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Update:June 20, 2019

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Grasslands have been preserved for a Hundred Thousand Years in Japan as a Forested country—Recent Radical Decrease in Grasslands Marks a Major Milestone on a Geological Time Scale


Article title

Genomic reconstruction of a 100,000-year history of grasslands in a forested country: population dynamics of specialist forbs

Author (affiliation)

Yuichi Yamaura (a), Ayu Narita (b), Yoshinobu Kusumoto (c), Atsushi Nagano (d), Ayumi Tezuka (d), Toru Okamoto (e), Hikaru Takahara (f), Futoshi Nakamura (g), Yuji Isagi (h), David Lindenmayer (i)

(a) Shikoku Research Center, FFPRI, Kochi, Japan.

(b) Hokkaido Research Organization, Bibai, Hokkaido, Japan.

(c) National Agriculture and Food Research Organization, Zentsuji, Kagawa, Japan.

(d) Ryukoku University, Otsu, Shiga Japan.

(e) Kansai Research Center, FFPRI, Kyoto, Japan.

(f) Kyoto Prefectural University, Kyoto, Japan.

(g) Hokkaido University, Sapporo, Hokkaido, Japan.

(h) Kyoto University, Kyoto, Japan.

(i) Australian National University, Canberra, ACT, Australia.

Publication Journal Biology Letters, 29 May 2019 DOI:10.1098/rsbl.2018.0577( External link )
Content introduction

Up to a century ago, grasslands*1 had accounted for more than 10% of Japan’s land area, serving as an essential site for the production of manure, livestock fodder, and roof thatch material. However, modernization has made these roles of grasslands obsolete. As a result of their conversion into artificial plantations or their transition into natural forests because of a lack of proper management, grasslands now occupy only 1% of Japan’s land area. Consequently, many species dependent on grasslands are presently on the verge of extinction. Then, what kind of impact does the decrease in grasslands and biodiversity have on a geological time scale, which is measured in 1,000–10,000-year increments?

Throughout the history of Japanese grasslands, “black soil,” which covers 17% of the total land area, has been attracting attention. It has been suggested that black soil develops in an environment where herbaceous vegetation has been thriving for an extended period. Thus, the fact that black soil is distributed throughout Japan likely indicates that grasslands have been preserved both extensively and continuously in the country. Conversely, pollen analysis, which has been performed to investigate the succession of vegetation, has produced no conclusive evidence that grasslands have been continuously maintained in Japan, leaving a major gap between facts and evidences. Moreover, no consensus has been reached on whether black soil is definitely derived from grasslands. Because pollen analysis is limited to deposited sediment in humid environments where pollen is not readily decomposed, reconstructing the history of dry grasslands based on black soil distribution and pollen analysis was an endeavor that was bound to reach an impasse.

In this study, we attempted to explore the history of grasslands by genetically analyzing four herbaceous plants that have been familiar to Japanese people and used to be distributed widely: Swertia japonica, Dianthus superbus, Patrinia scabiosifolia, and Sanguisorba officinalis (Figure 1, left). Specifically, we collected leaves of these species from 25 grasslands across the country (Figure 1, right). DNA extracted from these leaves were analyzed by a next-generation sequencer*2, yielding a large number of genome sequences. The information contained in these sequences was analyzed using population genetics to estimate past changes in the number of individuals (population size) of each species in each grassland.

We were able to track changes in population size back to several hundred thousand to hundred years ago, albeit with some variation depending on the species. This analysis revealed that the population sizes of the analyzed species have been maintained by a factor of 0.5–2.0-fold over the past hundred thousand years (Figure 2). These results suggest that Japanese grasslands have been stably maintained on a geological time scale. Therefore, the drastic decrease in grasslands during the past century is likely to constitute a major milestone from the geological perspective.

*1: Grasslands

Here grasslands refer to “semi-natural grasslands,” that are maintained by human hand without intensive interventions such as fertilization and sowing.

*2: Next-generation sequencer

An instrument capable of rapidly decoding genome sequences. Since their development in the 2000s, these instruments have revolutionized genetic research. This study employed next-generation sequencing to decode sequences of approximately 100 million base pairs for each species. The use of large-volume genetic information facilitates high-precision genetic analysis.

 Figure1. (Left) Four herbaceous plant species specialized

Figure 1. (Left) Four herbaceous plant species specialized to grasslands: (a) Swertia japonica, (b) Dianthus superbus, (c) Patrinia scabiosifolia, and (d) Sanguisorba officinalis. (Right) A typical grassland maintained by intentional burning (Soni Highlands, Nara).

Figure2. Changes in the population sizes of the four herbaceous

Figure 2. Changes in the population sizes of the four herbaceous plant species as estimated by genetic analysis

For each species, a survey was conducted in 10 grasslands to determine changes in the population size. The horizontal axis represents time (right to left, changes in the population size from the past to present). The vertical axis represents the ratio of the past population size to the population size from several hundred years ago. The bold gray line signifies the mean changes in the ten surveyed locations, with the gray area indicating the 95% confidence interval.
Except for S. japonica, the population sizes increased from a million years ago to hundred thousand years ago. Subsequently, the population size of D. superbus remained unchanged, whereas the population sizes of P. scabiosifolia and S. officinalis continued decreasing until ten thousand years ago. It was inferred that the population size of S. japonica increased from a hundred thousand years ago to ten thousand years ago, after which it was maintained at a constant level. The 95% confidence intervals of the 10 locations as depicted in the gray area suggest that the population sizes of the four species have been maintained within a factor of 0.5–2.0 over the past hundred thousand years.