Bayesian tracer mixing models and isotope data elephant diet

Supplementary information and carbon and nitrogen isotope data analysed in publication 'Timing of dietary switching by savannah elephants in relation to crop consumption'.<br>Data were collected with permission of the Republic of Botswana Ministry of Environment, Wildlife and Tourism, research permit EWT8/36/4 XXXI (49). Farmers' reports of elephant crop consumption were collected by community officers of the NGO the Ecoexist project.<br><br><b>Supplementary information</b><br>In the supplementary information we explain why we did not use Bayesian tracer mixing models in the final paper.<br><b>Isotope data</b><br>We air-dried the faecal and vegetation samples in an air-drying cabinet. After transportation, we dried samples for a further 24 h at 70 °C and ground to pass through a 1 mm mesh at the Okavango Research Institute laboratory. Samples were then shipped to the stable isotope laboratory housed in the archaeology department at the University of Cape Town, South Africa. There they were weighed in to tin cups to an accuracy of 1 mg on a Sartorius M2P microbalance.Sample weights were 2.5 mg for samples with potentially low nitrogen content, 2.1–2.2 mg for legumes and agricultural samples and 2.3 mg for other sample types. Samples were combusted in a Flash 2000 elemental analyser interfaced to a Delta V Plus isotope ratio mass spectrometer (IRMS) via a Conflo IV gas control unit (Thermo Scientific,Bremen, Germany). The in-house standards used were: Sucrose(“Australian National University (ANU)”sucrose), MG (Merck Gel), Acacia (Acacia saligna, Glencairn). All the in-house standards were calibrated against IAEA (International Atomic Energy Agency) standards,either at UCT or by other labs. Nitrogen was expressed in terms of its value relative to atmospheric nitrogen, while carbon was expressed in terms of its value relative to Pee-Dee Belemnite (VPDB).In our analyses we use stable isotopic values from faeces and their association to isotopic values of most likely consumed browse and grass species as proxies for elephant diet. In reality, diet content can vary from isotopic content due to issues as fractionation of isotopes during digestion, this is why we correct the results with fractionation values (Codron and Codron, 2009).<br><br>We used a linear two-source mixing model (see Supplementary Information). Following Codron et al., 2011, we used the following linear two-source mixing model in order to calculate the percentage of C3 plants(trees and sedges) and C4 (other grasses):<br><b>% C4 in diet = (d13C C3 plants + efaeces-diet - d13C faeces) / (d13C C3 plants - d13C C4 plants) *100</b><br>In this formula the difference between faeces and diet isotope values (εfaeces−diet) is −0.9‰ (Codron et al., 2005), while for the other values we used the average values for faeces and C4 plants, and weighted average for C3 plants, due to availability of data on proportions of trees species in the elephants' diet (Vogel et al., 2019). Grasses and sedges have similarδ13C values, so we include both in C4 plants. <br><br><b><i>Legend</i></b><br><br><b>Code: </b>elephant dung ID<b>Group: </b>data collection round<br><b>Month: </b>month of data collection<br><b>dN:</b> δ15N value of dung sample<b>dC:</b> δ13C value of dung sample<br><b>dung_Nitro: </b>nitrogen concentration dung sample<b>Sex: </b>elephant sex (BH: Breeding Herd, M: Male bull)<b>Season: </b>rain season period (LD: Late Dry, EW: Early Wet, LW: Late Wet, ED: Early Dry)<b>Crop raids</b>: crop consumption reported by farmers<b>Rainfall: </b>occurrence of rainfall (based on average mm of rain &gt;0 mm reported by Botswana Environmental Statistics at the closest weather station in the region), not included in the current study<b>Crop_phenology: </b>recorded crop phenology based on random selection of five farms across the study site, detailed data available from the first author, not included in the current study<b>C4_nitro: </b>weighted average nitrogen concentration of C4 vegetation (mainly grasses) included in elephant diet, per season. <b>C3_nitro: </b>weighted average nitrogen concentration of C3 vegetation (mainly trees) included in elephant diet, per season. <i><br></i><i>For more information on the data collection, calculation and interpretation of the C4_nitro and C3_nitro values please see this preprint: https://www.biorxiv.org/content/10.1101/673392v1. Details on calculation and data available of these, or other measures are available from the first author.</i>

