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. 2018 Apr 24;8(10):5069–5078. doi: 10.1002/ece3.4071

Daphnia diversity on the Tibetan Plateau measured by DNA taxonomy

Lei Xu 1,2,4,5,†, Qiuqi Lin 2,†, Shaolin Xu 2, Yangliang Gu 2, Juzhi Hou 3, Yongqin Liu 3, Henri J Dumont 2, Bo‐Ping Han 2,✉
PMCID: PMC5980554  PMID: 29876082

Abstract

Daphnia on the Tibetan Plateau has been little studied, and information on species diversity and biogeography is lacking. Here, we conducted a 4‐year survey using the barcoding fragment of the mitochondrial COI gene to determine the distribution and diversity of Daphnia species found across the Plateau. Our results show that species richness is higher than previously thought, with total described and provisional species number doubling from 5 to 10. Six of the taxonomic units recovered by DNA taxonomy agreed well with morphology, but DNA barcoding distinguished three clades each for the D. longispina (D. galeata, D. dentifera, and D. longispina) and D. pulex (D. pulex, D. cf. tenebrosa, and D. pulicaria) complexes. The sequence divergence between congeneric species varied within a large range, from 9.25% to 30.71%. The endemic D. tibetana was the most common and widespread species, occurring in 12 hyposaline to mesosaline lakes. The lineage of D. longispina is the first confirmed occurrence in west Tibet.

Keywords: COI, Daphnia, DNA taxonomy, Tibetan Plateau

1. INTRODUCTION

In the past decade, DNA sequencing has generated abundant molecular information, standard dataset platforms, and universal technical rules for modern taxonomic and biogeographical research (Ratnasingham & Hebert, 2007). DNA barcoding uses a short DNA sequence in an organism's DNA to compare against that of another organism to determine the degree of relatedness between two closely related organisms. The barcoding fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) is a popular marker used to identify and differentiate closely related species that are very similar in morphology. It has assisted in species‐level identity in many animal groups such as birds (Hebert, Stoeckle, Zemlak, & Francis, 2004), fishes (Ward, Zemlak, Innes, Last, & Hebert, 2005), spiders (Barrett & Hebert, 2005), butterflies (Hebert, Cywinska, Ball, & deWaard, 2003; Janzen et al., 2005), ants (Smith, Fisher, & Hebert, 2005), and crustaceans (Costa et al., 2007; Elías‐Gutiérrez, Jerónimo, Ivanova, Valdez‐Moreno, & Hebert, 2008), including marine decapods and euphausiids (Bucklin et al., 2007; Costa et al., 2007).

Cladocera is a monophyletic, primarily freshwater crustacean order, one of the three main components of the microcrustacean zooplankton (Dumont & Negrea, 2002). The genus Daphnia (Anomopoda: Daphniidae) has been studied in much detail (Lampert, 2011), and the full genome of two species (D. magna and D. pulex) has been sequenced (Colbourne, Singan, & Gilbert, 2005; Colbourne et al., 2011). Daphnia is most diverse and abundant in the temperate regions, but is present in all climate zones on all continents, and is often the dominant group in freshwater zooplankton (Benzie, 2005). Despite this, the taxonomy of the group remains uncertain because, inter alia, of a highly variable morphology that can be strongly modified by environmental conditions. Recently, molecular data have confirmed that some Daphnia cannot be identified to species by morphological means and its specific diversity remains underestimated. Analysis of sequences of mitochondrial COI and 12S rDNA genes by Hebert, Witt, and Adamowicz (2003b) revealed five phylogroups with more than 3% divergence in D. ambigua. Penton, Hebert, and Crease (2004) discriminated two cryptic species within the D. obtusa complex in North America. De Gelas and De Meester (2005) reported that populations of D. magna showed little COI divergence within Europe, but deep divergence was recovered in North American populations. So far in China, no barcode studies assessed Daphnia species diversity.

