Proceedings of the 19th IAHR-APD Congress 2014, Hanoi, Vietnam

ISBN 978604821338-1

A HYDROLOGICAL APPROACH TO REVEALING RELATIONSHIP BETWEEN PHYSICAL HABITAT AND GENETIC

DIVERSITY OF STREAM INVERTEBRATES

KEI NUKAZAWA(1), SO KAZAMA(1), AKIHIKO TAKASE(2) & KOZO WATANABE(3)

(1)
Graduate School of Engineering, Tohoku University, Sendai, Japan,
nukazawa@kaigan.civil.tohoku.ac.jp, kazama@kaigan.civil.tohoku.ac.jp
(2)
Tokyo metropolitan government, Tokyo, Japan,
(3)
Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan,
watanabe_kozo@cee.ehime-u.ac.jp

ABSTRACT
A vast number of researches in landscape genetics of river have been focused on how habitat fragmentation or
exogenous invasion ascribed to dam or stocking degrades native genetic diversity. However, there still is an unsolved
question in this arena; how are physical habitat characteristics related to genetic diversity. As the habitat nature arguably
contributes to not only faunal structure but intra-specific trait through gene flow, drift and selection, this association
needs to be revealed for future river management plan with a conservation perspective. In this study, we evaluated the
linkage between genetic diversity and habitat suitability index (HSI) of aquatic animals including freshwater fishes,
amphibians and macroinvertebrates in the Natori River basin located at the middle of Miyagi prefecture. The HSI has
been structured by hydraulic and thermal variables calculated from a distributed hydro-thermal model and GIS based
geographical variables. We found a strong positive correlation between genetic diversity and HSI in one caddisfly
(Hydropsychidae), indicating that a prospective habitat (i.e., locality which has high HSI) might contribute to increase in
genetic diversity. The genetic diversity of one caddisfly (Hydropsychidae) had significant positive correlations with the
HSIs of predatory fishes and aquatic insects. This result suggests that exposures to predation pressure can enhance
genetic diversity. We derived negative correlations between genetic diversity and the HSIs within niche competitors,
suggesting inter-species selective pressure constrains intra-species genetic diversity.

Keywords: distributed runoff model, functional feeding group, HSI, habitat value, landscape genetics, life types, Trichoptera

1. INTRODUCTION index (HSI) for quantifying habitat quality, normally

involved with application of hydrodynamic models (e.g.,
Genetic diversity, so called intra-specific diversity, is an
Leclerc et al., 1996; Muhlfeld et al., 2011). The HSI is
important concept to be internationally conserved and
determined by preference of focal organism to single or
retained in the Convention of Biological Diversity.
multiple local environmental factors. In landscape
Assessment of genetic diversity is necessary to sustain
genetics study, HSI was used for estimating gene flow of
robust natural population which has high potential of
spiny rat species (Wang et al., 2008). On the one hand,
evolution. Landscape genetics, a recently advocated
aquatic species diversity was estimated by HSIs of
discipline by Manel et al. (2003), devotes to reveal varying
multiple species and examined its connection to genetic
spatial pattern of genetic structure of natural population/
diversity of stream insects (Nukazawa et al., submitted).
individual in relation to ambient environmental
However, the use of HSI is limited in this arena ascribed
heterogeneity. Conventional approach of landscape
to difficulty in constructing integrated research
genetics for stream ecosystems covers negative effect of
framework assessing both habitat quality and genetic
habitat fragmentation by weirs on gene flow (e.g., Deiner
diversity from field survey.
et al., 2007; Watanabe et al., 2007), and impaired gene
attributed to exogenous invasions of same species such as A framework for deriving association between habitat
stocking (e.g., Vh et al., 2007). Although studies quality and genetic diversity in river should be limited to
focusing on a sole effect (e.g., exploring some organisms having poor dispersal ability (e.g., diatom and
environmental factors to determine genetic structure) is invertebrate) because defining stable habitat of strong
concise and relatively easy, more comprehensive attribute disperser in river (i.e., migrating fishes) is extremely
such as habitat quality for sole species is hardly difficult. Especially, stream invertebrates have several
considered. advantages for this purpose as they sensitively reflect
local ambient environments and are easily sampled.
A popular approach to quantify habitat quality in
Furthermore, benthic invertebrate species are possible to
streams is Physical habitat simulation approach
be classified to several groups in terms of functional
(PHABSIM) in Instream flow incremental methodology
feeding or life types. This enables us to discuss biological
(IFIM) (US Fish and Wildlife Service, 1980 and 1981). This
relationship in natural ecosystem such as niche
systematical method comprise of use of habitat suitability

