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. 2021 Oct 24;11(22):15664–15682. doi: 10.1002/ece3.8220

High diversity and local endemism in Aotearoa New Zealand's groundwater crustacean fauna

Graham D Fenwick 1, Michelle J Greenwood 1, Ian D Hogg 2,3,✉, Stacey J Meyer 2
PMCID: PMC8601929  PMID: 34824781

Abstract

We used DNA barcoding to assess the diversity and distribution of New Zealand's groundwater amphipods and isopods (Crustacea) and to determine whether biodiversity and endemism within tectonically active New Zealand are similar to those of more tectonically stable continents. Sixty‐five wells were sampled in seven aquifers across four regions within the North and South islands of New Zealand, and resident invertebrates were morphologically identified and then assessed using sequencing of the mitochondrial DNA cytochrome c oxidase subunit one (COI) gene. Invertebrates were found in 54 wells. Of the 228 individual amphipods and isopods found in 36 of the wells, 154 individuals were successfully sequenced for COI (68% success rate) from 25 wells, with at least one well in each aquifer containing sequenced individuals. Of the 45 putative species identified using Barcode Index Numbers (BINs), 30 BINs (78% of all taxa and 83% of amphipods) were previously unrecorded. Substantial morphologically cryptic, species‐level diversity was revealed, particularly within the amphipod Family Paraleptamphopidae. Similarly, one isopod taxon morphologically identified as Cruregens fontanus was assigned to five well‐separated BINs based on COI sequences. Endemism appeared high, with all taxa regionally endemic; 87% of species were restricted to one aquifer and more than 50% restricted to one well. Non‐saturated species accumulation curves indicated that, while additional sampling may increase the range of some currently identified taxa, additional range‐restricted taxa are also likely to be discovered. Patterns of diversity and short‐range endemism were similar to those found elsewhere, including locations which are more tectonically stable. The predominance of local endemism within New Zealand's groundwater fauna suggests that land‐use activities and groundwater extraction require careful evaluation to minimize threats to groundwater biodiversity.

Keywords: Amphipoda, cytochrome c oxidase subunit one (COI), diversity, endemism, groundwater, Isopoda, mitochondrial DNA, stygofauna

We used DNA sequencing of the cytochrome c oxidase subunit one (COI) gene to examine the diversity and distribution of New Zealand's groundwater amphipods and isopods (Crustacea) and to compare diversity and endemism within tectonically active New Zealand relative to more tectonically stable continents. Endemism appeared high, with all taxa regionally endemic; 87% of species were restricted to one aquifer and more than 50% restricted to one well. Patterns of diversity and short‐range endemism were similar to those observed elsewhere, including more tectonically stable locations.

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1. INTRODUCTION

Groundwater systems are often viewed as lifeless conduits of subsurface water flow (sensu Hancock & Boulton, 2008). However, research over the last few decades has identified a rich diversity of groundwater fauna (the stygofauna), which provide important ecosystem services (Griebler et al., 2019). Stygofaunal communities are typically dominated by invertebrates and are characterized by high levels of biodiversity, particularly Crustacea (Danielopol et al., 2000; Gibert & Culver, 2009), and by endemism over small spatial scales (Boulton, 2020; Gibert et al., 2009; Hancock & Boulton, 2008). Logistical difficulties in sampling groundwater ecosystems (Larned, 2012) and the often cryptic morphology of stygofauna (Bradford et al., 2010; Danielopol & Pospisil, 2001; Finston et al., 2007) have meant that biodiversity inventories of subterranean ecosystems are severely lacking in many locations (Ficetola et al., 2019; Gibert & Culver, 2009). Investigating the spatial scales of endemism within groundwater ecosystems is a critical step in understanding the implications of increasing threats, such as water abstraction and contaminant infiltration, as well as the efficacy of different management policies and practices (Boulton, 2020; Mammola et al., 2019).

Endemism over relatively small spatial scales appears to be high in most groundwater systems (Danielopol et al., 2003). For example, DNA sequencing of 14 nominal, widespread species indicated more than 50 morphologically cryptic amphipod lineages (Trontelj et al., 2009), most with highly restricted spatial distributions. Forty‐one percent of the stygobitic (obligate groundwater dwellers) species found across six European regions were reported from areas <500 km2 (Deharveng et al., 2009) and ranges of <200 km were common (Trontelj et al., 2009). Some taxa were even restricted to a single cave or sampling location (Gibert & Deharveng, 2002). Figure 1 shows a typical stygobitic crustacean, Paracrangonyx sp. (Amphipoda), which lacks any pigmentation or eyespots, reflecting its subterranean existence.

FIGURE 1.

FIGURE 1

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A typical groundwater (stygobitic) crustacean, Paracrangonyx sp. (Amphipoda), which shows the lack of pigmentation or eyespots. The head is to the lower right of the photo. Photo credit: N. Boustead

For stygobionts, low dispersal capabilities, coupled with geographical isolation over evolutionary time scales, will result in genetic divergences among populations, leading to small‐scale or short‐range endemism (Harvey, 2002; Harvey et al., 2011). Short‐range endemism has been identified in areas that are tectonically stable including Australia (e.g., Hancock & Boulton, 2008) and North America (Culver et al., 2000, 2009) and where physical barriers, such as glacial deposits or catchment shrinkage (due to aridity), subdivide aquifers and isolate populations. New Zealand's active tectonic environment, with relatively rapid uplift, subsidence, erosion, and deposition (Brown, 2001), provides a contrasting setting for stygofaunal evolution compared to that of other continents and could suggest an alternative to the emerging paradigm of short‐range endemism within stygofaunas.

Much of New Zealand's groundwater resides within alluvial aquifers underlying extensive plains comprising relatively young, unconsolidated, and often highly porous matrices, resulting in high hydraulic conductivities and high interstitial water velocities (Close et al., 2002; Pang et al., 1998). This might be expected to facilitate stygofaunal movement within or between aquifers. However, the country's mountainous terrain is also likely to provide physical barriers that would facilitate short‐range endemism. For example, New Zealand's spring and spring‐stream hydrobiid snails include several examples of allopatric, short‐range endemic species (Haase, 2008).

