Sample collection

In July–August 2018, fecal samples were collected from four locations in southern China (Fig. 6). The Jiumen cave with about 200 m elevation is located in Lengshuijiang City, Hunan Province, and is surrounded by evergreen broad-leaved forest and rice farmland (64). The Luohan cave with about 450 m elevation is located in Ganzhou City, Jiangxi Province, and is surrounded by evergreen broad-leaved forest (65). The Longxu cave and Xianren cave with about 2,100 m elevation are located in Kunming City, Yunnan Province. These two caves are located on the Yunnan–Guizhou Plateau and are surrounded by semi-humid evergreen broad-leaved forest and farmland (tobacco and corn) (66). Eight bat species were collected, including R. episcopus from the Jiumen (n = 12) and Luohan caves (n = 10); M. fuliginosus (n = 9), A. stoliczkanus (n = 6), and M. laniger (n = 12) from the Longxu cave; R. osgoodi (n = 12), R. ferrumequinum (n = 11), R. affinis (n = 12), R. pusillus (n = 10), and R. episcopus (n = 12) from the Xianren cave. Given that the Longxu and Xianren caves are located just slightly over 1 km apart, the sympatric distribution of the bats in the two caves was documented for this study (Table 3). The collection was conducted during the nonmating and nonlactating periods. From 21:00 in the evening to 4:00 the following morning, bats were captured with mist nets at the entrance of each cave as they returned to the cave. Species and gender were identified based on external morphological characteristics, and bats were judged as juveniles or adults based on epiphyseal fusions (67). First, juveniles were immediately released in situ after being identified. Next, captured bats were placed individually in sterilized kraft paper bags for 2 h while droppings were collected. The bags were checked frequently to ensure the collection of fresh droppings. The droppings were placed into lyophilized tubes containing RNAlater (RNA-EZ Reagents RNA-Be-Locked A, Sangon Biotech, China) using sterilized forceps. At least five droppings per bat were collected and stored at −80°C for DNA extraction. The body mass was determined with an electronic balance (ProScale LC-50, Accurate Technology, Asheville, USA, 0.01 g). The elevation and latitude of the sampling sites were measured using a global positioning instrument (GPSmap60CSx, GARMIN, Shanghai, China) (Table 3). The bats were released at the cave entrance immediately after droppings collection and measurements were finished.

Map of sampling site distribution and elevation, with pie charts showing samples per species composition and proportions within habitats.

Collection sites and species information of bats^a