1
competition or prey-predation balance within given
benthic community.
In this paper, we examined relationships between genetic
diversity of four stream invertebrates and HSIs of more
than 50 taxa. The genetic diversity of invertebrates has
been observed in Watanabe et al. (2014) and the HSI
models of benthic community, fishes and amphibians
have been developed using a distributed hydrological
model for a temperate basin in north-east Japan
(Nukazawa et al., 2011; Takase et al., 2013). Analyzing
relationship between genetic diversity and HSI, we aim
to reveal how habitat quality contributes to genetic
structure and which group of feedings or life types
relates to genetic diversity. Another goal is to clearly
shape usefulness of our approach to use HSI using
hydrological model for biodiversity evaluation
framework. them.
2. METHODS
2.1 Study area
The study catchment is the Natori River basin
encompassing approx. 1,000 sq km located in NE Japan
(Fig. 1). The region is classified to temperate climatic
zone with 12.1 C of the annual mean air temperature at
Sendai City. The main stem the Natori River is originated
in the Kamuro Mountain (ca 1,800 m in altitude) and
flows west to east. The catchment has high environmental
heterogeneity along steep headstreams, tributaries and
main stems. Upstream region is mountainous and
forested with beech and cedar, and subjects to snowfall in
winter. Corridors in middle stream are surrounded by an
urban area (Sendai City) which has a population of
approx. a million. Two main stems; the Natori River and
Hirose River merge inside of the city and the converged
stream finally drain into the Pacific Ocean. Downstream
plain is covered by crop and paddy fields (13% of the
basin). There are two multi-purpose major reservoir
dams; the Kamafusa Dam (approx. 50 years old) and the
Okura Dam (approx. 60 years old) regulating flow
regimes (Fig. 1).
2.2 Environmental data
The distributed runoff model described by Kazama et al.
(2007) and the stream temperature model described by
Nukazawa et al. (2011) were used to calculate current
velocity, water depth and water temperatures. These data
were calculated on a daily basis for 1,933 grids along the
water courses at a resolution of 250 m from July 2004 to
June 2005 (period 1) and through 2006 (365 days)
(period 2). The simulation covered the whole sampling
period from which the empirical genetic data were
collected (from September to November 2006, see
below). Meteorological data, including air temperature
and precipitation, from four stations were used as inputs
to the models (Fig. 1). These data were obtained from the
Automated Meteorological Data Acquisition System
(AMeDAS) established by the Japan Meteorological
Agency. The spatial distributions of air temperature and
precipitation were calculated using the weighted average
of the data from the three stations.
The distributed runoff model was separated into the slant
and river parts (Kazama et al., 2007). For the slant part
Fig. 1 Study area
model, the water flow consisted of direct flow, base flow
and snow accumulation/melt, which were calculated
using the kinematic wave method (Lighthill & Whitham,
1955a, b), the storage function method (Kimura, 1961)
and the degree-day method. For the river part model, the
dynamic wave method (Liggett, 1975; Liggett & Cunge,
1975; Fread, 1993) was employed. We used the observed
discharge and water temperature data from the outflow of
the Kamafusa and Okura Dams as boundary conditions.
The heat budget model consisted of the estimates of
groundwater and radiation levels as well as the heat
budget calculation (Nukazawa et al., 2011). Based on a
previous study (Kondo & Ishida, 1997), the bulk method
was employed to calculate the sensible and latent heat
using a value of 0.0011 as the bulk coefficient. The
hydro-thermal model was validated throughout the basin
(Nukazawa et al., 2011; submitted) based on the Nash-
Sutcliff sufficiency coefficient (Nash and Sutcliffe, 1970)
and agreement between the calculated and observed
runoff and water temperature.
After simulating the three hydro-thermal variables in
each grid during the period, we calculated four statistics
to characterize the local conditions for each variable:
annual average, maximum, minimum and variance. We
also calculated eight digital cartographic variables based
on elevation and land-use data from the Ministry of
Land, Infrastructure, Transport and Tourism (MLIT), as
described in Nukazawa et al. (2011). These variables
were slope, catchment area, urbanized area ratio, farm
area ratio, forested area ratio, distance to urbanized area,
distance to farm area, and distance to forested area.
2.3 Habitat suitability modeling