Previous work on New Zealand's stygofauna has largely relied on morphological identifications of taxa, with three families of amphipods and two families of isopods conspicuously present (e.g., Fenwick, 2001; Scarsbrook et al., 2003). This suggests either a smaller number of widespread taxa or a larger number of more restricted, morphologically cryptic taxa. Molecular markers, such as the mitochondrial DNA cytochrome c oxidase subunit one gene (COI), are particularly helpful for identifying morphologically conservative taxa, including Crustacea (Costa et al., 2007; Hogg et al., 2006; Watson et al., 2015). For example, molecular studies have revealed that several European stygofaunal species, previously considered widespread within karstic environments of southern and western Europe, actually comprise several morphologically cryptic taxa, each confined to single locations or catchments, with geographic ranges comprising single or multiple localities spanning no more than c. 180 km (e.g., Ferreira et al., 2007; Lefébure et al., 2006, 2007). Similarly, morphologically cryptic, subterranean stygofauna (e.g., amphipods, isopods, and water beetles) inhabiting groundwater calcretes in the arid Yilgarn region of Australia are actually endemic to single calcrete aquifers, with some ranges smaller than a few square kilometers (Cooper et al., 2007).

Here, we assess stygofaunal diversity across New Zealand using COI gene sequences. We focus on amphipod and isopod crustaceans, as they generally dominate the stygofaunal assemblages of shallow alluvial aquifers (Gibert & Deharveng, 2002) and compare stygofaunal diversity and endemism within New Zealand to more tectonically stable continents.

2. MATERIALS AND METHODS

2.1. Study sites

Sampling locations were stratified hierarchically, across: (1) North and South islands of New Zealand; (2) regions within the South Island; (3) aquifers within regions; and (4) elevation within an aquifer (Figure 1). Sampling was focused on larger alluvial aquifers in four regions along the drier, east coasts of both islands. The largely north–south orientation of New Zealand and its associated mountain ranges, in conjunction with predominantly westerly weather patterns, results in orographic precipitation on the west coast and a drier east coast. Further, we focused on alluvial aquifers to reduce variability in invertebrate communities potentially caused by geographical or hydrogeological differences. These aquifers generally extend from foothills to the coast and have high potentials to store and transport groundwater (Moreau et al., 2019; Tschritter et al., 2017). We collected from the uppermost aquifer at each location. Candidate aquifers were identified using a two‐dimensional aquifer map (Ministry for the Environment, 2015), which was generated using data from White (2001) and updated by Moreau and Bekele (2015). The location of major aquifers corresponds with a more recent map using finer‐scale GIS data (White et al., 2019). Given the unknown quantity of water exchange between aquifers at a small scale, we conservatively assigned wells to the major aquifers identified by both maps and named in Ministry for the Environment (2015). We caution that the “aquifers” identified in this report may comprise two or more smaller aquifers that are variously hydrologically connected.

We assigned a group of wells within the Moutere Valley aquifer to the adjacent Motueka River Terraces aquifer (Figure 1) because our sampling sites were close (440–630 m) and likely hydrologically connected to the Motueka River, which traversed both aquifers. Also, because the Waimea Plains are underlain by multiple major and minor aquifers with some hydrological inter‐connectivity (White, 2001), we assigned our sampling wells in this area to a composite “Waimea Plains” aquifer (Figure 1). There was no established name for the aquifer beneath the Southland wells, so we named this after the nearby Mataura River. Sampling locations within aquifers were restricted to existing wells where sampling equipment could be deployed. Candidate wells were identified with help from local groundwater monitoring agencies (regional and district councils) and had been installed for multiple purposes, including water quality monitoring and research, and for water abstraction.

Sixty‐two wells were sampled once across the four regions and two islands (Figure 2). Due to logistical constraints of finding and accessing suitable wells, the number of wells sampled varied between aquifers. However, at least two wells (and a maximum of 14 wells) were sampled within each aquifer. Where possible, these wells were located across a range of elevations within an aquifer (Appendix 1). We also included invertebrates collected during other sampling excursions from three Canterbury wells (Central Plains aquifer) because they contained specimens that complemented those from the current sampling program. This resulted in a total of 65 wells sampled. We use the term "well" to include both traditional wells (installed by excavation) as well as drilled bore holes. Sampling was undertaken between May 12, 2017, and December 1, 2017, with one well sampled on March 1, 2018.

FIGURE 2.

FIGURE 2

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Well locations across four regions of New Zealand with labeled aquifers (from Ministry for the Environment (2015)). Note that wells in the Moutere Valley aquifer were assigned to the Motueka River Terraces aquifer due to a surface water connection nearby (the Motueka River). Waimea is a composite label for multiple aquifers that have some degree of hydrological connectivity and Mataura is an unofficial aquifer name generated for this project. See Appendices 1 and 2 for well details

2.2. Invertebrate sampling

We used two main sampling methods to maximize capture rates. Firstly, we pumped 60 or 100 L (depending on well flow rate) of water from the screened (i.e., open to the aquifer via slots or perforations) section of the well through a 200‐µm mesh collecting bag. Neoprene flanges or inflatable packers were used to restrict pumping to the screened section of well. For shallower wells (water table < c. 8 m, 48 wells 77% of wells), we used a Bou‐Rouche pump (Malard et al., 2002). A pneumatic Bennett pump (Bennett Sample Pumps Inc., Amarillo, Texas; pumping rate c. 30 L/min. on average) was used for 11 deeper wells. Secondly, a plankton net (64 or 100 µm mesh, depending on the amount of suspended sediment) with a flexible rim was folded into a weighted bailer, lowered to bottom of the well, bounced to suspend sediment and any associated stygofauna, and retrieved slowly to filter the entire water column. The bailer was then retrieved, and its contents added to the contents of the net haul. This procedure was repeated three times. Contents of repeat net and bailer collections from each well were pooled. Sampling methods were modified for sampling very large and very small wells (casing internal diameters <50 and >500 mm diameter, 5% of wells) where the flanges or packers could not be used. Three samples were also collected coincidentally with other activities (e.g., well conditioning or purging) and employed other field methods and filtered larger volumes of groundwater. In all cases, stygofauna were collected and concentrated using a 200‐µm mesh bag. All samples were preserved in the field with 100% ethanol, chilled, transported to the laboratory, and stored in the dark at −20°C until needed for further processing. All equipment was washed thoroughly after sampling each well and air‐dried between regions to avoid transferring any specimens between wells.