The Tibetan Plateau is widely considered as a large natural experimental area for speciation and evolution. It is the world's highest and largest plateau and is surrounded by mountain ranges that source several of the longest rivers in Asia. The Plateau supports a variety of ecosystems that harbor an exceptionally diverse flora with about 4,385 species in 1,174 genera in 189 families (Wu, 1980). More than 25% of the total species identified are endemic (Wu, 1987). This reflects the age of the plateau, the central part of which started rising some 40 million years ago. Previous fragmentary taxonomic studies of Cladocera on the Tibetan Plateau including the genus Daphnia were based solely on morphology (Chiang, 1963; Chiang & Du, 1979; Shen & Sung, 1964). These were updated after several scientific expeditions to the area during the 1970s (Chiang & Chen, 1974; Chiang, Shen, & Gong, 1983). More recently, Möst et al. (2013) and Ma et al. (2015) used DNA sequences to study species diversity in the region. Their studies focused on the D. longispina complex that is often the dominant Daphnia taxa in freshwater lakes and ponds found in the northern temperate region. However, Möst et al.'s sampling sites covered only two alpine lakes in the Pamir and Himalaya mountains, and Ma et al.'s study were confined to just five Tibetan lakes. A more comprehensive coverage is required in this ecologically important region of the world.

In this study, we employed DNA barcoding and DNA taxonomy through analysis of the mitochondrial marker COI to determine species diversity of the Daphnia genus in lakes and ponds on the Tibetan Plateau. We also estimated the number of endemic species in the region and generated a phylogenetic tree based on our mtCOI data and those from GenBank. Our study will greatly improve our understanding of distribution and species diversity in Cladocera and may have important implications for the conservation of the Tibetan Plateau freshwater fauna.

2. MATERIALS AND METHODS

2.1. Sample collection

Sample collection covered a large geographical range (>2,200,000 km2) in different habitats that ranged from 2,700 m to about 5,000 m a.s.l. Zooplankton samples were collected between 2012 and 2015 from 26 permanent lakes and from several riparian temporary ponds (Table 1 and Figure 1). Samples were obtained by vertical hauls with a plankton net that has a mesh size of 100 μm. The collected samples were fixed in 70% ethanol. Specimens were examined under a dissecting microscope in the laboratory. Sorted individuals were transferred to a fresh tube and preserved in 95% ethanol at 4°C for genetic analysis. We followed Benzie (2005) for species identification and nomenclature of Daphniidae.

Table 1.

Geographic and environmental data for lakes and ponds where Daphnia populations were sampled

Lake and pond Latitude (N) Longitude (E) Altitude (m) Depth (m) pH Area (km2) Salinity (g/L) Predators Nma Morphological type
Biezuoze Co 32.429 82.933 4,407 2 8.97 33 27.5 Absence 3 D. tibetana
Dawa Co 31.233 84.967 4,628 2 9.30 114 19.2 Absence 3 D. tibetana
Dajiamang Co 29.650 85.733 5,069 7 8.69 9 0.1 Presence 6 D. galeata; D. cf. tenebrosa
Dong Co 32.183 88.733 4,398 2 8.81 88 46.2 Absence 3 D. tibetana
Dagze Co 31.883 87.533 4,470 34 9.96 245 17.0 Absence 3 D. tibetana
Gemang Co 31.583 87.283 4,610 48 9.72 61 6.5 Presence 3 D. tibetana
Jiang Co 31.533 90.816 4,603 20 9.29 41 14.1 Absence 3 D. tibetana
Nairiping Co 31.300 91.467 4,529 7 9.98 90 8.0 Absence 3 D. tibetana
Peng Co 31.533 90.967 4,534 6 9.91 175 8.5 Absence 3 D. tibetana
Sugan Lake 38.867 93.850 2,796 4 8.90 120 20.0 Absence 2 D. tibetana
Youbu Co 30.783 84.800 4,645 34 9.62 64 16.0 Absence 3 D. tibetana
Zigetang Co 32.067 90.867 4,573 15 10.0 191 13.5 Absence 3 D. tibetana
Pond near Lhasa river 29.684 91.317 3,740 0.3 NA 0.01 0.8 Presence 9 D. dentifera; D. similoides
Angrenjin Co 29.206 87.390 4,304 15 9.66 24 5.3 Presence 3 D. magna
Bangong Co 33.500 79.841 4,241 24 8.74 604 0.5 Presence 3 D. longispina
Chen Co 28.967 90.533 4,436 26 8.62 40 0.8 Presence 1 D. dentifera
Darebu Co 32.467 83.217 4,438 3 9.40 21 1.4 Presence 3 D. cf. himalaya
Daru Co 31.667 90.750 4,688 9 9.23 70 5.1 Presence 3 D. magna
Dongjicuona Lake 35.283 98.567 4,086 93 8.76 232 0.4 Presence 3 D. pulicaria
Keluke lake 37.286 96.897 2,817 13 8.50 57 0.7 Presence 3 D. magna
Lang Co 29.305 87.200 4,296 26 9.44 12 1.6 Presence 3 D. longispina
Qiagui Co 31.817 88.300 4,558 50 8.71 88 0.2 Presence 3 D. galeata
Songmuxi Co 34.600 80.250 5,057 8 8.50 27 0.3 Presence 3 D. cf. himalaya
Pond near Tanggula Pass 32.904 91.951 5,142 0.3 8.54 0.01 1.9 Presence 6 D. cf. himalaya
Zhuoyang Co 34.850 98.131 4,271 7 9.23 6 7.0 Absence 3 D. tibetana
Zhaling Lake 34.931 97.311 4,285 13 7.70 526 0.6 Presence 5 D. pulicaria; D. pulex
Co Ngoin Lake 31.600 88.776 4,568 27 8.79 253 0.2 Presence 3 D. galeata
Zongxiong Co 33.100 80.283 4,351 1 8.69 9 0.2 Presence 3 D. longispina
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a