To estimate the potential of aquatic species diversity we
developed the habitat suitability index (HSI) model. We
used inhabitation data of the studied animals including
benthic invertebrates, fishes and amphibians observed by
Hamamoto et al. (2007) and taken from a database of the
2
Natori City Office located in the SE study basin. This
governmental biological data which indicates spatially
distributed presence/absence of more than 1,000 animal
species in each grid with 250 m resolution was carried
out by experts in ecological field.
The HSI can provide the physical value of
habitat suitability (i.e., potential of occurrence) in focal
organisms along local environmental heterogeneity. As a
general procedure the HSI is synthesized with the set of
suitability index (SI) hinging on biological information
(e.g., numeric number of focal species and frequency)
along an environmental gradient or classifications. Here
we employed predictor variables for structuring SI; slope,
vegetation type, land-use, % urban, distance to urbanized
area, distance to forested area, distance to waterfront,
annual metrics (see Environmental data) of current
velocity, water depth and water temperature. We
structured frequency distribution graphs with the
numerical numbers of grid in which both presence and
absence in focal animals and the ranges (e.g., 0.0-0.2 m
for annual mean depth) or type (e.g., agricultural zone)
in the predictors. Subsequently, SIs were developed after
the frequencies in each range were normalized as 0-1 (0:
not suitable, 1: most suitable). The HSIs for the studied
taxa were then calculated by means of geometric mean of
the SIs for each predictor;
where SIxyi indicates suitability index in an environment
predictor i and p indicates numerical number of the
predictors (=15) at the grid (x, y).
2.4 Genetic diversity
We used the empirical AFLP genetic data for three
caddisflies (Insecta: Trichoptera), Hydropsyche orientalis
(Ho), Stenopsyche marmorata (Sm) and Hydropsyche
albicephala (Ha), and a mayfly (Insecta:
Ephemeroptera), Ephemera japonica (Ej) reported by
Watanabe et al. (2014). Whereas two caddisfly species,
Fig. 2 Correlations between genetic diversity
(%P: proportion of polymorphic loci) and
habitat suitability index in four aquatic species;
(a) Hydropsyche orientalis, (b) Stenopsyche
marmorata, (c) Hydropsyche albicephala and
(d) Ephemera japonica.
Ho and Sm, distributed broadly (present at 26 and 20 of
the 39 sampling sites), Ha and Ej were merely sampled at
upstream regions and small tributaries in the study basin.
All species occur throughout Japan except some remote
islands (e.g., Okinawa island) and have analogous habit
in feeding flowing particle organic matter (<1mm
diameter) in streams or accumulated on streambeds.
We calculated three genetic diversity indicators in
population level from the AFLP data. Proportion of
polymorphic loci (%P) was quantified using AFLP-SURV
v 1.0 (Vekemans 2002). Heterozygosity (He) was
computed at each locus from: He=1-ri2 , where r is
allele frequency at locus i estimated by the Bayesian
method with a uniform prior distribution of allele
frequencies (Zhivotovsky 1999) using AFLP-SURV v 1.0.
We employed a theta estimator (theta pi ()) (Tajima
1983), as a genetic diversity indicator using Arlequin v
3.0 (Excoffier et al. 2005).
2.5 Correlation analysis
We derived Pearsons and Spearmans correlation
coefficients between habitat suitability of 53 aquatic taxa
(49 taxa of benthic invertebrates, 3 taxa of fishes and 1
taxa of amphibian) and genetic diversity of 4
invertebrates using SPSS Statistics 17.0 (SPSS Inc.). The
results of benthic invertebrates were classified to
functional feeding groups (PR: predator, SH: shredder,
FC: filterer-collector, GS: grazer-scraper, GC: gatherer-
collector) (FFGs) and life types (CR: crawler excluding
glider, AT: attacher excluding net-spinner, NS: net-
spinner, GL: glider, BR: brawler, SW: swimmer) for
further discussion. Also, we applied multiple regression
analysis assigning the genetic diversity as objective
variable and HSI of 25 invertebrate taxa validated in
Takase et al. (2013) as predictor variable.
3
3. RESULTS
We found positive moderate correlation between genetic
diversity (%P: proportion of polymorphic loci) and HSI
in Hydropsyche albicephala (Ha) (R=0.50, P<0.10), while
correlations in other 3 species did not exhibit clear trend
(Fig.2).
correlated with HSIs of niche competitors (i.e., FC and
NS) (Table 1 & 2).
Multiple regression analysis revealed the genetic
diversity of Ho has negative correlation with the HSI of
Psepheridae taxon, which frequently dominates benthic
community and have similar longitudinal pattern of

