Pyramidal cell types drive functionally distinct cortical activity patterns during decision-making

Understanding how cortical circuits generate complex behavior requires investigating the cell types that comprise them. Functional differences across pyramidal neuron (PyN) types have been observed within cortical areas, but it is not known whether these local differences extend throughout the cortex, nor whether additional differences emerge when larger-scale dynamics are considered. We used genetic and retrograde labeling to target pyramidal tract, intratelencephalic and corticostriatal projection neurons and measured their cortex-wide activity. Each PyN type drove unique neural dynamics, both at the local and cortex-wide scales. Cortical activity and optogenetic inactivation during an auditory decision task revealed distinct functional roles. All PyNs in parietal cortex were recruited during perception of the auditory stimulus, but, surprisingly, pyramidal tract neurons had the largest causal role. In frontal cortex, all PyNs were required for accurate choices but showed distinct choice tuning. Our results reveal that rich, cell-type-specific cortical dynamics shape perceptual decisions.


March 2021
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We sequenced 2500 Ultraconserved Elements (UCEs) and the mitochondrial genome of the studied taxa, and used three different approaches to infer their demographic history. With a subsample of the UCEs and two mitochondrial markers we recovered the population size dynamics through time with Extended Bayesian Skyline Plots (EBSP) in BEAST 2.5. To compare with EBSP results, in DILS we used the whole genomic dataset to test the probability of different demographic models: population expansion, contraction or stability. Finally, with Ecoevolity we tested the probability of the recovered demographic expansions in all species having occurred concomitantly.
We focused on sampling taxa with broad distribution across the Amazonian floodplains and specialized on distinct floodplain environments. For each taxon, we searched for samples available at Scientific Collections in Brazil and the USA to cover as much as possible the taxon's whole distribution. We sampled 210 individuals belonging to 9 bird species specialized in Amazonian seasonally flooded habitats: Cranioleuca vulpecula, Furnarius minor, Knipolegus orenocensis, Mazaria propinqua, Stigmatura napensis, Attila bolivianus, Cranioleuca gutturata, Myiopagis flavivertex, and Nasica longirostris. All individuals have associated voucher specimens. Genomic sampling was based on a probe set targeting Ultraconserved Elements. We obtained an average of 2233 UCE loci and 1574 SNPs per individual.
For each of the 9 species, indiduals samples were chosen aiming to cover their known geographic distribution along seasonally flooded habitis in Amazonia.
Fresh tissue samples were obtained through loans from Scientific Collections. All field samplings in Brazil that contribute specimens for Scientific Collections are regulated by the Environmental Ministry / Brazilian Government through Collecting Permits issued by ICMBio/MMA. Eduardo D. Schultz extracted DNA from the tissues with QIAGEN Dneasy Blood and Tissue kits in laboratories at INPA and AMNH, prepared the plates and sent the extracts to Rapid Genomics for sequence capture following Brazilian legislation. All samples collected outside Brazil were loaned from US institutions following their loan policies. Sequences from each species were processed independently from raw reads to final UCE alignments through the Phyluce pipeline by Eduardo D. Schultz.
Not applicable. Specimens were deposited in Biological Collections, spatial scale is the Amazonian floodplains.
All obtained sequence data that passed through quality check was used.
All raw reads are deposited in Genbank and all analytical procedures are available through Github. All data deposited in Genbank have high read counts and have been processed successfully multiple times from first data explorations to final processing. On Github the input and config files contain all the set of parameters used for the analyses, ensuring reproducibility.
For the EBSP demographies, we used 50 random UCE loci for each species. Before final analyses, initial tests were made using different random UCEs and using the same priors and parameters of the present analyses, results were highly consistent. Moreover, each EBSP run starts with a random seed and, for all species, runs with different seeds recovered the same results. In DILS, although we provide all available loci as input, the program uses 1000 random loci to calculate the statistics. For all species, different runs, where different random loci were chosen to calculate the statistics were performed to check for consistency, and also resulted in highly consistent results.
Blinding is not applicable because we must know which taxon we are working with. However data processing and demographic analyses were performed independently for each taxon using the same approaches and without informing the habitat affinities of the taxa, all analyses recovered the distinct demographic histories between floodplain forest and island-specialists birds.