NEWS AND VIEWS
Measuring global fish species richness with eDNA
Christopher L. Jerde
Emily A. Wilson
Terra L. Dressler
Marine Science Institute, University of
California, Santa Barbara, California
Department of Ecology, Evolution, and
Marine Biology, University of California,
Santa Barbara, California
Christopher L. Jerde, Marine Science
Institute, University of California, Santa
United States Agency for International
Development, Grant/Award Number: AID-
Despite mounting threats to global freshwater and marine biodiversity, including cli-
mate change, habitat alteration, overharvesting and pollution, we struggle to know
which species are present below the water's surface that are suffering from these
stressors. However, the idea that a water sample containing environmental DNA
(eDNA) can be screened using high‐throughput sequencing and bioinformatics to
reveal the identity of aquatic species is a revolutionary advance for studying the
patterns of species extirpation, invasive species establishment and the dynamics of
species richness. To date, many of the critical tests of fisheries diversity using this
metabarcoding approach have been conducted in lower diversity systems (<40 fish
species), but in this issue of Molecular Ecology Resources, Cilleros et al. (2018)
described their eDNA application in the species‐rich French Guiana fishery (>200
fish species) and showed the greater potential and some limitations of using eDNA
in species‐rich environments.
biodiversity, environmental DNA, freshwater, marine
We performed a literature search in Google Scholar and Web of
Science to collect published papers using the metabarcoding
approach to estimate fish biodiversity. Key words used in the search
included variations of three terms: “environmental DNA,”“metabar-
coding”and “fish.”Only papers that attempted to estimate species
richness of fishes in natural systems were included in the analysis.
Since the first efforts (Thomsen, Kielgast, Iversen, Møller et al.,
2012; Thomsen, Kielgast, Iversen, Wiuf et al., 2012), over 24 studies
(53 unique observations) have been conducted in freshwater (Fig-
ure 1a; n= 46) and marine (Figure 1b; n= 7) systems. While the few
marine studies have ranged in measured species richness from 15 to
128 fish species, freshwater studies have all been less than 93 fish
species (Miya et al., 2015)—that is until Cilleros et al. (2018) con-
ducted a study in a system with an estimated fish species richness
So why have not metabarcoding approaches been applied to crit-
ical biodiversity regions? Many existing studies (38 of 53 unique
observations) have either concurrently measured species richness
using traditional fisheries capture methods (nets, electrofishing, etc.)
or formed a baseline from historical records from which to compare
results. In part, the metabarcoding approach is still working through
proof‐of‐concept development and demonstrating that eDNA‐recov-
ered species richness estimates are similar to traditional methods
(Olds et al., 2016). While many of the temperate freshwater diversity
studies have agreement in estimates of species richness and the spe-
cies identity recovered, Cilleros et al. (2018) noted that agreement in
species identity between the piscicide (chemical used to kill fish)
effort and metabarcoding was lacking in the species‐rich system. The
disparity has multiple explanations ranging from the timing between
eDNA and piscicide efforts, the geographic extent from which
eDNA‐based inferences are made compared to the piscicide treat-
ment, the incomplete inventories of fish species using traditional
methods or historical records, the inability of a single eDNA marker
to adequately discriminate between closely related species and the
Received: 9 June 2018
Accepted: 26 June 2018
Mol Ecol Resour. 2019;19:19–22. wileyonlinelibrary.com/journal/men ©2019 John Wiley & Sons Ltd
need for more fish sequences placed into genetic repositories to
provide reliable reference data. Yet, like Cilleros et al. (2018), we are
optimistic that many of these sources of uncertainty are actively
being addressed with methodological improvements, better experi-
mental design and the populating of databases with the genetic sig-
natures of additional fish species.
