Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding

DNA metabarcoding was employed to identify plant-derived food resources for the Japanese rock ptarmigan ( Lagopus muta japonica ), which is registered as a natural living monument in Japan, in the Northern Japanese Alps in Toyama Prefecture, Japan, in July to October, 2015–2018. DNA metabarcoding us...

Full description

Bibliographic Details
Published in:PLOS ONE
Main Authors: Fujii, Taichi, Ueno, Kaoru, Shirako, Tomoyasu, Nakamura, Masatoshi, Minami, Motoyasu
Other Authors: Šiler, Branislav T., JSPS Grant in Aid for Scientific Research, Chubu University Grant, DAIKO FOUNDATION
Format: Article in Journal/Newspaper
Language:English
Published: Public Library of Science (PLoS) 2022
Subjects:
Online Access:http://dx.doi.org/10.1371/journal.pone.0252632
https://dx.plos.org/10.1371/journal.pone.0252632
Description
Summary:DNA metabarcoding was employed to identify plant-derived food resources for the Japanese rock ptarmigan ( Lagopus muta japonica ), which is registered as a natural living monument in Japan, in the Northern Japanese Alps in Toyama Prefecture, Japan, in July to October, 2015–2018. DNA metabarcoding using high-throughput sequencing (HTS) of rbcL and ITS2 sequences from alpine plants found in ptarmigan fecal samples collected in the study area. The obtained sequences were analyzed using a combination of a constructed local database and the National Center for Biotechnology Information (NCBI) database, revealed that a total of 53 plant taxa were food plant resources for ptarmigans. Of these plant taxa, 49 could be assigned to species (92.5%), three to genus (5.7%), and one to family (1.9%). Of the 23 plant families identified from the 105 fecal samples collected, the dominant families throughout all collection periods were Ericaceae (99.0% of 105 fecal samples), followed by Rosaceae (42.9%), Apiaceae (35.2%), and Poaceae (21.0%). In all of the fecal samples examined, the most frequently encountered plant species were Vaccinium ovalifolium var. ovalifolium (69.5%), followed by Empetrum nigrum var. japonicum (68.6%), Kalmia procumbens (42.9%), Tilingia ajanensis (34.3%) and V . uliginosum var. japonicum (34.3%). A rarefaction analysis for each collection period in the study revealed that the food plant resources found in the study area ranged from a minimum of 87.0% in July to a maximum of 97.5% in September, and that 96.4% of the food plant taxa were found throughout the study period. The findings showed that DNA metabarcoding using HTS to construct a local database of rbcL and ITS2 sequences in conjunction with rbcL and ITS2 sequences deposited at the NCBI, as well as rarefaction analysis, are well suited to identifying the dominant food plants in the diet of Japanese rock ptarmigans. In the windswept alpine dwarf shrub community found in the study area, dominant taxa in the Ericaceae family were the major food plant ...