In the laboratory, the contents of each sample were concentrated on a 250‐µm sieve, sorted under a stereomicroscope into separate vials for each recognizable taxon, and stored in the dark at −20°C in 100% ethanol. Amphipods and isopods were identified as far as practicable, based on whole specimen morphology (dissection was avoided to retain material for DNA analyses) using existing literature and guides to the New Zealand stygofauna (Appendix 2).

2.3. Physical and chemical parameters

Two 250 ml water samples were collected in acid‐washed bottles from each well between pumping and plankton net sampling to determine dissolved organic carbon content and nutrient concentrations, respectively (nutrients were dissolved reactive phosphorus (DRP), nitrite‐nitrogen (NO2‐N), nitrate‐nitrogen (NO3‐N), ammoniacal nitrogen (NH4‐N), and total dissolved nitrogen (TDN) and total dissolved phosphorus (TDP)). Dissolved oxygen concentration was measured in a five‐liter container of gently pumped well water using a TPS WP‐82 meter (TPS Pty Ltd, Brisbane), and conductivity (µS/cm), temperature, and pH were measured in situ using a TPS WP‐81 meter (TPS Pty Ltd, Brisbane). Well depth and water column depth were measured in situ and information on well diameter and casing material extracted from local council databases.

2.4. DNA analyses

Individuals were photographed and loaded into single wells on 96‐well microplates for processing at the Canadian Centre for DNA Barcoding (CCDB). Total DNA was extracted from specimens using a glass fiber plate method (Ivanova et al., 2006, 2007). Following DNA extraction, residual cuticular material for each specimen was deposited with the NIWA (National Institute of Water and Atmospheric Research Ltd, Wellington) Invertebrate Collection (NIC) as museum vouchers available for morphological study.

Polymerase chain reaction (PCR) amplification of the mitochondrial cytochrome c oxidase subunit I (COI) gene region used the primer pairs LepF1 and LepR1 (Hebert et al., 2004) and LCO490 and HCO2198 (Folmer et al., 1994) according to CCDB standard protocols (Ivanova & Grainger, 2007). Successfully amplified products progressed to cycle sequencing using BigDye™ v3.1 terminator chemistry (Applied Biosystems™). Products were then cleaned using a semi‐automated AutoDTR™ method (EdgeBio®) before being sequenced in forward and reverse directions on an ABI 3730xl DNA Analyzer (Applied Biosystems™) using the same primers used for PCR amplification.

Specimen images, collection data, raw trace files, and edited sequences were all uploaded to and are available on the Barcode of Life Datasystems (BOLD) database (Ratnasingham & Hebert, 2007) (http://dx.doi.org/10.5883/DS‐GDWMS) and cross‐referenced to GenBank (accession numbers OK072722‐OK072875). Barcode Index Numbers (BINs; Ratnasingham & Hebert, 2013) assigned by BOLD were used to delineate putative species based on the sequence data (Milton et al., 2013).

2.5. Data processing and statistical analyses

The amphipod sequences were aligned in Geneious Prime 2020.0.4 (Kearse et al., 2012, https://www.geneious.com) using MUSCLE (Edgar, 2004) and trimmed to 462 bp. A Maximum‐likelihood (ML) phylogenetic tree was generated in MEGA7, (Kumar et al., 2016) with GTR+G+I used as the model of evolution and 1000 bootstrap replications. Similarly, the isopod sequences were aligned and trimmed to 488 bp and a ML phylogenetic tree was generated with TN93+G+I used as the model of evolution and 1000 bootstrap replications. The final trees were visualized in FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).

We calculated species accumulation curves using the abundance of BINs within each well to investigate how sampling effort (number of wells) affected the diversity of BINs both at the national and at regional scales. If most species within an area are collected, an asymptote in cumulative species richness is expected as sample number increases. The mean, median, and variance (quartiles and range) of species richness estimates for each additional well (1‐n wells with genetic sequences) were calculated from 100 permutations with wells added in random order using the package Vegan in the statistical program R (R Development Core Team, 2017).

Spearman rank correlation was used to assess whether the diversity of BINs detected within a well was positively correlated with the number of sequenced individuals. To investigate potential range restriction and, thus, endemism at different scales, the spatial occurrence of individual BINs between aquifers, regions, and islands was also assessed. Separate one‐way analyses of variance (ANOVA) were used to assess whether wells that contained specimens with successful COI sequences differed in physical and chemical parameters from wells that either contained no stygofauna or from which successful sequences were not generated. These parameters included well depth, spot measurements of water temperature, conductivity and pH, and nutrient concentrations (DRP, TDN, TDP, nitrate‐N, nitrite‐N, ammoniacal‐N). For each assigned aquifer, the diversity of amphipods per 1000 km2 of surface catchment area (from Booker & Whitehead, 2017) and aquifer area (from Ministry for the Environment, 2015) was calculated.

3. RESULTS

Of the 65 wells sampled, 54 (83%) contained stygofauna with amphipods found in 34 wells (52%) and isopods in 15 wells (23%) (Table 1). All amphipod and isopod specimens were considered to be stygobionts as they lacked body pigments or pigmented eyes (c.f., Marmonier et al., 1993). Other taxa that were found in more than five wells included cyclopoid and harpacticoid copepods, Syncarida, Ostracoda, Acarina, Annelida, Nematoda, and Gastropoda. From the wells containing amphipods and isopods, 186 amphipods and 42 isopods were collected and processed for their COI sequences, with successful sequences obtained from 154 individuals (68% overall success rate). Morphological identification to family or occasionally genus was possible for most specimens. Mounting and dissection of specimens for morphological assessment were largely precluded as many of the specimens were very small (e.g., adult, brooding amphipods <2 mm long) or their often damaged condition meant that any available tissue was required for DNA extraction. However, subsequent re‐examination of morphologies following COI sequencing (based on their clustering within trees; Figures 3 and 4), allowed us to allocate further specimens to established families or genera.

TABLE 1.