The georeferenced locations of published studies reveal that
metabarcoding research for freshwater fish has been concentrated in
well‐studied, temperate biomes and along the coastline of marine
systems (Figure 1c). The Pearson correlation between observed
freshwater species richness from metabarcoding and the minimum
projected species richness from the map is r=0.39 (p<0.01). While
FIGURE 1 Distribution of observed fish species richness for (a) freshwater and (b) marine systems and the (c) georeferenced location of the
studies. The Cilleros et al. (2018) study is the first to use the metabarcoding approach in a high‐diversity, freshwater system. For panel (c), the
basic world biomes were delineated using a map layer generated from Olson et al. (2001) and was used to visualize tundra (light blue), boreal
forest (dark blue), temperate forest (green), tropical forest (purple), savannah (yellow) and desert (orange). An additional layer was used to
visualize current estimations of worldwide freshwater biodiversity (Abell et al., 2008). This layer was colour‐scaled so that areas of high
biodiversity are represented by dark shading and areas with low biodiversity are represented by light shading. Circles represent the
georeferenced location of metabarcoding studies for freshwater (red) and marine (yellow) systems and size‐scaled according to the number of
species detected by eDNA analysis (largest points = highest number of species detected)
FIGURE 2 Freshwater systems, like the commercial fisheries on the (left) Tonle Sap River, Cambodia, have historical records of over 900
fish species but have been understudied using the metabarcoding approach. Restorations efforts, such as the (right) Los Angeles River, USA,
have far fewer fish species, but may also benefit from metabarcoding approaches by providing greater geographic coverage and detecting rare
and/or unexpected species
NEWS AND VIEWS
there is considerable uncertainty, this positive relationship, along
with the growing interest and application of eDNA‐related surveil-
lance efforts (Valentini et al., 2016), implies we are on the cusp of
producing a more cultivated mapping of global freshwater biodiver-
sity. However, there have been disproportionally few or no studies
in freshwater fish biodiversity hot spots or open oceans, where esti-
mating localized biodiversity using any detection method is difficult
and where information is needed to measure the impact of growing
So where specifically do we need better fish species richness
measurements to form baselines? Like the French Guiana fishery
(Cilleros et al., 2018), eDNA methods should be deployed in systems
likely to experience changes from immediate threats. The Mekong
River Basin is a biodiversity hot spot with over 900 species of fresh-
water, brackish and marine fish supporting the diets over 100 differ-
ent ethnic groups in seven countries (Valbo‐Jørgensen, Coates, &
Hortle, 2009) with a cumulative population of over 60 million peo-
ple. The scheduled completion of dams on the tributaries of the
Mekong River will likely have disastrous impacts on fish biodiversity
and food security (Ziv, Baran, Nam, Rodríguez‐Iturbe, & Levin, 2012;
Figure 2). While traditional fish capture methods, such as nets or
hook and line fishing, will provide useful estimates of species rich-
ness, the metabarcoding approach may complement these
approaches by detecting overlooked species that are missed due to
low capture probably resulting from any number of factors, including
bias size selection of gear (Millar & Fryer, 1999), feeding and move-
ment behaviour of the fish, or rarity within the system. In addition,
as has been demonstrated for eDNA application for single‐species
detection (Tucker et al., 2016), metabarcoding could provide broader
geographic coverage of species presence, and the eDNA approach
will not cause damage or death to any captured rare species through
In contrast, there are systems where changing policies regarding
water flow and restoration are leading to potential increases in spe-
cies richness. The concrete‐lined Los Angeles River (Figure 2), a once
relatively dead river with respect to fish biodiversity (Gumprecht,
2001), is being restored with particular attention to removing barri-
ers and providing seminatural riffles and pools for potential Southern
Pacific steelhead trout (Oncorhynchus mykiss) migration to upper
headwaters, yet very little monitoring beyond common species
caught by anglers is being conducted in the river or the upper head-
waters. The metabarcoding approach could provide routine monitor-
ing to measure the effectiveness of restoration efforts, particularly
for rare or elusive species (Gangloff, Edgar, & Wilson, 2016).
We have learned from Cilleros et al. (2018) that the metabarcod-
ing approach is applicable to more diverse systems and can comple-
ment traditional fisheries approaches. The ground‐truthing in 36
biodiversity‐limited study areas has been successful in building confi-
dence that metabarcoding reveals estimates of species richness on
par with, and potentially better than (Olds et al., 2016), traditional
fisheries methods, and now, it is time to expand into more biologi-
cally diverse areas of conservation concern. Clearly, we should fur-
ther develop our eDNA collection, genetic sequencing and
bioinformatic screening components of the metabarcoding approach,
but if we wait for the methods to be further improved before
deploying in areas of conservation concern with greater species rich-
ness, we will miss global opportunities to motivate the protection of
rare species and prevent fishery collapses.
C. L. J. is interested in the application of quantitative tools for
resource management of rare species and estimation of species rich-
ness. This work supported by USAID (AID‐OAA‐A‐16‐00057). E. A.
W. is interested in the effects of invasive species on restoration and
STEM education to promote scientific literacy. T. L. D. is interested
in the persistence of fish populations in extreme conditions near
their native range limits, in particular those affected by wildfire.
Christopher L. Jerde http://orcid.org/0000-0002-8074-3466
(*denotes literature used in metabarcoding fish species richness
Abell, R., Thieme, M. L., Revenga, C., Bryer, M., Kottelat, M., Bogutskaya,
N., …Petry, P. (2008). Freshwater ecoregions of the World: A new
map of biogeographic units for freshwater biodiversity conservation.
BioScience,58, 403–414. Digital media at: www.feow.org. https://doi.
*Balasingham, K. D., Walter, R. P., Mandrak, N. E., & Heath, D. D. (2018).
Environmental DNA detection of rare and invasive fish species in
two great lakes tributaries. Molecular Ecology,27(1), 112–127.