本数据集为发表于论文《Timing of dietary switching by savannah elephants in relation to crop consumption》（《稀树草原大象饮食转变时机与农作物盗食关联》）中所分析的补充信息及碳、氮同位素数据。本数据的采集已获得博茨瓦纳共和国环境、野生动物与旅游部许可，研究许可编号为EWT8/36/4 XXXI (49)。大象盗食农作物的农户上报数据由非政府组织生态共存项目（the Ecoexist project）的社区专员收集。

<b>补充信息</b>
本补充信息将说明最终论文未采用贝叶斯示踪混合模型的原因。
<b>同位素数据</b>
研究人员首先在风干柜中对粪便与植被样本进行风干。样本经运输后，于70℃下再次烘干24小时，并在奥卡万戈研究所实验室中研磨至可通过1mm孔径的筛网。随后，样本被运往位于南非开普敦大学考古系的稳定同位素实验室。在该实验室中，样本被称入锡杯，使用赛多利斯M2P微量天平（Sartorius M2P microbalance）称重，精度达1mg。其中，氮含量潜在较低的样本称重为2.5mg，豆科与农业样本称重为2.1~2.2mg，其余样本类型称重为2.3mg。
样本通过Flash 2000元素分析仪进行燃烧，该分析仪通过Conflo IV气体控制单元与Delta V Plus同位素比率质谱仪（IRMS，Delta V Plus isotope ratio mass spectrometer）相连，设备制造商为德国不来梅的赛默飞世尔科技（Thermo Scientific）。
本研究使用的内部标准物质包括：澳大利亚国立大学（ANU, Australian National University）蔗糖、默克凝胶（MG, Merck Gel）、细叶金合欢（Acacia saligna, Glencairn）。所有内部标准物质均在开普敦大学或通过其他实验室，与国际原子能机构（IAEA, International Atomic Energy Agency）的标准物质完成校准。
氮同位素值以相对于大气氮的比值表示，碳同位素值以相对于佩迪箭石（VPDB, Pee-Dee Belemnite）的比值表示。
本分析以粪便的稳定同位素值，及其与最可能被取食的木本植物与草本植物的同位素值的关联，作为大象饮食的替代指标。实际饮食组成与同位素组成可能存在差异，原因包括消化过程中的同位素分馏，因此研究人员通过分馏值对结果进行了校正（Codron & Codron, 2009）。

研究使用线性双源混合模型（详见补充信息）。参考Codron等人2011年的研究，本研究采用如下线性双源混合模型，以计算饮食中C3植物（树木与莎草）与C4植物（其余草本）的占比：
<b>% 饮食中C4植物占比 = (δ¹³C_C3植物 + ε_粪便-饮食 - δ¹³C_粪便) / (δ¹³C_C3植物 - δ¹³C_C4植物) × 100</b>
该公式中，粪便与饮食同位素值的差值（ε_粪便-饮食）为−0.9‰（Codron et al., 2005）；其余数值方面，研究使用了粪便与C4植物的平均值，以及C3植物的加权平均值——这是由于已有关于大象饮食中树木物种占比的公开数据（Vogel et al., 2019）。草本与莎草的δ¹³C值相近，因此将二者均归入C4植物范畴。

<b><i>变量说明</i></b>

<b>Code: </b>大象粪便编号
<b>Group: </b>数据采集轮次
<b>Month: </b>数据采集月份
<b>dN:</b> 粪便样本的δ¹⁵N值
<b>dC:</b> 粪便样本的δ¹³C值
<b>dung_Nitro: </b>粪便氮浓度
<b>Sex: </b>大象性别（BH：繁殖象群，M：成年公象）
<b>Season: </b>雨季分期（LD：晚旱季，EW：早雨季，LW：晚雨季，ED：早旱季）
<b>Crop raids</b>: 农户上报的大象盗食农作物情况
<b>Rainfall: </b>降雨量情况（基于研究区域最近气象站报告的平均降雨量>0mm的数据，本研究未纳入该变量）
<b>Crop_phenology: </b>基于研究区域内5个随机选取农场记录的作物物候期，详细数据可联系第一作者获取，本研究未纳入该变量
<b>C4_nitro: </b>按季节划分的、纳入大象饮食的C4植被（主要为草本）的加权平均氮浓度
<b>C3_nitro: </b>按季节划分的、纳入大象饮食的C3植被（主要为树木）的加权平均氮浓度
<i>如需了解C4_nitro与C3_nitro值的数据采集、计算与解释的更多信息，请参阅该预印本：https://www.biorxiv.org/content/10.1101/673392v1。上述指标及其他指标的计算与数据详情可联系第一作者获取。</i>