Table 1 Correlations between genetic diversity of four aquatic insects and habitat suitability index
classified to five categories of functional feeding groups (FFGs) (Merrit and Cummins, 1996) (PR:
predator, SH: shredder, FC: filter feeder, GS: scraper, GC: collector-gatherer). Bracketed numeric
values following each FFG acronym indicate number of taxon belonging to each FFG. Numeric
values and following bracketed numeric values indicate number of significant correlation (P<0.05)
and its symbol (+: positive, -: negative), and upper and lower hands indicate results from
Pearsons correlation analysis and Spearmans correlation analysis.

Table 2 Correlations between genetic diversity of four aquatic insects and habitat suitability index
classified to six categories of life types (Merrit and Cummins, 1996) (CR: crawler, AT: attacher,
NS: net-spinner, GL: glinder, BR: burrower, SW: swimmer). Bracketed numeric values following
each life type indicate number of taxon belonging to each life type. See caption of Table 1 for
instructions of numeric values and following bracketed numeric values.

Correlations between genetic diversity (He: inhabitation and microhabitat preference to Ho.
heterozygosity, Tp: theta pi) of Hydropsyche orientalis
(Ho) and the HSIs in benthic assemblage classified in line 4. DISCUSSION
with FFGs and fishes, clearly underlined strong positive
In principle, population density of focal species is
connection (P<0.05) of the genetic diversity and HSI of
probably high in which habitat seems to be preferable for
predatory invertebrates and fishes (Table 1). This result
this species (i.e., HSI is high). Simultaneously, effect of
implies genetic diversity of Ho is relatively high in
genetic drift causing decline of genetic diversity can be
habitat having strong predation pressure. Furthermore,
small where density of local population is large. Given
we found the genetic diversity of Ho negatively
intra-specific diversity is mainly /partly characterized by