*Cannon, M. V., Hester, J., Shalkhauser, A., Chan, E. R., Logue, K., Small,
S. T., & Serre, D. (2016). In silico assessment of primers for eDNA
studies using PrimerTree and application to characterize the biodiver-
sity surrounding the Cuyahoga River. Scientific Reports,6, 22908.
*Cilleros, K., Valentini, A., Allard, L., Dejean, T., Etienne, R., Grenouillet, G.,
…Brosse, S. (2018). Unlocking biodiversity and conservation studies in
high‐diversity environments using environmental DNA (eDNA): A test
with Guianese freshwater fishes. Molecular Ecology Resources,19(1),
*Civade, R., Dejean, T., Valentini, A., Roset, N., Raymond, J. C., Bonin, A.,
…Pont, D. (2016). Spatial representativeness of environmental DNA
metabarcoding signal for fish biodiversity assessment in a natural
freshwater system. PLoS ONE,11(6), e0157366. https://doi.org/10.
*DiBattista, J. D., Coker, D. J., Sinclair-Taylor, T. H., Stat, M., Berumen,
M. L., & Bunce, M. (2017). Assessing the utility of eDNA as a tool to
survey reef‐fish communities in the Red Sea. Coral Reefs,36(4),
*Dudgeon, D., Arthington, A. H., Gessner, M. O., Kawabata, Z. I., Knowler,
D. J., Lévêque, C., …Sullivan, C. A. (2006). Freshwater biodiversity:
Importance, threats, status and conservation challenges. Biological
Reviews,81(2), 163–182. https://doi.org/10.1017/S1464793105
*Evans, N. T., Li, Y., Renshaw, M. A., Olds, B. P., Deiner, K., Turner, C. R.,
…Pfrender, M. E. (2017). Fish community assessment with eDNA
NEWS AND VIEWS
metabarcoding: Effects of sampling design and bioinformatic filtering.
Canadian Journal of Fisheries and Aquatic Sciences,74(9), 1362–1374.
Gangloff, M. M., Edgar, G. J., & Wilson, B. (2016). Imperilled species in
aquatic ecosystems: Emerging threats, management and future prog-
noses. Aquatic Conservation: Marine and Freshwater Ecosystems,26(5),
Gumprecht, B. (2001). The Los Angeles River: Its life, death, and possible
rebirth. Baltimore, MD: JHU Press.
*Hänfling, B., Lawson Handley, L., Read, D. S., Hahn, C., Li, J., Nichols, P.,
…Winfield, I. J. (2016). Environmental DNA metabarcoding of lake
fish communities reflects long‐term data from established survey
methods. Molecular Ecology,25(13), 3101–3119. https://doi.org/10.
*Keskin, E., Unal, E. M., & Atar, H. H. (2016). Detection of rare and inva-
sive freshwater fish species using eDNA pyrosequencing: Lake Iznik
ichthyofauna revised. Biochemical Systematics and Ecology,67,29–36.
*Li, Y., Evens, N. T., Renshaw, M. A., Jerde, C. L., Olds, B. P., Deiner, K.,
…Pfrender, M. E. (2018). Estimating the distribution of fish and
diversity along a longitudinal stream gradient with environmental
DNA metabarcoding. Metabarcoding and Metagenomics,2,1–11.
*Lim, N. K., Tay, Y. C., Srivathsan, A., Tan, J. W., Kwik, J. T., Baloğlu, B.,
…Yeo, D. C. (2016). Next‐generation freshwater bioassessment:
eDNA metabarcoding with a conserved metazoan primer reveals spe-
cies‐rich and reservoir‐specific communities. Royal Society Open
Science,3(11), 160635. https://doi.org/10.1098/rsos.160635
Millar, R. B., & Fryer, R. J. (1999). Estimating the size‐selection curves of
towed gears, traps, nets and hooks. Reviews in Fish Biology and Fish-
eries,9(1), 89–116. https://doi.org/10.1023/A:1008838220001
*Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., …
Kondoh, M. (2015). MiFish, a set of universal PCR primers for
metabarcoding environmental DNA from fishes: Detection of more
than 230 subtropical marine species. Royal Society Open Science,2(7),
*Nakagawa, H., Yamamoto, S., Sato, Y., Sado, T., Minamoto, T., & Miya,
M. (2018). Comparing local‐and regional‐scale estimations of the
diversity of stream fish using eDNA metabarcoding and conventional
observation methods. Freshwater Biology,63(6), 569–580. https://doi.
*Olds, B. P., Jerde, C. L., Renshaw, M. A., Li, Y., Evans, N. T., Turner, C.
R., …Pfrender, M. E. (2016). Estimating species richness using envi-
ronmental DNA. Ecology and Evolution,6(12), 4214–4226. https://doi.