Nm = sample size for mitochondrial analysis.

Figure 1.

Figure 1

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Geographic location of sample collection sites. Color dots: lakes or ponds inhabited by Daphnia species. The background map was generated using SRTM 90 m elevation data

2.2. DNA extraction

Total genomic DNA was extracted using a genomic DNA isolation kit (Wizard® Genomic DNA, Purification Kit type A1225; Promega, USA). We modified the standard protocol as follows: for DNA extraction, specimens were picked out from 95% ethanol, rinsed with double‐distilled water, transferred individually to a reaction tube and stored on ice. Next, we added 200 μl warm Cell Lysis solution and 3 μl Proteinase K (20 mg/ml). We vortexed and subsequently incubated the mixture for 2 hr at 65°C and then for 2–3 days at 55°C with daily addition of 2 μl of fresh Proteinase K. Next, we added 100 μl of Precipitation Solution, vortexed vigorously at middle speed for 20 s and put on ice for 2 min, then centrifuged at RCF 15,321 g for 10 min at room temperature. We carefully removed the supernatant and transferred it to a clean 500 μl microcentrifuge tube containing 200 μl of isopropanol at room temperature. We centrifuged at RCF 15,321 g for 1 min at room temperature and carefully decanted the supernatant. Finally, the pellet was washed with 70% ethanol, dissolved in 40 μl DNA hydration solution and stored at −20°C.

2.3. Amplification and sequencing of the mitochondrial gene

The barcoding fragment of the mitochondrial cytochrome oxidase I (COI) gene was amplified from total genomic DNA using polymerase chain reaction (PCR) (Hajibabaei et al., 2005). Primers used for PCR were CO1490F and CO2198R (Folmer, Black, Hoeh, Lutz, & Vrijenhoek, 1994). Each 50 μl PCR reaction consisted of 31.25 μl dd H2O, 5 μl PCR buffer, 5 μl Coralload concentrate, 4 μl of 25 μmol/L MgCl2, 1 μl of 10 μmol/L dNTPs, 0.5 μl of 25 μmol/L solution of each primer, 2.5 μl DNA template, and 0.25 μl TopTaq DNA polymerase (QIAGEN, Germany). The PCR conditions for amplification were as follows: 40 cycles set at 30 s at 96°C (denaturation), 30 s at 51°C (annealing), and 60 s at 72°C (extension), followed by 7 min at 72°C (final‐extension) on a 2720 Thermal Cycler (Applied Biosystems, USA). We also used a set of primers specific for zooplankton (Prosser, Martínez‐Arce, & Elías‐Gutiérrez, 2013) for samples that responded unsuccessfully with Folmer primers. The PCR products were sequenced on an ABI 3130XL automatic sequencer. Whenever possible, we sequenced at least three individuals of each species from each population.

