Hosts winnow symbionts with multiple layers of absolute and conditional discrimination mechanisms

In mutualism, hosts select symbionts via partner choice and preferentially direct more resources to symbionts that provide greater benefits via sanctions. At the initiation of symbiosis, prior to resource exchange, it is not known how the presence of multiple symbiont options (i.e., the symbiont social environment) impacts partner choice outcomes. Furthermore, little research addresses whether hosts primarily discriminate among symbionts via sanctions, partner choice or a combination. We inoculated the legume, Acmispon wrangelianus, with 28 pairs of fluorescently labeled Mesorhizobium strains that vary continuously in quality as nitrogen-fixing symbionts. We find that hosts exert robust partner choice, which enhances their fitness. This partner choice is conditional such that a strain's success in initiating nodules is impacted by other strains in the social environment. This social genetic effect is as important as a strain's own genotype in determining nodulation and has both transiti..., We transformed eight Mesorhizobium strains to express fluorescent markers. We grew Mesorhizobium in symbiosis with a single genotype of the native Acmispon wrangelianus host plant as both 1-strain inoculations (8 treatments) and all possible 2-strain combinations (28 treatments), replicated over 8 blocks. Rhizobia and host plant fitness data were measured in the greenhouse experiment (symbiosis_phenotype_data.csv).  We also measured reproductive fitness of rhizobia in nodules (cfu_data.csv) and measured each strains intrinsic axenic growth rate (growth_data.csv)., We provide three datasets as csv files and one R code file that contains code for analyzing the data in these files. In addition, two more csv files are provided to save time but these files can also be regenerated using code in the R file. See the README file for metadata for each data set. The contents of each file are as follows:
* symbiosis_phenotype_data.csv contains Mesorhizobium and host plant fitness data from the greenhouse experiment. This file contains a metadata description in the first column.
* cfu_data.csv contains nodule culturing data (counts of colony forming units). This file contains a metadata description in the first column.
* growth_data.csv contains each of the eight Mesorhizobium strains growth rate. This file contains a metadata description in the first column.
* noduleproportion_models_randomized.csv is an extra file that is provided to save time when reproducing part of figure S2 (nodule proportion), or the code that generated this output file is included in ...

在互利共生体系中，宿主通过伴侣选择（partner choice）筛选共生体，并通过制裁机制优先向提供更高收益的共生体分配更多资源。在共生起始阶段、资源交换发生之前，宿主面对多种共生体可选对象（即共生体社会环境）时，其伴侣选择的结果会受到何种影响，目前尚不明确。此外，鲜有研究探讨宿主主要通过制裁机制、伴侣选择，还是二者结合来区分共生体。

我们以28组荧光标记的中慢生根瘤菌（Mesorhizobium）菌株组合接种豆科植物Acmispon wrangelianus，这些菌株作为固氮共生体的质量呈连续梯度变化。研究发现宿主可实施稳健的伴侣选择，这一过程可提升宿主的适合度。该伴侣选择具有条件依赖性：菌株启动结瘤的成功率会受到社会环境中其他菌株的影响。这种社会遗传效应在调控结瘤过程中的重要程度与菌株自身基因型不相上下，且兼具……

我们对8株中慢生根瘤菌进行了荧光标记转化。我们以单一基因型的本土宿主植物Acmispon wrangelianus与中慢生根瘤菌构建共生体系，设置两种接种处理：单菌株接种（共8组处理）以及所有可能的双菌株组合接种（共28组处理），每组处理设置8次生物学重复。在温室实验中测定了根瘤菌与宿主植物的适合度数据（文件symbiosis_phenotype_data.csv）。此外，我们还测定了根瘤菌在根瘤内的繁殖适合度（cfu_data.csv，即菌落形成单位计数数据），并测定了8株菌株的纯培养生长速率（growth_data.csv）。

本数据集包含3个CSV格式数据文件与1个R代码文件，后者用于实现上述数据的分析流程。此外，为节省复现时间，我们额外提供了2个CSV文件；用户也可通过R代码文件中的代码重新生成这些文件。各数据集的元数据详见README文件，各文件内容说明如下：
* symbiosis_phenotype_data.csv：包含温室实验中获取的中慢生根瘤菌与宿主植物适合度数据，该文件的第一列包含元数据说明。
* cfu_data.csv：包含根瘤培养数据（菌落形成单位计数），该文件的第一列包含元数据说明。
* growth_data.csv：包含8株中慢生根瘤菌的生长速率数据，该文件的第一列包含元数据说明。
* noduleproportion_models_randomized.csv：额外提供的文件，用于节省复现补充图S2（根瘤占比）部分流程的时间；生成该文件的代码已包含在……