Olson, D. M., Dinerstein, E., Wikramanayake, E. D., Burgess, N. D., Pow-
ell, G. V., Underwood, E. C., …Loucks, C. J. (2001). Terrestrial ecore-
gions of the World: A new map of life on earth: A new global map of
terrestrial ecoregions provides an innovative tool for conserving bio-
diversity. BioScience,51(11), 933–938. https://doi.org/10.1641/0006-
*Sato, H., Sogo, Y., Doi, H., & Yamanaka, H. (2017). Usefulness and limi-
tations of sample pooling for environmental DNA metabarcoding of
freshwater fish communities. Scientific Reports,7(1), 14860. https://
*Shaw, J. L., Clarke, L. J., Wedderburn, S. D., Barnes, T. C., Weyrich, L. S., &
Cooper, A. (2016). Comparison of environmental DNA metabarcoding
and conventional fish survey methods in a river system. Biological Con-
*Sigsgaard, E. E., Nielsen, I. B., Carl, H., Krag, M. A., Knudsen, S. W., Xing,
Y., …Thomsen, P. F. (2017). Seawater environmental DNA reflects
seasonality of a coastal fish community. Marine Biology,164(6), 128.
*Simmons, M., Tucker, A., Chadderton, W. L., Jerde, C. L., & Mahon, A. R.
(2015). Active and passive environmental DNA surveillance of aquatic
invasive species. Canadian Journal of Fisheries and Aquatic Sciences,
Stoeckle, M. Y., Soboleva, L., & Charlop-Powers, Z. (2017). Aquatic envi-
ronmental DNA detects seasonal fish abundance and habitat prefer-
ence in an urban estuary. PLoS ONE,12(4), e0175186. https://doi.
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C., & Willerslev, E.
(2012). Towards next‐generation biodiversity assessment using DNA
metabarcoding. Molecular Ecology,21, 2045–2050. https://doi.org/10.
Takahara, T., Minamoto, T., Yamanaka, H., Doi, H., & Kawabata, Z.
(2012). Estimation of fish biomass using environmental DNA. PLoS
ONE,7, e35868. https://doi.org/10.1371/journal.pone.0035868
*Thomsen, P. F., Kielgast, J., Iversen, L. L., Møller, P. R., Rasmussen, M.,
& Willerslev, E. (2012). Detection of a diverse marine fish fauna using
environmental DNA from seawater samples. PLoS ONE,7(8), e41732.
*Thomsen, P. F., Kielgast, J., Iversen, L. L., Wiuf, C., Rasmussen, M., Gil-
bert, M. T. P., …Willerslev, E. (2012). Monitoring endangered fresh-
water biodiversity by environmental DNA. Molecular Ecology,21,
*Thomsen, P. F., Møller, P. R., Sigsgaard, E. E., Knudsen, S. W., Jørgensen,
O. A., & Willerslev, E. (2016). Environmental DNA from seawater
samples correlate with trawl catches of subarctic, deepwater fishes.
PLoS ONE,11(11), e0165252. https://doi.org/10.1371/journal.pone.
Tucker, A. J., Chadderton, W. L., Jerde, C. L., Renshaw, M. A., Uy, K.,
Gantz, C., …Sieracki, J. L. (2016). A sensitive environmental DNA
(eDNA) assay leads to new insights on Ruffe (Gymnocephalus cernua)
spread in North America. Biological Invasions,18(11), 3205–3222.
*Ushio, M., Murakami, H., Masuda, R., Sado, T., Miya, M., Sakurai, S., …
Kondoh, M. (2018). Quantitative monitoring of multispecies fish envi-
ronmental DNA using high‐throughput sequencing. Metabarcoding
and Metagenomics,2, e23297.
Valbo-Jørgensen, J., Coates, D., & Hortle, K. (2009). Fish diversity in the
Mekong River basin (pp. 161–196). Amsterdam: Elsevier. In The
*Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P.
F., …Gaboriaud, C. (2016). Next‐generation monitoring of aquatic
biodiversity using environmental DNA metabarcoding. Molecular Ecol-
ogy,25(4), 929–942. https://doi.org/10.1111/mec.13428
*Yamamoto, S., Masuda, R., Sato, Y., Sado, T., Araki, H., Kondoh, M., …
Miya, M. (2017). Environmental DNA metabarcoding reveals local fish
communities in a species‐rich coastal sea. Scientific Reports,7, 40368.
Ziv, G., Baran, E., Nam, S., Rodríguez-Iturbe, I., & Levin, S. A. (2012).
Trading‐off fish biodiversity, food security, and hydropower in the
Mekong River Basin. Proceedings of the National Academy of Sciences,
109(15), 5609–5614. https://doi.org/10.1073/pnas.1201423109
How to cite this article: Jerde CL, Wilson EA, Dressler TL.
Measuring global fish species richness with eDNA
metabarcoding. Mol Ecol Resour. 2019;19:19–22.
NEWS AND VIEWS