2.4. DNA taxonomy

The authenticity of all mitochondrial COI sequences was verified by a BLAST search in GenBank. The sequences were assembled and edited in BioEdit (Hall, 1999) and aligned using the CLUSTALW multiple algorithm. The first 20 and last 10 bp were not included because they were missing in some sequences. We added the COI sequences available in public databases to our analysis to ensure that our nomenclature is reliable for each Daphnia species (see Table S1). We used two different approaches to identify taxonomic units from DNA taxonomy, namely the Automatic Barcode Gap Discovery (ABGD) (Puillandre, Lambert, Brouillet, & Achaz, 2012) and Generalized Mixed Yule Coalescent (GMYC) model (Fujisawa & Barraclough, 2013; Pons et al., 2006) to infer putative species boundaries on COI dataset. The ABGD approach tests for a gap in the distribution of the pairwise genetic distances and then identifies groups of individuals united by genetic distances that are shorter than the gap. The method was performed on the COI alignment through an online tool (http://wwwabi.snv.jussieu.fr/public/abgd/abgdweb.html) with default settings with P (prior limit to intraspecific diversity) ranged between 0.001 and 0.1 and X (gap widths) = 1 using the available models JC86 (Jukes‐Cantor) and K80 (Kimura). The GMYC uses a maximum likelihood approach to optimize the shift in the branching patterns of the gene tree from interspecific branches (Yule model) to intraspecific branches (neutral coalescent), thereby identifies clusters of sequences corresponding to independently evolving entities. The ultrametric tree with terminals representing haplotypes, which are needed for the GMYC method, was reconstructed using BEAST1.8.0 (Drummond, Suchard, Xie, & Rambaut, 2012). Parameters for BEAST were set in BEAUti 1.8.0 assuming coalescent model with constant population size, uncorrelated relaxed clock model, general time reversible (GTR) substitution model, and gamma shape site model with a chain length of 100,000,000 iterations for Markov chain Monte Carlo (MCMC). The GMYC model was performed with the R package splits version 1.0‐19 (Ezard, Fujisawa, & Barraclough, 2009).

2.5. Genetic divergence and phylogenetic analysis

Distances between COI sequences were calculated using the Kimura two‐parameter (K2P) substitution model in MEGA, version 6 (Kumar, Nei, Dudley, & Tamura, 2008). We used uniform rates, and standard error estimates were obtained by a neighbor‐joining (NJ) bootstrap procedure with 10,000 replicates. Before phylogenetic analysis, we used MrModeltest v.2.3 (Nylander, 2004) to select the best‐fitting models of nucleotide substitution under the Akaike information criterion (AIC). Analyses were performed using Bayesian inference and maximum likelihood. Bayesian analysis was performed using MrBayes v.3.1.2 (Huelsenbeck & Ronquist, 2001; Huelsenbeck, Ronquist, Nielsen, & Bollback, 2001). The MCMC analysis was run in four parallel chains for 2,000,000 generations, sampling every 1,000 generations. For maximum likelihood analysis, we used PhyML 3.0 (Guindon et al., 2010), assuming a GTR model (Lanave, Preparata, Saccone, & Serio, 1984) with four gamma‐distributed rate categories, as suggested by ModelGenerator 0.851 (Keane, Creevey, Pentony, Naughton, & Mclnerney, 2006). We used NNI moves for tree topology searching and fast likelihood‐based parameter aLRT SH‐like for branch support. Majority rule consensus trees were reconstructed after discarding the burn‐in of 500 and displayed with treeview v.1.6.6.

