Phylogenetic and biogeographical data of the southern hemisphere temperate tree flora

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.

本数据集收录了南半球温带森林的全套木本树种名录，其编制基于各国官方名录，并通过公开及私有渠道获取的地理参照数据完成空间制图。本数据集同时提供针对该区域内所有含木本类群的属，基于贝叶斯推断分析及两个质体区域序列构建的系统发育重建结果。
本数据集涵盖的区域为Olson等人（2001年）定义的温带森林，分布于南美洲及大洋洲：南美洲范围为南纬32.8°至56.0°，澳大利亚为南纬23.9°至43.6°，新西兰为南纬34.4°至47.3°。
澳大利亚树种名录源自Boland与McDonald（2006）及Krisch（2015）的研究；新西兰树种名录则基于Dawson等人（2011）、De Lange等人（2006）以及Breitwieser等人（2010）的成果；南美洲树种名录取自García与Ormazabal（2008）的研究。
本数据集采用Beech等人（2017）提出的树种定义标准：通常具有单一主干且高度至少达2米的木本植物；若为多主干，则至少存在一根垂直主干，其胸径不小于5厘米。
各物种的地理参照数据源自全球生物多样性信息设施（Global Biodiversity Information Facility, GBIF，www.gbif.org）、Scherson等人（2017）的研究、智利标本馆（CONC、SGO）以及智利大学系统与植物生态实验室的数据库。
系统发育重建最初以属为分类单元开展，所用序列包含从GenBank下载的271条遗传序列，以及本实验室针对Myrceugenia和Porlieria获取的另外2条序列。研究中将质体区域rbcL（1519 bp）与matK（2849 bp）进行序列拼接，并借助CIPRES科学网关V.3.3门户（www.phylo.org）完成贝叶斯推断分析。
基于赤池信息准则（Akaike Information Criterion, AIC），分别为rbcL和matK选用对应的核苷酸替换模型：rbcL采用GTR+G模型，matK采用GTR+I+G模型。马尔可夫链共采样20×10^6代，并舍弃前25%的抽样结果作为燃烧期。使用Tracer软件v1.7.1（Rambaut等人，2014）对输出参数进行可视化，以验证参数平稳性并评估重复运行的收敛性，两次重复运行的平均似然值分别为3268.6和35975.0。
当系统发育树存在拓扑结构不一致时，将分支约束为符合APG IV拓扑结构（Chase等人，2016）。后验概率不低于0.95的节点被视为具有支持度（Huelsenbeck等人，2002）。为构建物种水平系统发育树，本研究借助R v4.0.3环境下的phytools工具包（Revell，2012），为属水平树的每个物种分支末端添加0.0001的分支长度。
访问本数据集需使用常用电子表格软件（如Microsoft Excel）、地理信息系统（GIS）软件（如QGIS）以及任意支持系统发育分析的软件（如R语言）。