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

Taichi Fujii,Tomoyasu Shirako,Masatoshi Nakamura,Motoyasu Minami,Kaoru Ueno,Branislav T Šiler

doi:10.1371/journal.pone.0252632

Taichi Fujii, Tomoyasu Shirako + Show 4 more

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https://doi.org/10.1371/journal.pone.0252632

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Journal: PloS one	Publication Date: Mar 10, 2022
Citations: 11	License type: CC BY 4.0

Affiliation: Chubu University

Abstract

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 s for Japanese rock ptarmigans from July to October. This plant community therefore needs to be conserved in order to protect the food resources of Japanese rock ptarmigans in the region.

Highlights

There is concern that changes in the habitat of alpine flora due to global warming will result in the extinction of endangered animals that utilize endemic alpine plants that grow above the tree line in the alpine meadow zone as food resources
Some taxa could only be identified to the genus or family level due to having the same rbcL sequences; three species in family Asteraceae (Cirsium otayae, Hieracium japonicum, and Solidago virgaurea subsp. asiatica), two species in genus Rhododendron (R. brachycarpum and R. tschonoskii subsp. trinerve), and three species in genus Vaccinium (V. shikokianum, V. smallii var. smallii, and V. uliginosum var. japonicum) [22]
For the four out of six ITS2 sequences that could not be amplified in this study, the sequences used in our local database of ITS2 sequences were obtained from National Center for Biotechnology Information (NCBI) (Cornus canadensis, MG218733, accession no.; E. vaginatum, JX566737; Maianthemum dilatatum, KY908558; and Polytrichum juniperinum, MF180404)

Summary

Introduction

Global climate change will alter the current distribution patterns of alpine biota, threatening many of the endemic species that are adapted to alpine ecosystems with extinction [1]. There is concern that changes in the habitat of alpine flora due to global warming will result in the extinction of endangered animals that utilize endemic alpine plants that grow above the tree line in the alpine meadow zone as food resources. During the breeding season (April to May), the male occupies a territory of 0.015 to 0.072 km2 [6] The female builds her nest at the base of P. pumila trees from June to July, and lays her eggs in July [4,7]. The female alone incubates the eggs and raises the chicks until October, at which time they become independent [4] When their habitat (alpine meadow zone) is covered with snow (November to April), the Japanese rock ptarmigan migrates to the forest zone, returning to the alpine meadow zone as the snow begins to melt [8]

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