3. RESULTS

3.1. Morphological survey and DNA taxonomy

Our survey identified six morpho‐species or complexes: D. tibetana, D. similoides, D. magna, D. longispina complex, D. cf. himalaya, and D. pulex complex. The most common morpho‐species was D. tibetana, found in 12 water bodies, followed by D. longispina complex (found in eight water bodies); D. magna, and D. pulex complex (found in three water bodies). Daphnia cf. himalaya was also found in three water bodies: two permanent and one temporary. The rarest species were D. similoides and D. pulex, found only in one population each (Table 1). Sequences of COI were obtained from 93 animals (GenBank accession numbers MG544001–MG544093). Comparing each of our COI sequences with sequences in GenBank, we identified all animals as Daphnia (sequence divergence < 5%). The ABGD model detected a barcode gap in the alignment and suggested that the 93 individuals included 10 taxonomic units (named S1–S10). The GMYC model also supported the scenario that all analysed individuals represented 10 taxonomic units (confidence interval: 8–11). The likelihood of the null model of only one species (likelihood = 721.29) was significantly worse (likelihood ratio test = 12.73, P = 0.001) than that with more than one species (likelihood = 727.66). Six of the 10 taxonomic units matched morphology well. However, the D. longispina complex was split up into three clades—D. galeata, D. dentifera and D. longispina—and the D. pulex complex also split up into three clades—D. pulex, D. cf. tenebrosa, and D. pulicaria (Figure 2).

Figure 2.

Figure 2

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COI phylogenetic tree for Daphnia in Tibetan Plateau obtained from MrBayes, with the scale bars proportional to substitution rates; support values are Bayesian Posterior Probabilities support/Maximum Likelihood; ML supports are for the clades present also in the ML trees; support values below 0.7 and for short branches are not shown. The results of ABGD are shown as blue open circles and those of GMYC as red open stars on the branches

3.2. Patterns of genetic divergence and phylogenetic analysis

The total length of the sequenced segment after alignment was 677 bp. The average base composition was A = 21.70%, C = 20.41%, G = 22.36%, T = 35.53%, and transition/transversion (ti/tv) ratio = 1.751. The uncorrected K2P pairwise distances among species in this study varied between 9.25% and 30.71% and the average pairwise distance was 25.23%. The highest distance was between D. cf. tenebrosa and D. magna, a value which is slightly higher than the maximum congeneric distance of 30.65% recorded earlier in Daphnia by Costa et al. (2007). Two species of the D. longispina complex, viz. D. longispina, and D. dentifera, recorded the lowest distance. The uncorrected K2P pairwise distances within species varied between 0% and 1.72%. High pairwise distances within species, found in D. tibetana and D. pulicaria, reached 1.60% and 1.72%, respectively (Table 2).

Table 2.

Genetic diversity, assessed by Kimura two‐parameter distance (median, in %) within/between the ten taxonomic units of Daphnia with uniform rates; standard error estimates obtained by neighbor‐joining bootstrap procedure with 10,000 replicates

Speciesa D. tibetana D. cf. tenebrosa D. similoides D. magna D. longispina D. dentifera D. galeata D. cf. himalaya D. pulicaria D. pulex
D. tibetana (12/35) 1.60 ± 0.25
D. cf. tenebrosa (1/3) 28.77 ± 2.44 0.00
D. similoides (1/3) 23.68 ± 2.15 27.56 ± 2.39 0.00
D. magna (3/9) 24.64 ± 2.19 30.71 ± 2.61 17.02 ± 1.67 0.56 ± 0.21
D. longispina (3/9) 29.22 ± 2.48 28.06 ± 2.43 25.63 ± 2.24 25.93 ± 2.24 0.38 ± 0.12
D. dentifera (2/7) 29.20 ± 2.51 27.97 ± 2.52 26.05 ± 2.33 26.81 ± 2.46 9.25 ± 1.13 0.55 ± 0.21
D. galeata (3/9) 28.75 ± 2.47 27.72 ± 2.36 25.56 ± 2.25 21.50 ± 1.91 17.24 ± 1.67 16.50 ± 1.78 0.68 ± 0.21
D. cf. himalaya (3/12) 26.71 ± 2.36 26.64 ± 2.34 22.95 ± 2.13 26.60 ± 2.15 27.40 ± 2.27 27.19 ± 2.39 25.18 ± 2.16 1.46 ± 0.29
D. pulicaria (2/6) 27.72 ± 2.38 11.39 ± 1.35 24.08 ± 2.15 28.14 ± 2.34 25.31 ± 2.21 25.14 ± 2.24 24.90 ± 2.12 24.81 ± 2.11 1.72 ± 0.41
D. pulex (1/2) 29.83 ± 2.48 24.37 ± 2.19 24.99 ± 2.20 28.04 ± 2.34 27.99 ± 2.42 27.54 ± 2.44 26.73 ± 2.41 30.47 ± 2.56 23.55 ± 2.15 0.00
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a

Number of lakes and individuals per taxonomic unit were showed in the head column (lakes/individuals).