Numbers of wells within the four New Zealand regions and seven aquifers that were sampled for stygofauna, in which stygofauna (all stygofauna, amphipods, and isopods) were collected, and from which COI gene sequences were successfully obtained (amphipods, isopods, and combined amphipods and isopods)

Island Region Aquifer(s) Sampled Taxa present Successful COI sequences
All stygofauna Amphipoda Isopoda Amphipoda Isopoda Total
North Hawke's Bay (9 wells)
Ruataniwha 9 4 2 1 1 0 1
South Tasman (19 wells)
Motueka R Terraces 7 7 2 1 1 1 2
Waimea Plains* 12 10 4 3 3 2 3
Canterbury (35 wells)
Waimakariri‐Ashley Plains 12 9 7 3 6 2 6
Central Plains 14 13 9 5 5 4 6
Rangitata Levels Plains 9 9 8 2 5 2 5
Southland (2 wells)
Mataura** 2 2 2 0 2 0 2
Total 65 54 34 15 23 11 25
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Aquifer names are modified from Ministry for the Environment (2015). * refers to complex of multiple aquifers; ** “Mataura” is the name of a nearby river and not an official aquifer name.

FIGURE 3.

FIGURE 3

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Species accumulation curves showing average cumulative taxa richness (combined amphipod and isopod BINs) against the number of wells sampled for wells within Canterbury (blue line, n = 17) and for all wells sampled (black line, n = 25 wells with BINs). Boxplots show the variance of species richness estimates from 100 permutations with wells added in random order for all wells (black bar =median, box indicates first to third quartile, with outliers indicated by a cross)

FIGURE 4.

FIGURE 4

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Maximum‐likelihood tree (MEGA7; GTR+G+I) based on aligned and trimmed COI sequences (462 bp) of groundwater amphipods. Supporting bootstrap values >0.7 (1000 replicates) are provided. Labels are color‐coded according to region/aquifer and symbols are used to differentiate sites within the regions: Hawke's Bay, light blue (RU, Ruataniwha); Tasman, dark blue (MT, Motueka, circle (Inline graphic); WM, Waimea, square (Inline graphic)); Canterbury, orange (WA, Waimakariri‐Ashley, triangle (Inline graphic); CP, Central Plains, plus sign (Inline graphic); RL, Rangitata Levels, pentagon (Inline graphic)), Southland, red (MA, Mataura). Tentative morphological identifications are provided at the far right of the figure. Barcode of Life Datasystems (BOLD) Barcode Index Numbers (BINs) are shown at the branch tips. Different BINs represent putative species‐level differences. Aquifer and well codes as well as number of individuals (in parentheses) are shown following each BIN. For further details on well locations, see Figure 2 and Appendix 3

Of the 228 individual crustaceans collected, successful sequences were obtained from 129 amphipods (69% success) and 25 isopods (60% success). These sequences were obtained from a total of 25 wells, with amphipods and isopods successfully sequenced from 23 and 11 wells, respectively (Table 1). Seventeen of the wells were in Canterbury, with 5–6 wells in each of the aquifers (Table 1). Although sequences from the Canterbury region were over‐represented, most aquifers, apart from the Ruataniwha aquifer in Hawke's Bay, contained at least two wells where sequences were obtained (Table 1). Individually, amphipod taxa were successfully sequenced from at least one well in each aquifer. However, isopod sequences were available only for the Canterbury and Tasman aquifers (Table 1).

The 154 COI sequences were assigned to 45 BINs, comprised of nine isopod BINs and 36 amphipod BINs (Table 2). The number of specimens available for sequencing and success of sequencing differed between regions, catchments, and wells within catchments (Table 2). The number of sequenced individuals per well ranged from one to 23 (median three), with six wells having only one sequenced individual. The number of BINs per well ranged from one to eight (median two), with 11 wells containing a single BIN. Wells with more sequenced individuals had greater BIN diversity (r = 0.84, p < .001). Species accumulation curves (based on BINs) were unsaturated both for the Canterbury region and for all wells combined (Figure 3).

TABLE 2.

Numbers of successfully sequenced individuals and BINs for amphipods and isopods within each region (bolded values) and aquifer

Region Aquifer Amphipoda Isopoda TOTALS
Seq. BINs Seq. BINs Seq. BINs
Hawke's Bay Ruataniwha 1 1 0 0 1 1
Tasman 34 14 6 2 40 16
Motueka R Terraces 7 4 1 1 8 5
Waimea Plains 27 10 5 1 32 11
Canterbury 90 20 19 7 109 27
Waimakariri‐ Ashley 31 9 (33%) 3 2 (80%) 34 12 (42%)
Central Plains 44 12 (58%) 13 5 (50%) 57 17 (64%)
Rangitata Levels 15 6 (67%) 3 1 18 7 (71%)
Southland Mataura 4 1 – 4 1
TOTALS 129 36 (83%) 25 9 154 45
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The en dash indicates no specimens analyzed. Amphipoda and region BINs (bolded) exclude occurrences in more than one aquifer. Numbers in parentheses within the BIN columns indicate the percentage of amphipod, isopod, and total BINs unique to each aquifer. If no number is included, then all BINS are unique (100%).

Thirty‐five amphipod BINs (78% of all taxa and 83% of amphipods) were new records on BOLD. Of these, only three could be attributed to known morphologically described genera. The endemic amphipod genus Ringanui was assigned to three BINs (Figure 3). The Canterbury/Rangitata Levels BIN (ADL2688, Figure 3) probably comprised one of the two described species (reported range Waimakariri‐Ashley to Rangitata Levels aquifers and Temuka; Fenwick, 2006), whereas two other BINs (ADL5144, ADL5178) are probably undescribed species endemic to the Waimea aquifer. Substantial morphologically cryptic diversity was identified at the family level. The Family Paraleptamphopidae includes three described genera, two of which are hypogean, whereas our analysis found 27 BINs representing several potential genera within a large paraleptamphopid clade (Figure 3).

Cryptic diversity was also apparent within the Isopoda. Eight specimens that were originally morphologically identified as Cruregens fontanus were assigned to five well‐separated BINs (>92% support, Figure 5), one each in Motueka and Waimea aquifers (BINs ADP0923, 3149), one shared between aquifers within the Canterbury region (ADL3492) and two appear to be single‐aquifer endemics (ADL2602, ADP4594) within the Central Plains aquifer (Figure 5). Similarly, three BINs of the phreatoicid isopods were distinguished (>91% support) from specimens initially identified as Phreatoicus typicus and P. orarii (Figure 5).

FIGURE 5.

