DOI: 10.5061/dryad.9ghx3ffr8
title: Data from: Evaluating the impact of historical climate and early human groups in the Araucaria Forest of Eastern South America

description: It has been hypothesized that the Araucaria Forest in Southern Brazil
 underwent expansions in the past, driven either by human groups or by
 climate fluctuations of the Holocene and Pleistocene. Fossil pollen
 records of the Paraná Pine (Araucaria angustifolia), a dominant tree in
 that forest, provide some insights into when those may have occurred.
 Still, the timing of those expansions has never been estimated. To infer
 past range shifts and shed light on their main drivers, we employed
 next-generation DNA sequencing (ddRADseq), machine learning, and a
 comprehensive database of fossil pollen records in a study of historical
 demographic inference and paleo-distribution modeling of the Paraná Pine.
 We found that A. angustifolia comprises two populations expanding at
 different times: one in the Mantiqueira mountain chain, and the other in
 the southern Brazilian plateau. The Southern population began to expand
 during the Last Glacial Period ~70kya, long before human arrival in South
 America. Still, genetic analyses support that humans later impacted this
 population, resulting in lower genetic diversity, higher inbreeding, and
 high levels of gene flow over large distances with a weak pattern of
 isolation by distance. It is possible this resulted from human influence
 on seed dispersal and germination on the Southern Brazilian plateau. The
 Mantiqueira population, in contrast, expanded only recently (~3kya). This
 timing coincides with Holocene climatic changes and human settlements
 established further south, although, to date, there is little
 archeological evidence of human impact in the Mantiqueira. In addition,
 multitemporal species distribution models built from a combination of
 present-day and pollen records infer range expansion of the Araucaria
 Forest during glacial times until the cold humid HS1 event (~16kya), when
 the forest was most widespread, with no evidence of glacial refugia. The
 combination of genomic and spatial analyses suggests that both human and
 climatic controls played a role in the dynamics of the Araucaria Forest.
description: # Evaluating the impact of historical climate and early human groups in
 the *Araucaria* Forest of Eastern South America
 [https://doi.org/10.5061/dryad.9ghx3ffr8](https://doi.org/10.5061/dryad.9ghx3ffr8) ## Description of the data and file structure * Fossil_pollen_reference_list.pdf – complete list of references from which fossil pollen data were retrieved and used in the multitemporal species distribution models of *Araucaria angustifolia*. * Fossil_pollen_data_Araucaria.xlsx – spreadsheet containing two tabs: [data] with the data retrieved from the reference list above, and [colunm_description] with explanations of the column names. Each row of data refers to a sediment layer covering a period described in the 'sedim_young' and 'sedim_old' columns, which might portray a discontinuous distribution of *Araucaria* pollen in the core over time (if more than one row). Columns named in gray describe data directly retrieved from each reference and columns named in yellow contain our calibrated dates including (+ or -) error estimates from which the occurrence matrix for each time frame was built. Sites (1 to 38) where *Araucaria* occurred at any point in time are shown in blue and sites (39 to 64) where *Araucaria* was never recorded are shown in red. * AraucariaOccurrenceData.csv – georeferenced occurrence data (latitude and longitude) for *Araucaria angustifolia* trees in the present. GPS data from field collections. * arauc-SE-10X_n46.ustr – input file with the unlinked SNPs (a single SNP per locus) used for the genetic structure analysis (STRUCTURE). This file was generated after the assembly in ipyrad and it includes, in addition to the data, a column of locality numbers right after the individual's names and a first row with marker names. * arauc-SE-10X_n46_mod.nex – input nexus file (interleaved) with the assembled sequence loci across all individuals (missing data = N). This file was generated after the assembly in ipyrad and modified to include the individual's names in the right format to be imported in the SplitsTree software. * arauc-SE-10X_n46.vcf – input VCF file of all SNPs recovered across the 3517 loci. This file was generated after the assembly in ipyrad and used in VCFtools to calculate pairwise *Fst* and inbreeding coeficient *Fis* for the landscape genetic analyses. * arauc-SE-10X_n46.alleles – input file used in the demographic analyses of PipeMaster with the entire sequence loci for the individuals included in each locus. This file includes both alleles (0 and 1), and it was generated after the assembly in ipyrad and processed using the function iPyrad.alleles.loci2fasta() in PipeMaster to convert the alleles file into several fasta files (one for each locus). ## Sharing/Access information If using this dataset, please cite: Vasconcellos MM, Varela S, Reginato M, Gehara M, Carnaval AC, Michelangeli FA. 2024. Evaluating the impact of historical climate and early human groups in the *Araucaria* Forest of Eastern South America. *Ecography*. [https://doi.org/10.1111/ecog.06756](https://doi.org/10.1111/ecog.06756)