The best‐fitting model selected by MrModeltest 2.3 was GTR+I+G with a relative AIC weight of 0.982 and gamma distribution shape parameter 1.556. Two species of Simocephalus (KF484574 and KF960069) were used as outgroups to root the phylogenetic trees. Phylogenetic calculations (Bayesian inference and ML) resulted in trees of similar topology (Figure 2). COI phylogenetic tree revealed six well‐supported main clades: D. tibetana, D. similoides, D. magna, D. longispina complex, D. cf. himalaya, and D. pulex complex. Clade D. longispina complex contains three distinct genetic clusters: D. longispina, D. galeata, and D. dentifera. The D. pulex complex also contains three well‐supported sublineages: D. pulex, D. cf. tenebrosa, and D. pulicaria.

4. DISCUSSION

4.1. Species diversity and genetic divergence

Cladocera have been traditionally regarded as cosmopolitan, but there is mounting evidence for the existence of numerous sibling and cryptic species. In the past 10 years, DNA barcoding has accumulated much molecular information in support of this idea. Among examples on cladocerans, Elías‐Gutiérrez et al. (2008) applied COI barcoding to show that in Mexico and Guatemala, five species can be distinguished in the Diapahanosoma birgei group, while two or three taxa each were identified for Ceriodaphnia cf. rigaudi, and Moina cf. micrura. Xu et al. (2011) reconstructed the phylogeographic history of the Holarctic carnivorous cladoceran Leptodora and uncovered at least three species in this previously monotypic genus. In Australia, Sharma and Kotov (2013) identified three sibling species in the Ceriodaphnia cornuta complex. Other studies have revealed deep genetic divergences among allopatric populations of single species (De Gelas & De Meester, 2005; Thielsch, Brede, Petrusek, de Meester, & Schwenk, 2009). Recently, DNA barcoding was used to document cryptic speciation and species diversity in the sub‐Arctic region of Canada (Jeffery, Elías‐Gutiérrez, & Adamowicz, 2011), Mexico (Elías‐Gutiérrez & Valdez‐Moreno, 2008; Quiroz‐Vázquez & Elías‐Gutiérrez, 2009), Guatemala (Elías‐Gutiérrez, Kotov, & Garfias‐Espejo, 2006), and in other parts of North America (Penton et al., 2004). DNA barcoding in the present study also revealed that Daphnia species diversity on the Tibetan Plateau is much higher than previously thought (Chiang, 1963; Chiang & Chen, 1974; Chiang & Du, 1979; Chiang et al., 1983; Shen & Sung, 1964), doubling the described and provisional species number from 5 (D. magna, D. tibetana, D. pulex, D. similoides, and D. dentifera) to 10. Recently, an updated checklist of Chinese Cladocera was released based on literature analysis and our molecular data (Xiang et al., 2015). Approximately 19 species of Daphnia are now found in China. At least 10 of these species occur on the Tibetan Plateau, with some species such as D. cf. himalaya, D. cf. tenebrosa, D. longispina, and D. pulicaria being the first records identified by molecular data. Morphological similarity in some clades was the cause for hidden species diversity. Alternatively, species in the D. longispina clade show strong morphological plasticity (Laforsch & Tollrian, 2004; Petrusek, Tollrian, Schwenk, Haas, & Laforsch, 2009) compounded by the possibility of hybridization and introgression (Ishida et al., 2011; Keller, Wolinska, Tellenbach, & Spaak, 2007; Schwenk & Spaak, 1995). Morphology‐based taxonomy is insufficient for distinguishing the underlying genetic units. A lack of investigation has long delayed an appreciation of the diversity of Daphnia in Tibet. Only recently have studies begun to reveal the region's hidden species (Ma et al., 2015) and the impact of environmental change on cladoceran species richness and composition (Lin et al., 2017).