FIGURE 5

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Maximum‐likelihood tree (MEGA7; TN93+G+I) based on aligned and trimmed COI sequences (488 bp) of groundwater isopods. Supporting bootstrap values >0.7 (1000 replicates) are provided. Labels are color‐coded according to region/aquifer and symbols are used to differentiate sites within the regions: Tasman, dark blue (WM, Waimea, square (Inline graphic)); Canterbury, orange (WA, Waimakariri‐Ashley, triangle (Inline graphic); CP, Central Plains, plus sign (Inline graphic); RL, Rangitata Levels, pentagon (Inline graphic)), Southland, red (MA, Mataura). Tentative morphological identifications are provided at the far right of the figure. Barcode of Life Datasystems (BOLD) Barcode Index Numbers (BINs) are shown at the branch tips. Different BINs represent putative species‐level differences. Aquifer and well codes as well as number of individuals (in parentheses) are shown following each BIN. For further details on well locations, see Figure 2 and Appendix 3

Each of the 45 genetically distinct isopod and amphipod BINs was restricted to one region; 27 BINs were unique to Canterbury, 16 to Tasman, one to Hawke's Bay, and one to Southland (Table 2). Each BIN from the Tasman region was found in a single aquifer only: 11 BINs were unique to the Waimea aquifers and five to the Motueka River terrace aquifer. In Canterbury, 11 BINs were specific to the Central Plains aquifer, five to the Waimakariri‐Ashley, and five to the Rangitata Levels aquifer (Table 2). Six BINs (one isopod and five amphipods) were found in both the Waimakariri‐Ashley and Central Plains aquifers, and two of these occurred across the three Canterbury aquifers. Many amphipod BINs (86%) were apparently endemic to single aquifers (Figure 4, Table 2). However, in more intensively collected aquifers (Waimakariri‐Ashley and Central Plains), single‐aquifer endemics only comprised 46% and 33% of BINs, respectively. These aquifers shared five amphipod BINs, two of which spanned all Canterbury aquifers sampled (Ashley to Rangitata Levels, c. 100 km; Figure 4). Most isopod BINs (89%) were also from single aquifers while specimens assigned to one BIN (ADL3492) were collected in two aquifers (Central Plains, six specimens; Waimakariri‐Ashley, two specimens) (Figure 4).

Of the 39 BINs (87%) restricted to individual aquifers, 29 (64% of all BINs) were found at one well within the aquifer, and nine (20%) BINs confined to a single aquifer were found in two wells. Three BINs occurred at three wells within an aquifer.

Increasing spatial separation was commonly correlated with greater genetic variability. For example, specimens of the Family Paracrangonyctidae from the Motueka aquifer (ADL3783) were genetically distinct from Waimea specimens (ADL2540) (Figure 4), and those from Canterbury's Waimakariri‐Ashley system (ADL5568) were even more genetically divergent, reflecting the much greater geographic distance of the Waimakariri‐Ashley system from the two Tasman aquifers (c. 150 km cf. <1 km between adjacent headwater tributaries).

We found very high amphipod diversity in four aquifers within two of the regions studied. Comparisons based on estimated numbers of BINs per 1000 km2 of aquifer area and catchment area (Table 3) reveal very low relative richness in the two largest, but poorly sampled aquifers (<1.5; Tukituki, Mataura), intermediate richness (3.9 BINs/1000 km2) in the most intensively sampled Selwyn/Central Plains aquifer, and high richness in the three more intensively sampled aquifers (>6.0 BINs/1000 km2). Highest estimated richness (>80 BINs/1000 km2) was within the Waimea aquifer.

TABLE 3.

Total number of amphipod BINs (putative species) from each catchment and aquifer sequenced during present investigation, total land area for each sampled catchment and aquifer (from Booker & Whitehead, 2017), and estimated amphipod species richness per 1000 km2 each catchment and aquifer. Moteuka = Moutere Valley aquifer + Motueka River Terraces

Catchment/aquifer Amphipod species/BINs Catchment Aquifer
Total area km2 Amphipod species/1000 km2 Total area km2 Amphipod species/1000 km2
Tukituki/Ruataniwha 1 2500 0.4 806.61 1.2
Motueka 4 2056 2.0 387.75 10.3
Waimea 10 770 13.0 120.25 83.1
Ashley/ Waimakariri‐Ashley Plains 9 4758 1.9 1358.08 6.6
Selwyn/ Central Plains 12 974 12.3 3045.59 3.9
Orari/ Rangitata Levels Plains 6 715 8.4 971.28 6.2
Mataura 1 5356 0.2 4337.99 0.2
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3.1. Physical and chemical parameters

The sixty‐five sampled wells varied in physical size (depth range: 2.7–39 m, diameter range: 50–1200 mm), chemical parameters (e.g., conductivity range 1.2–1014 μS), and nutrient status (e.g., NO3‐N range 1.0–11,000 mg/m3, Appendix 1).

The water in wells from which specimens with successful genetic sequences were collected was cooler (median spot water temperature 12.9°C) than wells where either taxa were not collected or genetic sequencing failed (median water temperature 13.5°C, ANOVA: F 1,53 = 7.1, p = .03). Likewise, conductivity was lower in wells that yielded successful sequences (median 120.9 μS) than those that did not (median 167.2 μS, ANOVA F 1,53 = 4.3, p = .04, Appendix 3). There were no differences in well depth or nutrient concentrations between wells that had specimens resulting in successful COI sequences compared with wells where no successful sequences were obtained, or from which no amphipods or isopods were collected. Seventy percent (n = 18) of the wells from which successful COI sequences for amphipods and isopods were processed had steel casings, while six wells had PVC casings and two were undetermined. No amphipod or isopod specimens were collected from the larger (>400 mm diameter) concrete wells. The elevation of wells with COI sequences ranged from 4 to 216 m a.s.l. (median 82.5 m) and well depth ranged from 2.7 to 26 m (median 9.7 m; Appendix 3).

