Occurrence records of ten Southern Ocean myctophid species with associated sea surface and depth-specific environmental conditions

This dataset contains occurrence records for ten Southern Ocean myctophid fish species that have been downloaded and cleaned from the online biodiversity repository GBIF. As well as providing GBIF documented metadata for each occurrence record, this dataset provides environmental conditions - specifically bathymetry, temperature, salinity, dissolved oxygen and net primary productivity - for each record. Both sea-surface and depth-specific values for the temperature, salinity and oxygen variables are given in separate data files. A third data file of corresponding background points and their associated environmental conditions is also provided. Together these data were used as input files for the MaxEnt ecological niche models within the peer reviewed article: Freer JJ, Tarling GA, Collins MA, Partridge JC, Genner MJ (2020) Estimating circumpolar distributions of lanternfish using 2D and 3D ecological niche models, Marine Ecology Progress Series.,Occurrence records and environmental data were downloaded from online and open access sources (see the Reference section). For the 2D model approach, occurrence and background points were matched to the appropriate environmental conditions using the "prepareSWD" function from the R package "SDMTUNE". Sea surface conditions are matched to all records, regardless of the depth they were caught at. For the 3D model approach, occurrence and background points were matched to the appropriate environmental conditions using the "depth_extract" function from Duffy and Chown (2017) source code available at: https://figshare.com/articles/Duffy_Chown_MEPS12011_model_virtualspecies/4315052. This ensures each occurrence or background point is only matched to the environmental conditions from the depth closest to the depth from which the record came from. File: occurrence_data_2D.csv Volume: 6 megabytes Contents: This file contains the cleaned and processed occurrence records of the ten myctophid species modelled in the study and the sea surface environmental conditions associated to each presence locality. Data columns and units: NAME = species LON = longitude (decimal degrees) LAT = latitude (decimal degrees) DEPTH = depth of catch information (metres) BATHYMETRY = bathymetry (metres) O2 = dissolved oxygen at the sea surface (mmol-m3) PP = primary organic carbon production by all types of phytoplankton in the upper 150m (nmol m-2 s-1) SAL = sea surface salinity (PSU) TEMP = sea surface temperature (degrees celcius) ALL OTHER COLUMNS = STANDARD GBIF METADATA File: occurrence_data_3D.csv Volume: 4.5 megabytes Contents: This file contains the cleaned and processed occurrence records of the ten myctophid species modelled in the study and the depth-specific environmental conditions associated to each presence locality. Data columns and units: NAME = species LON = longitude (decimal degrees) LAT = latitude (decimal degrees) DEPTH = depth of catch information (metres) BATHYMETRY = bathymetry (metres) O2 = depth-specific dissolved oxygen at (mmol-m3) PP = primary organic carbon production by all types of phytoplankton in the upper 150m (nmol m-2 s-1) SAL = depth-specific salinity (PSU) TEMP = depth-specific temperature (degrees celcius) ALL OTHER COLUMNS = STANDARD GBIF METADATA File: background_data_2D_AND_3D.csv Volume: 1.2 megabytes Contents: This file contains the coordinates of the background data generated for the study. Both the 2D (suface) and 3D (depth-specific) environmental conditions are given for each point. Data columns and units: NAME = identifier for background data "bg" LON = longitude (decimal degrees) LAT = latitude (decimal degrees) DEPTH = depth assigned to each point (metres) BATHYMETRY = bathymetry (metres) PP = primary organic carbon production by all types of phytoplankton in the upper 150m (nmol m-2 s-1) O2_2D = dissolved oxygen at the sea surface (mmol-m3) SAL_2D = sea surface salinity (PSU) TEMP_2D = sea surface temperature (degrees celcius) O2_3D = depth-specific dissolved oxygen (mmol-m3) SAL_3D = depth-specific salinity (PSU) TEMP_3D = depth-specific temperature (degrees celcius) File: GBIF_citations.txt Volume: 6 kilobytes Contents: A citation list of all contributing datasets for occurrence records downloaded from GBIF, generated in 2020 via R package "rgbif".,All analyses were carried out in R version 3.5.3.,Occurrence records for all ten species were downloaded from the Global Biodiversity Information Facility (GBIF). These occurrence records represent those remaining after undertaking following quality assurance and control processes. Unreliable data, which included records with identical latitude and longitude, and records with a latitude and longitude corresponding to a terrestrial location, were removed. Due to high sampling bias towards austral spring and summer seasons, only records from the months October-March were kept for analyses. Furthermore, only occurrence records from 1960 to 2010 were retained, to correspond to a similar baseline period of available environmental data. Duplicate records were excluded from model runs. Citations for all data (occurrence and environmental data) are given in the Reference section.,