The genomic region of the COI gene sequence is used not only in DNA barcoding (Costa et al., 2007; Hebert, Cywinska, et al., 2003), but also in detecting speciation. The level of sequence divergence between congeneric species of crustaceans averaged 17.16%, the highest value so far in animals. As a comparison, congeneric species of lepidopterans show just 6.1% variation (Hebert, Cywinska, et al., 2003), birds 7.93% (Hebert et al., 2004), and fishes 9.93% (Ward et al., 2005). Congeneric divergences in Daphnia are reported by Costa et al. (2007) to be extremely high at 13.18%–30.65%, which is supported by our data (9.25%–30.71%; the highest divergence being between D. cf. tenebrosa and D. magna). The average interspecific divergence between Daphnia species on the Tibetan Plateau of 25.23% is similar to that reported in Argentina (25.28%, Adamowicz, Hebert, & Marinone, 2004), but significantly higher than values reported from Churchill, Canada (14.1%, Jeffery et al., 2011). Difference in average interspecific divergence may be related to species richness: 10 congeneric species occurred in Tibet and 11 South American endemics in Argentina, against only five species in the Churchill region.

The level of intraspecific variation in crustaceans averaged 0.69%, a value that is slightly higher than those reported in other groups (most range from 0.25% to 0.30%). High intraspecific variations in our study were found in D. tibetana (1.60%) and D. pulicaria (1.72%). We collected one population of D. tibetana and D. pulicaria from Zhaling Lake, which is more than 1,600 km away from the other investigated lakes, indicating the elevated divergence values came from Zhaling Lake samples. Possibly the high values reflect limited gene flow between the two species caused by physical barriers such as mountains that separate the Tibetan lakes from Zhaling Lake, followed by adaptation to local environmental pressure in the lake.

4.2. Biogeographic patterns of Daphnia on the Tibetan Plateau

Six of the 10 taxonomic units from DNA taxonomy in our study matched those determined by morphological taxonomy. However, our analysis distinguished three clades each for the D. longispina (D. galeata, D. dentifera, and D. longispina) and D. pulex (D. pulex, D. cf. tenebrosa, and D. pulicaria) complexes. Distributions of Daphnia species on the Tibetan Plateau were mostly nonoverlapping, with the exception of D. cf. tenebrosa, D. pulex, and D. similoides (Figure 1). Daphnia tibetana was the most common species in our investigation, being present in 12 of 28 water bodies without fish predators. Daphnia tibetana is endemic to the Tibetan Plateau, previously recorded as Daphniopsis tibetana Sars, 1903 (Chiang & Du, 1979). Glagolev (1983) and Benzie (2005) regard Daphniopsis as a junior synonym of Daphnia. There has long been confusion about the status of D. tibetana and D. fusca, but D. fusca was absent from our samples. Daphnia tibetana is distinguished from D. fusca by having rounded rather than angled fornices, combs on the postabdominal claws that are not strongly differentiated, fewer anal spines, no spines on the carapace margins, a sinuate anterior margin to the head in some specimens, no dorsal ridge and a short rostrum, and two well developed postabdominal processes (Benzie, 2005). Previous investigations showed that D. tibetana is a halobiont, living at more than 4,000 m in hyposaline to mesosaline lakes in Tibet, Mongolia, and India. Our sample area covered a large geographical range (>2,200,000 km2) containing different habitats located at latitudes ranging from 2,700 m to about 5,000 m asl. Water temperatures at which the samples were collected ranged from 2°C to 20°C, salinity varied from 9 to 35 g/L, and pH ranged from 9.0 to 10.4 (Zhao, Wang, Zheng, Zhao, & Wang, 2002). However, a recent study (Lin et al., 2017) reported an even wider salinity range (6.4–46.2 g/L) for D. tibetana. The northernmost population in our investigation was found in Sugan Lake, a closed inland ecosystem located to the north of Qaidam Basin at an altitude of 2,796 m, the lowest known altitude where D. tibetana occurs. Sugan Lake is situated more than 1,200 km from where other D. tibetana are found, and is an important habitat for migratory birds. Thirty‐eight bird species have been observed in the wetlands around this lake (Bao, Zhang, Liu, Song, & Zhao, 2007). Bird migration is the most likely explanation for D. tibetana presence in the lake, although research is required to identify which birds are the vectors involved in long‐distance dispersal of the cladoceran.