4. DISCUSSION

Of the 45 putative species (BINs) identified from the COI sequences, 78% were previously unrecorded on BOLD. Of these, only three could be attributed to established genera, indicating that current knowledge of New Zealand's stygofaunal diversity is extremely low. Morphologically cryptic taxa were common, as has been found in other genetic studies of groundwater taxa (e.g., Delić et al., 2017; Eme et al., 2018). For example, one currently recognized isopod species (Cruregens fontanus) was assigned to five well‐separated BINs, and over 20 species were found within the Family Paraleptamphopidae, particularly within the genus Paraleptamphopus. Six specimens of phreatoicid isopods also showed cryptic diversity. Specifically, three BINs were found in the vicinity of the Central Plains aquifer, whereas Chilton (1894), and Wilson and Fenwick (1999) previously reported a single species within the Central Plains and Waimakariri‐Ashley aquifers. The few examples of taxa found in more than one aquifer were possibly stygophilic, migrating between aquifers via permanent and/or intermittent surface water connections.

Endemism appeared high, with all species found in only one region, 87% attributed to single aquifers and more than 50% recovered only from single wells. However, we caution that the actual levels of local endemism (e.g., well, aquifer) are likely to be somewhat lower, as our sampling within individual wells and aquifers was not comprehensive (we obtained successful sequences for isopods and amphipods from 38% (n = 25) of the 65 wells sampled). Due to their subterranean nature, the sampling of groundwater ecosystems is inherently challenging (Hancock & Boulton, 2009; Korbel et al., 2017). Specifically, collection is often restricted to pre‐existing wells that are predominantly located in areas of human activities. Likewise, it can be difficult to effectively deploy sampling equipment within a well and samples may not adequately represent invertebrate biodiversity within the surrounding aquifer (Ficetola et al., 2019; Larned, 2012), particularly when sampling is only possible on a single occasion. For example, in the Pilbara region of Australia, multiple sampling methods and multiple visits were required to capture most of the species present within a given well (Eberhard et al., 2009).

In our study, only aquifers that were better sampled (i.e., more wells and more sequenced individuals), such as the Canterbury aquifers, yielded taxa that were not aquifer specific. This implies that further sampling is likely to increase the geographic range of some of the apparent single‐aquifer endemic taxa. However, between 42% and 71% of taxa in our most intensively sampled region (Canterbury) were aquifer‐specific indicating that additional sampling would also reveal additional species, many of which are likely to be range‐restricted. In the United States, sampling over nearly 40 years after an early survey of cave fauna led to a <20% decline in frequency of reported county‐specific endemism, while the absolute number of endemic species increased nearly threefold (Culver et al., 2000). While we are unable to definitively identify aquifer‐specific taxa based on our study, other studies of groundwater stygofauna indicate that aquifer‐specific endemism is likely to be common (e.g., Culver & Sket, 2000; Ferreira et al., 2007; Gibert et al., 2009; Bradford et al., 2010; Murphy et al., 2013).

We identified 36 putative stygofaunal amphipod species, 20 in Canterbury region aquifers, and at least 12 within the Central Plains aquifer (Appendix 4). Assuming similar aquifer‐specific endemism across New Zealand's 15 regions and the 220 larger, named aquifers (Moreau et al. (2019), simple extrapolation suggests there could be as many as 300 to 2600 species of groundwater amphipods across New Zealand. Future collecting, particularly repeated sampling and more accurate diversity extrapolation techniques (Eberhard et al., 2009), would assist in more accurately quantifying the diversity of New Zealand groundwater stygofauna, as simple extrapolation techniques are likely to be somewhat limited (Culver et al., 2012). However, the likely diversity identified here is within the range of total stygofaunal diversity in other regions across the world. The described (named) groundwater biodiversity of all aquatic stygofauna in France, after 200 years of study, stands at 380 species, although this is likely to be an under‐estimate due to incomplete sampling (Ferreira et al., 2007) and the presence of several morphologically cryptic species (e.g., Wattier et al., 2020; Westram et al., 2011). In the United States, 300 species of cave‐dwelling aquatic groundwater species are known (Culver et al., 2000). Extrapolating sampling effort and species caught suggests that the Pilbara region of Western Australia may contain 500–550 species (Eberhard et al., 2009) and 21 species of amphipods were present in Australia's smaller Yilgarn region (Cooper et al., 2007).

We found high richness of stygofaunal amphipods in three of the more intensively sampled aquifers (>6.0 BINs/1000 km2). We also estimated extremely high stygofaunal amphipod richness (>80 BINs/1000 km2) within the Waimea aquifer, probably resulting from its interconnectedness with two other aquifers and the extremely high hydraulic transmissivity (20,000 m2/day) reported for parts of this aquifer, including adjacent to the rivers (White & Rosen, 2001). These amphipod richness values are similar to the highest reported for total stygofaunas elsewhere: 6.6 total stygofaunal species/1000 km2 for karst in the Balkan Peninsula (Deharveng et al., 2009; Gibert et al., 2009), although those measures of richness preceded DNA investigations which revealed substantial cryptic stygofaunal diversity. The New Zealand stygofaunal amphipod richness is twice that reported for the total stygofauna in the Pilbara region of Australia (or 3.1 species/1000 km2) and much greater than that reported for amphipods from Australia's Yilgarn region (0.05 species/1000 km2; Cooper et al., 2007). The higher richness found in these New Zealand aquifers is more remarkable because it does not include other taxa such as isopods, copepods, ostracods, syncarids, platyhelminths, and oligochaetes known from these New Zealand aquifers (e.g., Fenwick, 2000; Larned et al., 2014; Scarsbrook & Fenwick, 2003; Scarsbrook et al., 2003).

As with stygofaunas elsewhere, many of described and new species of amphipods and isopods inhabiting New Zealand's alluvial groundwater likely have restricted geographic distributions. The number, size, and complexity of New Zealand's aquifer systems, hydrologically separated by extensive hills and mountains, are probable reasons for the country's high stygofaunal diversity. This appears true even where headwater tributaries almost join (e.g., Motueka and Waimea catchments). Stygofaunal populations also appear genetically isolated between aquifers within the relatively homogeneous landscape of Canterbury Plains, where there are no obvious geohydrological barriers. However, the complexity of the plains’ subsurface geology and hydrogeology (Bradshaw & Soons, 2008; Davey, 2006) may hydrologically separate individual aquifers, leading to genetic isolation and at least some, short‐range, endemism.

