Title

Longitudinal and microhabitat distributions of fishes, amphibians, and reptiles and the environmental characteristics in the upper Yura River, Kyoto, Japan

Author

Hikaru Nakagawa¹

¹Field Science Education and Research Center, Kyoto University, Kyoto, JP

Correspondence

Hikaru Nakagawa, Field Science Education and Research Center, Kyoto University, 1 Onojya, Miyama, Nantan, Kyoto, JP, 601-0703

E-mail: hikarunakagawa@icloud.com (Corresponding Author)

Funding information

Ministry of Education, Culture, Sports and Technology, Japan, Global COE Program, A06 ‘Formation of a Strategic Base for Biodiversity and Evolutionary Research: from Genome to Ecosystem’

Abstract

Quantitative data on the distribution of aquatic vertebrate species along environmental gradients at multiple spatial scales are useful for assessing habitat quality, understanding habitat selection, and predicting the population structures of focal species. In addition, comparable datasets for multiple species enable the examination of the interspecific differences in habitat niches and their differentiation or aggregation patterns in a stream assemblage, as well as the theory of species coexistence. The distributions of aquatic vertebrates and environmental characteristics on longitudinal and microhabitat scales were investigated at 21 sites in a temperate stream, the Yura River, Kyoto, Japan, during the day and at night from August to September 2009. The sites were located from the headwaters to about 40 km downstream along the main channel of the river. Snorkeling observations were conducted using the line-transect method following a standardized procedure at each sampling site with a detailed description of the spatial structure of aquatic vertebrate habitats. The microhabitat environments (water depth, current velocity, substratum characteristics, and presence/absence of vegetation cover) could be determined for all observed individuals. A total of 11,724 individuals belonging to 28 fish, two amphibian, and one reptile species were observed. The data can be used to examine the spatial patterns of focal aquatic vertebrate species and assemblages, and interspecific differences in habitat use among sympatric aquatic vertebrate species at multiple spatial scales.

Keywords

amphibians, assemblage, line-transect, microhabitat, reach, reptile, snorkeling, stream environment, stream fish

1 | INTRODUCTION

Quantitative data on the distribution of aquatic vertebrate species along environmental gradients at multiple spatial scales (Frissell et al., 1986) are useful for assessing habitat quality, understanding habitat selection mechanisms, and predicting the population structures of focal species (Fausch et al., 1988; Simonson et al., 1993; Maddock, 1999). In addition, comparable datasets for multiple species enable the examination of the interspecific differences in habitat niches and their differentiation or aggregation patterns in a stream fish assemblage (Simonson et al., 1993; Maddock, 1999), as well as the theory of species coexistence (i.e., habitat niche theory, Hutchinson, 1959).

 The utility of datasets of aquatic vertebrate distributions depends on the use of methodologically unified quantitative observations and having sufficient sample size (Simonson et al., 1993; Maddock, 1999). Comparisons of the quantitative density of focal species or assemblages require systematically planned sampling, such as using quadrat or line-transect methods that standardize the expectation of the number of individuals observed with the same sampling effort (Simonson et al., 1993; Maddock, 1999), removal methods, or mark and recapture methods that mathematically estimate the total number of individuals within an area (Schwarz & Seber, 1999). In addition, the patterns of species distributions are often autocorrelated due to the migration of individuals among local populations (Hanski, 1998). For example, migration events that are less frequent than extinction events generate a habitat patch without a focal species, even if the patch is suitable for that species. By contrast, a focal species may be observed in an unsuitable habitat patch because of frequent migrations from a neighboring source population (Leibold et al., 2004; Holyoak et al., 2005). To consider the autocorrelation of species distributions, the spatial structure of the unit of sampling (i.e., local habitat patch) should be described (Peres-Neto et al., 2012).

 This paper reports the distribution data for 28 fish, two amphibian, and one reptile species observed at 21 sites along the Yura River, northern Kyoto Prefecture, central Japan, during the day and at night from August to September 2009. The sites were located from the headwaters to about 40 km downstream along the main channel of the river. Microhabitat environments could be determined for observed individuals. Snorkeling observations were conducted using the line-transect method following a standardized procedure at each sampling site, with detailed descriptions of the spatial structures of the aquatic vertebrate habitats that covered the microhabitat and longitudinal scales. The data can be used to examine the spatial patterns of focal aquatic vertebrate species and assemblages, and interspecific differences in habitat niche use among sympatric aquatic vertebrate species at multiple spatial scales.

