DOI: 10.57760/sciencedb.01856
title: Phylogenetic and biogeographical data of the southern hemisphere temperate tree flora
title: Phylogenetic and biogeographical data of the southern hemisphere temperate tree flora

description: Dataset contains a comprehensive lists of tree species of temperate forests in the southern hemisphere, constructed upon national checklists and mapped using georeferences obtained from open and private sources. Phylogenetic reconstructions based on a Bayesian inference analysis and two plastidial regions for all the genera containing woody taxa in these forests is also available.The area included in the dataset corresponds to Temperate Forests as defined by Olson et al. (2001) in South America and Oceania, from 32.8°S to 56.0°S in South America, 23.9°S to 43.6°S in Australia and 34.4°S to 47.3°S in New Zealand.Australian tree species were compiled from Boland & McDonald (2006) and Krisch (2015), The New Zealand list was based on Dawson et al. (2011), De Lange et al. (2006) y Breitwieser et al. (2010). The South American list was obtained from García y Ormazabal (2008). The Beech et al. (2017) criterion was used to define tree species as “a woody plant with usually a single stem growing to a height of at least two meters, or if multi-stemmed, then at least one vertical stem five centimeters in diameter at breast height”. Georeferences for each species were obtained from Global Biodiversity Information Facility (www.gbif.org), Scherson et al. (2017), Chilean herbaria (CONC, SGO) and databases from the Systematic and Plant Ecology Laboratory, University of Chile.Phylogenetic reconstruction was initially conducted at the genus level based on 271 genetic sequences downloaded from GenBank and two additional sequences that were obtained in our lab for Myrceugenia and Porlieria. A concatenation of plastidial regions rbcL (1519 bp) and matK (2849 bp) was used in a Bayesian inference analysis performed in the CIPRES Science Gateway V. 3.3 Portal (www.phylo.org). The nucleotidic substitutions models for rbcL GTR+G y matK GTR+I+G were applied based on the Akaike Information Criterion. Parameters were sampled 20 x 106 generations and 25% of the first samples were discarded. The Tracer program v1.7.1 (Rambaut et al., 2014) was used to visualize output parameters to prove stationarity and assess convergence of duplicated runs on the same mean likelihood, attaining values of 3268.6 y 35975.0. When there were inconsistencies the ordinal-level, branches were constrained to reflect the APG-IV topology (Chase et al. 2016). Nodes with 0.95 were considered supported for posterior probabilities (Huelsenbeck et al. 2002). To obtain a species-level tree, 0.0001 branch lengths were added to the tips of the generic-level tree for each species in a genus using the package phytools (Revell 2012) on R v.4.0.3 (R Core Team 2020). Common use spredsheet processator, like Microsoft Excel, GIS software, like QGIS, and any software that allows phylogenetic analysis, like R, are required to acces to the data.
description: Dataset contains a comprehensive lists of tree species of temperate forests in the southern hemisphere, constructed upon national checklists and mapped using georeferences obtained from open and private sources. Phylogenetic reconstructions based on a Bayesian inference analysis and two plastidial regions for all the genera containing woody taxa in these forests is also available.The area included in the dataset corresponds to Temperate Forests as defined by Olson et al. (2001) in South America and Oceania, from 32.8°S to 56.0°S in South America, 23.9°S to 43.6°S in Australia and 34.4°S to 47.3°S in New Zealand.Australian tree species were compiled from Boland & McDonald (2006) and Krisch (2015), The New Zealand list was based on Dawson et al. (2011), De Lange et al. (2006) y Breitwieser et al. (2010). The South American list was obtained from García y Ormazabal (2008). The Beech et al. (2017) criterion was used to define tree species as “a woody plant with usually a single stem growing to a height of at least two meters, or if multi-stemmed, then at least one vertical stem five centimeters in diameter at breast height”. Georeferences for each species were obtained from Global Biodiversity Information Facility (www.gbif.org), Scherson et al. (2017), Chilean herbaria (CONC, SGO) and databases from the Systematic and Plant Ecology Laboratory, University of Chile.Phylogenetic reconstruction was initially conducted at the genus level based on 271 genetic sequences downloaded from GenBank and two additional sequences that were obtained in our lab for Myrceugenia and Porlieria. A concatenation of plastidial regions rbcL (1519 bp) and matK (2849 bp) was used in a Bayesian inference analysis performed in the CIPRES Science Gateway V. 3.3 Portal (www.phylo.org). The nucleotidic substitutions models for rbcL GTR+G y matK GTR+I+G were applied based on the Akaike Information Criterion. Parameters were sampled 20 x 106 generations and 25% of the first samples were discarded. The Tracer program v1.7.1 (Rambaut et al., 2014) was used to visualize output parameters to prove stationarity and assess convergence of duplicated runs on the same mean likelihood, attaining values of 3268.6 y 35975.0. When there were inconsistencies the ordinal-level, branches were constrained to reflect the APG-IV topology (Chase et al. 2016). Nodes with 0.95 were considered supported for posterior probabilities (Huelsenbeck et al. 2002). To obtain a species-level tree, 0.0001 branch lengths were added to the tips of the generic-level tree for each species in a genus using the package phytools (Revell 2012) on R v.4.0.3 (R Core Team 2020). Common use spredsheet processator, like Microsoft Excel, GIS software, like QGIS, and any software that allows phylogenetic analysis, like R, are required to acces to the data.