Climatic events appear to be the main factor in changing hydrological connectivity and genetic isolation for tectonically stable continents like Europe, North America, Australia, and Africa (Collins et al., 2019; King & Leys, 2014; Lefébure et al., 2006; Witt et al., 2006). Both glaciations and aridity are strongly implicated in creating hydrological barriers that isolated populations of stygofauna, leading to genetic divergence and speciation. These two types of climatic events are also likely to be important drivers of hydrological and genetic isolation of aquifers within New Zealand's alluvial plain systems.

Tectonic events may also have a role via lateral and/or vertical displacement creating barriers and/or changing groundwater flow directions (Trontelj et al., 2009; Craw & Waters, 2007). For example, most (if not all) of New Zealand's larger plain systems are fragmented with recent and historic faults, including the Pacific–Australian tectonic plate boundary. The effect of active faulting (e.g., the Greendale Fault responsible for the 2011 Christchurch eartquake), on dispersal and gene flow is unknown, although it may create physical barriers within an aquifer. Shearing and shaking could consolidate alluvium, reduce interstitial pore spaces and hydrological connectivity, or uplift may misalign strata to subdivide an aquifer (Cox et al., 2012; Rutter et al., 2016). Alternatively, tectonic activity may breach existing hydrological barriers between adjacent aquifers (e.g., bedrock fractures through ranges or breaks in confining layers may create new hydrological connections) and facilitate gene flow.

4.1. Summary

There have been repeated calls for accelerated scientific work to identify groundwater biodiversity, which is threatened with extinction before being discovered, identified, and ideally assigned a conservation status and protected (Gladstone et al., 2021; Mammola et al., 2019). Like most countries, knowledge of groundwater fauna is exceptionally poor in New Zealand. Our results support common findings of high biodiversity and short‐range endemism in groundwater faunas internationally (e.g., Boulton, 2020; Gladstone et al., 2021) and likewise for the use of genetic data in identifying morphologically cryptic species, which are common in groundwaters (Boulton, 2020; Delic et al., 2017; Eme et al., 2018; Gladstone et al., 2021). By contributing to knowledge of the biodiversity and spatial distributions of groundwater taxa, we hope to help address some of the knowledge gaps inhibiting conservation of groundwater biodiversity (e.g., Boulton, 2020; Mammola et al., 2019, 2020).

CONFLICT OF INTEREST

The authors declare no conflicting interests.

AUTHOR CONTRIBUTION

Graham D. Fenwick: Conceptualization (lead); Funding acquisition (lead); Investigation (equal); Methodology (equal); Project administration (equal); Resources (equal); Supervision (equal); Validation (equal); Visualization (equal); Writing‐original draft (lead). Michelle J. Greenwood: Formal analysis (equal); Investigation (equal); Methodology (equal); Project administration (equal); Validation (equal); Visualization (equal); Writing‐review & editing (equal). Ian D. Hogg: Data curation (equal); Formal analysis (equal); Investigation (equal); Methodology (equal); Project administration (equal); Resources (equal); Supervision (equal); Validation (equal); Writing‐review & editing (lead). Stacey J. Meyer: Data curation (equal); Formal analysis (equal); Investigation (equal); Methodology (equal); Visualization (equal); Writing‐review & editing (equal).

ACKNOWLEDGMENTS

We are extremely grateful to S. Mammola and an anonymous reviewer for their valued and constructive comments on the manuscript. Our thanks to NIWA colleagues Simon Howard, who coordinated and led the field sampling, Brian Smith for assistance with fieldwork, Paul Lambert for sample sorting, and Julian Sykes and Amy Whitehead for assistance with mapping and GIS data. Thanks also to Phil Abraham and others at the New Zealand Institute of Environmental Science and Research who assisted with fieldwork and provided environmental data. Joseph Thomas and his team (Tasman District Council), Hamish Carrad and Duncan Gray (Environment Canterbury), and staff at Hawkes Bay Regional Council helped to identify and access candidate bores and wells, provided well data, and assisted in the field. We also thank the land owners in Hawkes Bay, Tasman, Canterbury, and Southland for generous access to bores and wells on their land. Funding for this project was provided by New Zealand’s Biological Heritage National Science Challenge (Contract No. 1617‐44‐019 A).

APPENDIX 1.

Summary environmental characteristics for the 65 sampled wells. The number of sites in each category is listed in the median column for categorical variables. Some wells were missing environmental data owing to logistical sampling constraints and equipment failure

Parameter Description No. of wells missing data (%) Median Range
Well depth (m) Depth of well in meters 0 9.2 2.7–38.7
Water column depth (m) Depth of water within the well 2 (3%) 6.4 0.8–37.9
Well diameter (mm) Diameter of the well 1 (1.5%) 143 51–1200
Casing material Material of the well casing

4 (6%)

Steel: 34 wells

PVC: 16 wells

Concrete: 11 wells

 NA
Conductivity (uS/cm) Specific conductance spot measurement 7 (11%) 138 1.2–1014
Water temperature (°C) Water temperature spot measurement 7 (11%) 13.2 9–15.3
pH Scale of water acidity or basicity (0–14) spot measurement 7 (11%) 6.8 5.3–11.8
Dissolved oxygen (ppM) Amount of dissolved oxygen spot measurement 7 (11%) 4.5 0.4–8.6
DOC (g/m3) Dissolved organic carbon spot measurement 15 (24%) 2.1 0.2–23.6
DRP (mg/ m3) Dissolved reactive phosphorus spot measurement 14 (23%) 0.003 0.001–0.06
NH4‐N (mg/ m3) Ammoniacal nitrogen spot measurement 14 (23%) 11.5 2.0–774
NO3‐N (mg/ m3) Nitrate nitrogen spot measurement 14 (23%) 1900 1.0–11000
TDN (mg/ m3) Total dissolved nitrogen spot measurement 14 (23%) 2.04 0.02–10.9
TDP (mg/ m3) Total dissolved phosphorus spot measurement 14 (23%) 0.003 0.001–0.06
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APPENDIX 2.

The following keys are available and were used to morphologically identify amphipods and isopods:

Scarsbrook, M. R., G. D. Fenwick, I. C. Duggan, and M. Haase. 2003. A guide to the groundwater invertebrates of New Zealand. ISSN 1173–0382.

Fenwick, G.D. 2007. Quick guide to New Zealand freshwater amphipods. http://www.niwa.co.nz/sites/niwa.co.nz/files/amphipoda.pdf

Fenwick, G.D.; John, A. 2007. Quick guide to New Zealand freshwater Isopoda.