2 | METADATA

1. TITLE

Longitudinal and microhabitat distributions of fishes, amphibians, and reptiles and the environmental characteristics in the upper Yura River, Kyoto, Japan

2. IDENTIFER

ERDP-2018-09

3. CONTRIBUTER

A. Dataset owner

Hikaru Nakagawa

Field Science Education and Research Center, Kyoto University, 1 Onojya, Miyama, Nantan, Kyoto, 601-0703, Japan, hikarunakagawa@icloud.com

B. Dataset creator

Hikaru Nakagawa

Field Science Education and Research Center, Kyoto University, 1 Onojya, Miyama, Nantan, Kyoto, 601-0703, Japan, hikarunakagawa@icloud.com

4. PROGRAM

A. Title

Doctoral thesis of Hikaru Nakagawa

B. Personal

Hikaru Nakagawa

Field Science Education and Research Center, Kyoto University, 1 Onojya, Miyama, Nantan, Kyoto, 601-0703, Japan, hikarunakagawa@icloud.com

C. Funding

This study was supported by Global COE Program A06 ‘Formation of a Strategic Base for Biodiversity and Evolutionary Research: from Genome to Ecosystem’ from the Ministry of Education, Culture, Sports and Technology, Japan.

D. Objectives

Detailed data were collected to evaluate how aquatic vertebrate species were distributed along environmental gradients at longitudinal and microhabitat scales, whether there were any patterns, and which environmental factors correlated with the distributions of aquatic vertebrate species and their assemblages, even given spatial autocorrelations. The data can be used to examine theoretical assumptions that predict the importance of habitat niche and spatial autocorrelation for the distribution of each aquatic vertebrate species and their assemblage patterns at multiple spatial scales.

5. GEOGRAPHIC COVERAGE

A. Geographic description

Upper reaches of Yura River, Ashiu Forest Research Station of the Kyoto University Field Science Education and Research Center, Japan

B. Geographical position

35.25694N–35.3737N, 135.52410E–135.77270E (WGS84)

6. TEMPORAL COVERAGE

A. Begin

August 2009

B. End

September 2009

7. TAXONOMIC COVERAGE

^a Anadromous fish introduced by a local fisheries society.

^b Introduced from Northern America.

8. METHODS

A. Study site

Aquatic vertebrates were observed along the main channel of the Yura River, at 21 sites ranging from the headwaters to about 40 km downstream in northern Kyoto Prefecture, central Japan (fig. 1). A large dam separates the research area from the lower part of the river. The Yura River flows from the Sugio Ridge (750 m a.s.l.), located on the border between Kyoto and Fukui Prefectures. The river is about 146 km long with a catchment area of about 1880 km². The regional climate is warm-temperate with monsoon effects. In the upper quarter of the research area (35°18'N, 135°43'E, 356 m a.s.l.), the annual mean temperature is 11.9°C, annual precipitation is 2298 mm, and snow depth in winter is approximately 1 m. The catchment area in the upper part of the research area (0–15 km from the headwaters; sampling sites 1–7; fig. 1c) is covered by plantations of the conifer Cryptomeria japonica and deciduous broad-leaved forests dominated by Fagus crenata and Quercus crispula (data from the Ashiu Forest Research Station, Field Science Education and Research Center, Kyoto University, http://www.ashiu.kais.kyoto-u.ac.jp, last accessed January 9, 2018). Artificial protective structures are relatively rare along the riverbanks, and the riverbanks in most areas are bordered by forest. There are some sediment-control dams in the middle part of the research area (around sampling sites 13–18, fig. 1c), but all of these dams have fishways. Some of the data on the distribution and ecology of the fishes at the study site have been reported (Nakagawa et al., 2012; Nakagawa, 2014, 2018a,b).

