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Title: Dataset 2 - Reconstructed Values Open Access Deposited

http://creativecommons.org/licenses/by-nc/4.0/
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  • Species’ Range Occurrences The geographic distributions (or range) of the modern African species were downloaded as GIS shapefiles from the IUCN Red List  https://wwww.iucnredlist.org. Each shapefile was loaded into QGIS version 2.18. A point-based sampling method was used following Polly (2010). Points were spaced at 50 km intervals over a map of Africa (points and map available at  https://www.pollylab.org/publications). The geographic distribution shapefile of a given species was superimposed over the 50 km intervals and the points of overlap between the two were extracted as the species’ range occurrence (Figure 4.1; Lawing & Polly, 2011). Climate Envelope Modeling To construct the climate envelopes of the modern species, global climate data were downloaded from the WorldClim database version 2.0 ( www.worldclim.org) at 2.5 arc-minute resolution (Hijmans et al., 2005). The data consists of nineteen bioclimatic (BIOCLIM) variables that describe the mean, minimum, and maximum temperature, and precipitation on a monthly, quarterly, and annual basis from 1970 to 2000 (Nix, 1986). All bioclimate values were calculated but only four of the nineteen variables were used for this study (Table 4.3). These are the variables commonly used in other studies on Olduvai paleoenvironments (e.g. Bonnefille & Riollet, 1980; Bonnefille, 1984; Cerling & Hay, 1986; Magill, et al., 2012, 2013; Farrugia & Njau, 2022; Schap et al., 2024). The data were then imported into QGIS as raster layers. Values for each of the nineteen BIOCLIM variables were extracted for each species at each grid point of their range occurrence (Figure 4.1). Ancestral Climate Envelope Reconstruction The remainder of the analysis was conducted in Mathematica 11.3 using Phylogenetics for Mathematica, version 6.9 (Polly, 2023). Phylogenetic trees for each extinct species were created using data from published sources (Appendix 4.3). Trees that included non-African species were pruned using the PruneTree function in Phylogenetics for Mathematica Version 6.9 (Polly, 2023) to include only their African relatives. The phylogenetic matrices needed for ancestral node reconstructions were then created using the PhylogeneticMatrices function in Phylogenetics for Mathematica Version 6.9 (Polly, 2023). These matrices are described by Martins & Hansen (1997). To construct the ancestral climate envelopes for extinct species, the mode (mean was used for all instances where there was no mode or more than one mode) of each BIOCLIM variable for each modern species was mapped onto composite phylogenies of the corresponding clade (Figure 4.2) using the ReconstructNodes function in Phylogenetics for Mathematica Version 6.9 (Polly, 2023). The ancestral reconstruction is based on a Brownian motion model of evolution following Martins & Hansen (1997). This approach determines the most likely value at each node and returns the rate, node reconstructions, and standard deviations of the nodes. The estimated value at any given point in time along a lineage is derived through a linear interpolation between neighboring nodes or tips and nodes (Lawing & Polly, 2011; Polly, 2023). For any given time bin, the paleoclimate was estimated as follows: 1) Identify the vertebrate taxa present at Olduvai during the bin in question. 2) Collect climate data and create climate envelopes for the close relatives of each fossil taxon. 3) Utilize Brownian motion ancestor state reconstruction to map the median values of the four climate variables from Table 4.3 onto the respective phylogenetic tree. 4) For each fossil taxon, reconstruct its climate variables by tracing back the length of time in question (ex. 1.8 Ma) along the branch of its closest living relative. 5) Compute the average of all the reconstructions for each fossil taxon within each Olduvai time bin as the best estimate of the paleoclimate variable for that bin and calculate the variance of those reconstructions as an estimate of the standard error. The climate envelopes consist of the mean, minimum, and maximum values of each BIOCLIM variable for all species occurring during that period (Table 4.4). Time periods were selected based on known Tuff dates from Deino (2012); Deino et al., (2021); Smedley et al., (2024). The specific time periods selected for this study are outlined in Table 4.5.
Description
  • Paleoclimate values for Olduvai Gorge obtained through ancestral state reconstructions using a Brownian model of evolution,
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  • pfarrugi@iu.edu
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  • 04/14/2024
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To Cite this Work:
Paul Farrugia Dataset 2 - Reconstructed Values [Data set]. Indiana University - DataCORE.

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