4

habitat suitability, the theoretical process driven by
genetic drift is probably dominant in natural local
population of focal species. On the one hand, exploring
relationship between genetic diversity of a species and
HSI of other species, genetic variation mediated by biotic
interactions can be revealed.
A positive association between genetic diversity and
HSI in Ha implies that habitat quality might constrain
population genetic structure, presumably caused by
spatially different extent of genetic drift. Note genetic
diversity in Fig. 2 varies where HSI indicates 0. This
attributes to possible consequence of HSI (potential of
inhabitation); even if HSI indicates extremely low value,
natural population can successfully colonize there
because of other local preferable factor than ours. The
HSIs of Ho and Sm, mainly ranging around 0.3 to 0.6, did
not show correlating pattern with genetic diversity
(Fig.2). To further understand genetic trend along broad
range of HSI gradient, empirical genetic data observed in
stream reaches in which HSI shows higher value should
be taken together.
Genetic diversity of Ho exhibited strong significant
correlations with the HSIs of predatory fishes and
invertebrates (table 1 and 3). This result is clear evidence
that spatial genetic diversity pattern of Ho is
characterized by existence of predatory animals, giving
predation pressure on focal habitat colonized by
relatively small invertebrates. Possible interpretations of
this fact are dominating nature of Ho in natural
community. Since relative size of Ho population density
is large compared with other niche competitors
throughout this basin, predation pressure impairing
population size of Ho might be weak.
Table 3 Correlations between genetic diversity of 2
aquatic insects and 4 aquatic taxa (3 freshwater fish
species and 1 taxon of frog). Symbol indicates significant
positive (+) or negative (-) correlation found with
Pearsons correlation analysis (upper hand) and
Spearmans correlation analysis (lower hand). Number of
symbol (1 or 2) indicates level of significance (1: P<0.10,
2: P<0.05).
Table 4 Results of multiple regression analysis based on
objective variables of genetic diversity of four aquatic
insects and predictor variables of habitat suitability index
(HSI) of each taxon from benthic assemblage. Name of
taxon selected as significant predictor variable is listed in
this table with its symbol (+: positive, -: negative).
We found negative significant correlations between
genetic diversity of Ho and HSIs of its niche competitors
(i.e., filter-feeders and net-spinners) (table 2). Niche
competitive species is known to share their habitat in
local to broad scale (Imanishi, 1941), thereby balance of
abundance can directly reflect spatial genetic patterns
within the groups of filter-feeders and net-spinners.
Lankau and Strauss (2007) reported positive mutual
effect of species diversity of competitors on genetic
diversity in plant community. While a comparison in
different biomes is exactly difficult, these studies are
implying feedback of competitors can differ between
different biomes.
Multiple regression analysis derived the HSIs of
Psephenidae (-) and Ephemeridae (2+) were significant
predictors of genetic diversity of Ho (Table 4).
Psephenidae often dominates local benthic community
specifically in middle portion of stream, mostly similar
nature to Ho species. This competitive relationship can
depress the genetic diversity as well as shown in negative
correlations of competitors with respects to FFGs and life
types.
We also found many significant correlations between
genetic diversity of Ephemera japonica (Ej) and the HSIs.
5
The positive correlations of the genetic diversity with the
HSIs of GC express that preferable habitat with low flow
velocity potentially storing much fine organic matters
enhance the genetic diversity of Ej.
5. CONCLUSIONS
In this paper, we evaluated association between genetic
diversity of four stream insects and habitat suitability of
around 50 aquatic taxa including fishes and invertebrates.
Habitat suitability model based on a hydrological model
enabled us to test the relationship in basin scale.
Furthermore, habitat suitability of benthic assemblage
classified to functional feeding groups and life types
revealed cryptic attributes of niche competitions and
prey-predators to genetic diversity. This study will be a
significant implication of future modeling frameworks
which aim to take biotic interactions into account.
ACKNOWLEDGMENTS
This research was partially supported by the Ministry of
Education, Science, Sports and Culture through a Grant-
in-Aid for Scientific Research (grant #: 24254003,
25241024, 26820196, 26630247) and Japan Society for the
Promotion of Science (JSPS) Research Fellowship (grant
#: 256493).
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