本数据集包含从在线生物多样性知识库全球生物多样性信息机构（Global Biodiversity Information Facility，GBIF）下载并清洗后的10种南大洋灯笼鱼的物种出现记录。本数据集不仅为每条物种出现记录提供GBIF元数据，还为每条记录提供了对应的环境条件数据，具体包括水深地形、温度、盐度、溶解氧与净初级生产力。温度、盐度与溶解氧变量的海表值及水深分层值分别存储于不同的数据文件中。此外还提供了第三份数据文件，包含对应的背景点及其关联的环境条件数据。上述所有数据均作为输入文件，用于同行评议论文《使用二维与三维生态位模型估算灯笼鱼环极分布范围》（Freer JJ, Tarling GA, Collins MA, Partridge JC, Genner MJ, 2020, *Marine Ecology Progress Series*）中的最大熵（MaxEnt）生态位模型构建。

物种出现记录与环境数据均从公开在线数据源下载（详见参考文献部分）。针对二维模型方法，本研究使用R软件包"SDMTUNE"中的"prepareSWD"函数，将物种出现点与背景点匹配至对应的环境条件数据；无论采样记录的实际捕获水深，所有记录均匹配海表环境条件。针对三维模型方法，本研究使用Duffy与Chown（2017）公开于https://figshare.com/articles/Duffy_Chown_MEPS12011_model_virtualspecies/4315052 的源代码中的"depth_extract"函数，将物种出现点与背景点匹配至对应的环境条件数据，此举可确保每个出现点或背景点仅匹配至与该记录采样水深最接近的水深层的环境条件。

文件：occurrence_data_2D.csv，大小：6兆字节
内容：本文件包含本研究建模所用的10种灯笼鱼的清洗与预处理后的物种出现记录，以及各采样点对应的海表环境条件数据。
数据列与单位：
NAME = 物种名称
LON = 经度（十进制度数）
LAT = 纬度（十进制度数）
DEPTH = 采样捕获水深（米）
BATHYMETRY = 水深地形（米）
O2 = 海表溶解氧（mmol·m⁻³）
PP = 上层150米内所有浮游植物产生的有机碳初级生产量（nmol·m⁻²·s⁻¹）
SAL = 海表盐度（实用盐度单位，PSU）
TEMP = 海表温度（摄氏度）
其余所有列 = 标准GBIF元数据

文件：occurrence_data_3D.csv，大小：4.5兆字节
内容：本文件包含本研究建模所用的10种灯笼鱼的清洗与预处理后的物种出现记录，以及各采样点对应的水深分层环境条件数据。
数据列与单位：
NAME = 物种名称
LON = 经度（十进制度数）
LAT = 纬度（十进制度数）
DEPTH = 采样捕获水深（米）
BATHYMETRY = 水深地形（米）
O2 = 水深分层溶解氧（mmol·m⁻³）
PP = 上层150米内所有浮游植物产生的有机碳初级生产量（nmol·m⁻²·s⁻¹）
SAL = 水深分层盐度（实用盐度单位，PSU）
TEMP = 水深分层温度（摄氏度）
其余所有列 = 标准GBIF元数据

文件：background_data_2D_AND_3D.csv，大小：1.2兆字节
内容：本文件包含本研究生成的背景数据坐标信息，每个点均附带二维（海表）与三维（水深分层）环境条件数据。
数据列与单位：
NAME = 背景数据标识符"bg"
LON = 经度（十进制度数）
LAT = 纬度（十进制度数）
DEPTH = 分配给各点的水深（米）
BATHYMETRY = 水深地形（米）
PP = 上层150米内所有浮游植物产生的有机碳初级生产量（nmol·m⁻²·s⁻¹）
O2_2D = 海表溶解氧（mmol·m⁻³）
SAL_2D = 海表盐度（实用盐度单位，PSU）
TEMP_2D = 海表温度（摄氏度）
O2_3D = 水深分层溶解氧（mmol·m⁻³）
SAL_3D = 水深分层盐度（实用盐度单位，PSU）
TEMP_3D = 水深分层温度（摄氏度）

文件：GBIF_citations.txt，大小：6千字节
内容：本文件包含从GBIF下载的物种出现记录所涉及的所有贡献数据集的引用列表，于2020年通过R软件包"rgbif"生成。

所有分析均在R 3.5.3版本中完成。本研究所有10个物种的物种出现记录均下载自全球生物多样性信息机构（GBIF）。这些出现记录均经过质量保证与质控流程筛选后保留：移除了经纬度完全一致的记录、以及经纬度对应陆地区域的不可靠记录。由于采样存在偏向南半球春季与夏季的偏差，本研究仅保留10月至次年3月的记录用于分析。此外，仅保留1960年至2010年的物种出现记录，以匹配现有环境数据的基准时段。模型运行过程中剔除了重复的出现记录。所有数据（物种出现记录与环境数据）的引用信息详见参考文献部分。