Figure 1 (a) Locations of the Yura River (b) Location of the research area (c) Location of the sampling sites (d) Arrangement of the transects and plots

B. Research methods

a. Sampling site

A total of 21 sampling sites were established: sites 1 (uppermost) to 21 (lowest) (fig. 1c). No sampling sites were established in the river between 4 and 10 km from the headwaters because of access difficulties. The Yura River originates from a spring in the forest floor. The uppermost site was 1.5 km downstream from the origin. The lowest sampling site was located just upstream from the dam reservoir.

At each sampling site, ten line transects were set perpendicular to the water flow along the channel (fig. 1d). The interval between transects was adjusted according to river size: 5-m intervals at the upper four sites (sites 1–4); 20-m intervals at sites 14, 20, and 21; and 10-m intervals at all other sites. Each sampling site included at least one pool–riffle unit (range 1–3 units). Plots were established along each transect at regular intervals (four to eight plots per transect; fig. 1d). Plots were the minimum unit of observation and measurement. The number of observation plots along a transect was adjusted according to the channel width, with four plots at the upper four sites (sites 1–4; mean wet width < 5.5 m), eight plots at sites 14, 20, and 21 (mean wet width > 20 m), and six plots at the other sites (mean wet width 5.5–20 m). A red sounding lead was placed at the center of each observation plot as a landmark for aquatic vertebrate observations and environmental measurements.

b. Aquatic vertebrate observations

Aquatic vertebrates were observed in the summer from August 20 to September 27, 2009. During this season, the water temperature of the river is at its annual maximum, and all aquatic vertebrate species are active (Nakagawa, unpublished). Observations were conducted by snorkeling during the day (10:00–15:00) and at night (22:00–3:00), because some aquatic vertebrate species are active at night. Water temperature was measured at the start of each observation. The snorkeling observations were conducted using the line-transect method with the following procedure. First, I dove into the right or left side of the stream channel and moved 1 m downstream from a transect. Five minutes later, the aquatic vertebrates showed normal behavior, and I quietly moved along the transect and observed the aquatic vertebrates. When an individual aquatic vertebrate was found, I recorded its species, standard length (<5, 5–10, 11–20, >20 cm), age (larva, yearling, 1 year, or older), swimming status (stays on streambed, cruises in the bottom, middle, or surface layer of the water column) and the nearest landmark lead. I grouped small larva (standard length <1 cm) of Tribolodon hakonensis, Rhynchocypris oxycephalus, Zacco platypus, and Nipponocypris temminckii as ‘Cyprinidae Gen. sp.’, because they were difficult to identify during underwater observations. All observations were conducted by the author. A waterproof hand light and headlight were used for night observations.

c. Measurements of environmental characteristics

Water depth, current velocity, and substrate characteristics were measured at each landmark lead (i.e., each observation plot) after the aquatic vertebrate observations. Water depth was measured to 1 cm using a meter stick. Current velocity was measured at the surface, 60% of the depth, and the bottom of the water column using a portable tachometer (Model 3651 Pocket Tachometer; Cosmo-Riken, Osaka, Japan). To measure substrate characteristics, a 50 × 50 cm quadrat with 10 × 10 cm cells (total 25 cells) was placed at the center of a plot. The main substrate type was recorded, as characterized by sediment particle size, in each cell based on the Udden–Wentworth particle scale (<2 mm, sand; 2–4 mm, granules; 5–64 mm, pebbles; 65–256 mm, cobbles; >256 mm, boulders; bedrock; Wentworth, 1922). I calculated the relative frequency of each substrate type as the number of cells occupied by each substrate divided by the total number of cells (25 cells) for each plot. The presence/absence of vegetation cover was recorded at the nearest observation plot from the river sides or bars. Vegetation cover was defined as branches and leaves of terrestrial plants that overhung the river by more than 50 cm.

C. Data verification procedures

The data were manually digitized and checked for typographical errors by the investigators.

9. DATA STATUS

A. Latest update

30 August 2018

B. Metadata status

The metadata are complete for this period and stored with the data.

10. ACCESSIBILITY

A, License and usage rights

This dataset is provided under a Creative Commons Attribution 4.0 International License (CC BY 4.0; https://creativecommons.org/licenses/by/4.0/legalcode).