The Daphnia longispina complex was found in eight water bodies from the westernmost Ngari Prefecture to Lhasa River. The lineage of D. longispina was found in Bangong co and Lang co, Ngari area, western Tibet, near to the recently confirmed easternmost locality of Pamir Mountains (Möst et al., 2013). Its distribution extends to western China. In contrast to previous taxonomic studies based solely on morphology (Chiang & Du, 1979), our finding suggests widespread presence of the D. longispina complex across the whole of China. Daphnia galeata was reported from northern and southwestern China and from the Yangtze Basin (Xu, 2013), and presumably coexists with D. longispina in east China. But because D. galeata, D. dentifera and D. longispina have similar morphologies, classification errors are likely. Thus, D. longispina phenotypes reported from the 1970s are suspect and may have been incorrectly identified (Wei et al., 2015). Moreover, D. longispina has been documented to typically occur in alpine oligotrophic lakes (Hamrová, Krajicek, Karanovic, Černý, & Petrusek, 2012; Ventura et al., 2014). The absence of D. longispina phenotypes in lowland China may be related to the rareness of oligotrophic lakes in eastern China caused by eutrophication. Our molecular results also confirm recent reports on the D. longispina complex across China, in which D. galeata was the only lineage found in the eastern low‐altitude plain, whereas D. dentifera dominated in lakes of the Tibetan Plateau and D. longispina was absent from east China (Ma et al., 2015). Daphnia cf. himalaya is especially intriguing, as it was found in two permanent lakes and one temporary pond along the Nyenchenthanglha Mountain in the center of the Tibetan Plateau. The morphology of D. cf. himalaya in our collection is similar to the dark‐pigmented Daphnia‐like species described by Manca, Martin, Peñalva‐Arana, and Benzie (2006) and named Daphnia himalaya from the Khumbu Region in Nepal. However, the absence of males in our samples suggests further investigation is needed.

5. CONCLUSION

Our study is the first to use DNA barcoding as a tool to delineate species and their distribution pattern in Tibet. The technique revealed 10 described and provisional species of Daphnia on the Tibetan Plateau. This diversity is double of that shown by previous checklists. The sequence divergence among Daphnia was high and varied between 9.25% and 30.71%. Two species, D. tibetana and D. cf. himalaya, are endemic to the plateau and the Himalayas. The hygrophile D. tibetana, presumed to be the result of local speciation, was the most common species that was found in 12 hyposaline to mesosaline lakes. Our study is the first time to confirm the presence of the D. longispina lineage in western Tibet.

CONFLICT OF INTEREST

None declared.

AUTHOR CONTRIBUTIONS

L. Xu sampled the zooplankton samples, analyzed the data, and wrote the manuscript. Q. Lin performed the research, sampled the zooplankton samples, and wrote the manuscript. S. Xu, Y. Gu, J. Hou, and Y. Liu sampled the zooplankton samples. H. J. Dumont wrote the manuscript. B.‐P. Han designed the research, supported the fieldwork, and wrote the manuscript.

DATA ACCESSIBILITY

DNA sequences: GenBank accessions: MG544001–MG544093.

Supporting information

 

Click here for additional data file. (18.8KB, docx)

ACKNOWLEDGMENTS

This work was supported by the National Basic Research Program of China (grant number 2012CB956100) and the National Natural Science Foundation of China (grant number 31670460). We thank all colleagues and students in the field station for their help with sampling. We are grateful to Dr. Mingda Wang of Institute of Tibetan Plateau Research for supplying the sampling map using SRTM 90 m elevation data.

Xu L, Lin Q, Xu S, et al. Daphnia diversity on the Tibetan Plateau measured by DNA taxonomy. Ecol Evol. 2018;8:5069–5078. https://doi.org/10.1002/ece3.4071

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Associated Data

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Supplementary Materials

 

Click here for additional data file. (18.8KB, docx)

Data Availability Statement

DNA sequences: GenBank accessions: MG544001–MG544093.

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