorinia from interplots. Ask Partick Heuret and Eric Nicolini.

Check flux cytometry confidence: plot second against first sampling for confidence envelope (Fig. ??)
choose what to sequence
get in touch asap sequencing company
High molecular DNA extraction at CNRGV
Bionano with CNRGV
PacBio for HiFi reads

PacBio HiFi best contiguity
hifiasm separate haplophase
different apporaches for optical map
- calssical assembly with bionano software (only 3% of N recently)
- if issues (gaps or N), local tools to make it better

UVs can have a different signal than direct light exposure measured by Accupar or currently modeled with lidar data (up to 20-30% uncertainty according to G. Vincent)
lidar gave a hieght of 50.6m against 51.25 with tree climbing. This erros below the meter is very encouraging.
Herrera CM 2019 on the phenotypic variability within individual trees or plants
Screwdriver can be good to initiate the auger (O. Martin)

Branch dating
- discuss with Patrick and perhaps Romain methodology, sampling points, tools etc
- plan a mission with climbers
- send samples to Patrick
Direct light measurement: not primordial to do aside from a mission if time
Mutation detection: continue with the plan
Offspring genotyping: meet with geneticists to discuss samples and techniques, dimensions of the assay.
Data management: discuss archiving with everybody, e.g. NCBI for raw genomic data, Zenodo for cleaned genomic data, GitHub for codes, what for the others (lidar) ?

Patrick, Niklas, moi

Niklas, Myriam, Thibault, me

Globally: don’t follow archi, no signal in UVs, and the estimate gives a high # of low AF mutations + evidence the difficulty to estimate mutations # comparing with previous studies
Next steps: annotation (w transcripts, contact Christophe & Isabelle) & transmission (suggest a number of shared mutations in branches with position in the genome + ranking)
Meeting: schedule a meeting with everybody to discuss valorisation
3 papaers: 2 genomes, 1 mutations
Save data
Follow mutations sharing along architecture (cell surfing idea)
Add architecture when comparing phylogenies
Add comparisons with oka if possible