B. Contact

Hikaru Nakagawa

Field Science Education and Research Center, Kyoto University, 1 Onojya, Miyama, Nantan,

Kyoto, 601-0703, Japan, hikarunakagawa@icloud.com

C. Storage location

JaLTER Database

Raw data sheets and digital data are stored with H. Nakagawa on multiple hard drives in two physical locations.

11. DATA STATUS

A. Data tables

B. Format type

The data files are in ASCII text, tab delimited.

C. Header information

Headers corresponding to variable names (see section 11.D) are included as the first row in the data file. The format of data follows Darwin Core Archive format (GBIF 2010).

D. Variable definitions

12. ACKNOWLEDGEMENTS

I thank Koji Tominaga for helping field survey, and members of Laboratory of Animal Ecology, Graduate School of Science, Kyoto University for many helpful comments. I thank the staffs of Ashiu Forest Research Station, Field Science Education and Research Center of Kyoto University, and the staff of Miyama Gyokyo (Fisheries Cooperative of Miyama, Yura River), Kyoto, Japan. This study was supported by Global COE Program A06 ‘Formation of a Strategic Base for Biodiversity and Evolutionary Research: from Genome to Ecosystem’ from the Ministry of Education, Culture, Sports and Technology, Japan.

13. CONFLICT OF INTEREST

The author declares that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.

14. REFFERENCES

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Frissell, C. A., Liss, W. J., Warren, C. E. & Hurley, M. D. (1986) A hierarchical framework for stream habitat classification: Viewing streams in a watershed context. Environmental Management, 10, 199–214.

Hanski, I, Metapopulation dynamics. Nature, 396, 41–49.

Holyoak, M., Leibold, M. A. Monquet, N. M., Holt, R. D. & Hoops, M. S. (2005) Metacommunities: a framework for medium scale community ecology. Metacommunities: spatial dynamics and ecological communities. (eds M. Holyoak, M. A. Leibold & R. D. Holt) pp. 1–31. The University of Chicago Press, Chicago, USA.

Hutchinson, G. E. (1959) Homage to Santa Rosalia or why are there so many kind of animals. American Naturalist, 93, 145–159.

Leibold, M. A., Holyoak, M., Mouquet, N., Amarasekare, P., Chase, J. M., Hoopes, M. F., Holt, R. D., Shurin, J. B., Law, R., Tilman, D., Loreau, M., & Gonzalez, A. (2004) The metacommunity concept: a framework for multi-scale community ecology. Ecology Letters 7, 601–613.

Maddock, I. (1999) The importance of physical habitat assessment for evaluating river health. Freshwater Biology, 41, 373–391.

Nakagawa, H., Yamane, H., Yasugi, M., Fujita, T., Yokoi, K., Ashiwa, H., Kitada, N., Takano, H., Suzuki, N., Kishimoto, J., Maeda, H., Yamano, H., Ito, T., Maruyama, H., Tominaga, K., Hatakeyama, E., Goto, M. & Takahashi, D. (2012) Diel changes in resource use and diet overlap in temperate stream fishes. Ecological Research, 27, 417–426.

Nakagawa, H. (2014) Contribution of environmental and spatial factors to the structure of stream fish assemblages at different spatial scales. Ecology of Freshwater Fish, 23, 208–223

Nakagawa, H. (2018a) Temperature-dependent gastric evacuation rate of the Japanese delicate loach Niwaella delicata (Cobitidae), Ichthyologycal Research, 65, 172–174.

Nakagawa, H. (2018b) Fish–prey interactions in, and associated data from, a temperate stream of the Yura River, Kyoto, Japan, Ecological Research, 33, 823–823.

Peres-Neto, P. R., Leibold, M. A. & Dray, S. (2012) Assessing the effects of spatial contingency and environmental filtering on metacommunity phylogenetics. Ecology, 93, S14–S30.

Schwarz, C. J. & Seber, G. A. (1999) Estimating Animal Abundance: Review III. Statistical Science, 14, 427–456.

Simonson, T. D., Lyons, J. & Kanchi, P. D. (1993) Guidelines for evaluating fish habitat in Wisconsin streams. United States Department of Agriculture, Forest Service, North Central Forest Experiment Station, General Technical Report, NC-164.

Wentworth, C. K. (1922) A Scale of Grade & Class Terms for Clastic Sediments. The Journal of Geology, 30, 377–392.