Fenwick, G.D.; Wilson, G.D.F. 2007. Field guide to New Zealand phreatoicid isopods. NIWA Biodiversity Report. 24 pp.

APPENDIX 3.

Sampling locations used in this study including North or South Island, region, aquifer and site (well) code, latitude, longitude, elevation, well depth, well casing type, sampling date, and availability of usable COI sequences obtained from the site (Yes/No)

Island Region Aquifer Site Latitude Longitude Elev (m) Depth Casing Date COI
North Hawkes Bay Ruataniwha RU1 −39.9812 176.3265 250 23.5 Steel 18/10/2017 N
RU2 −40.0082 176.3237 250 11.9 Steel 18/10/2017 N
RU3 −39.8097 176.4742 232 7.7 NA 18/10/2017 N
RU4 −39.8503 176.4525 215 21.2 Steel 18/10/2017 N
RU5 −39.9019 176.4575 185 8.9 PVC 18/10/2017 N
RU6 −39.9025 176.5147 160 6.3 Steel 19/10/2017 Y
RU7 −39.9736 176.4914 150 6.9 Steel 17/10/2017 N
RU8 −39.9654 176.644 110 38.7 Steel 19/10/2017 N
RU9 −39.9653 176.644 110 7.9 Steel 19/10/2017 N
South Canterbury Central Plains CP1 −43.483 171.9519 250 15 Steel 4/10/2017 N
CP2 −43.4851 171.9516 245 15 Steel 4/10/2017 N
CP3 −43.5015 171.9838 216 2.7 Steel 4/10/2017 Y
CP4 −43.5017 171.9836 216 7.7 Steel 4/10/2017 Y
CP5 −43.5629 171.9834 169 11.9 Steel 4/10/2017 Y
CP6 −43.6084 172.0977 117 7 Steel 12/05/2017 Y
CP7 −43.6076 172.0982 116 6.8 Steel 12/05/2017 N
CP8 −43.6201 172.3091 60 18.3 PVC 5/10/2017 N
CP9 −43.6202 172.3094 60 16.3 PVC 5/10/2017 N
CP10 −43.6746 172.3217 35 6.5 Steel 12/05/2017 N
CP11 −43.6743 172.3218 35 5.9 Steel 12/05/2017 N
CPA −43.6203 172.309 57 17.2 PVC 9/06/2015 N
CPB −43.6471 172.2298 67 18.3 Steel 30/05/2017 Y
CPC −43.7054 172.3606 21 15 Steel 1/03/2018 Y
Rangitata Levels RL1 −44.006 171.2551 192 9.4 Steel 8/11/2017 Y
RL2 −44.0482 171.306 143 9.8 Steel 11/12/2017 N
RL3 −44.0576 171.267 141 8.6 Steel 29/11/2017 Y
RL4 −44.072 171.3319 117 12 Steel 29/11/2017 Y
RL5 −44.1265 171.2723 82 7.6 Steel 8/11/2017 N
RL6 −44.1477 171.2988 67 8.2 Steel 29/11/2017 Y
RL7 −44.1645 171.3915 42 13.4 Steel 11/12/2017 Y
RL8 −44.1922 171.3294 37 14.4 Steel 8/11/2017 N
RL9 −44.2241 171.4141 7 6.3 Steel 29/11/2017 N
Waimakariri‐Ashley WA1 −43.2284 172.2278 220 6.8 PVC 16/06/2017 N
WA2 −43.2338 172.405 130 5.3 Steel 6/11/2017 N
WA3 −43.2492 172.49 105 5.8 PVC 6/11/2017 Y
WA4 −43.3129 172.4826 75 26 PVC 14/11/2017 Y
WA5 −43.2985 172.6162 27 15.2 Steel 6/11/2017 Y
WA6 −43.2768 172.6142 25 5.3 Steel 16/06/2017 Y
WA7 −43.2712 172.6272 21 6.3 PVC 9/11/2017 N
WA8 −43.283 172.6412 20 14.1 Steel 11/12/2017 Y
WA9 −43.274 172.6284 19 21.8 Steel 9/11/2017 N
WA10 −43.3126 172.4822 18 19 PVC 14/11/2017 N
WA11 −43.4165 172.6536 4 23.9 Steel 9/10/2017 Y
WA12 −43.3443 172.4099 106 30 Steel 14/11/2017 N
Tasman Motueka MT1 −41.477 172.8371 210 6.9 Steel 23/05/2017 N
MT2 −41.2515 172.8217 78 7.3 Concrete 24/05/2017 N
MT3 −41.2531 172.8225 75 6.8 Concrete 24/05/2017 N
MT4 −41.1049 172.9994 8 19 Steel 24/05/2017 Y
MT5 −41.1051 172.9992 8 18 uPVC 24/05/2017 N
MT6 −41.1049 172.9998 8 21.5 uPVC 24/05/2017 N
MT7 −41.1042 172.9996 8 10 uPVC 24/05/2017 Y
Waimea WM1 −41.4546 172.9574 143 4 Concrete 23/05/2017 N
WM2 −41.4499 172.9595 140 4.3 Concrete 23/05/2017 N
WM3 −41.4533 172.9577 139 3.9 Concrete 23/05/2017 N
WM4 −41.4502 172.9622 132 3.4 Concrete 23/05/2017 N
WM5 −41.3817 173.0811 90 9.2 PVC 25/05/2017 Y
WM6 −41.3819 173.0813 90 9.2 PVC 25/05/2017 Y
WM7 −41.3823 173.0817 90 8.6 PVC 25/05/2017 Y
WM8 −41.3574 173.098 24 5 Concrete 23/05/2017 N
WM9 −41.3568 173.097 23 5 Concrete 23/05/2017 N
WM10 −41.2885 173.1243 3 10 PVC 23/05/2017 N
WM11 −41.292 173.1195 3 6.4 Concrete 23/05/2017 N
WM12 −41.2998 173.1412 3 14 NA 23/05/2017 N
Southland Mataura MA1 −46.2981 168.8129 34 15.5 NA 26/10/2017 Y
MA2 −46.3469 168.7855 28 15 NA 24/10/2017 Y
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APPENDIX 4.

List of taxa and associated molecular operational taxonomic units (MOTU) based on Barcode of Life Datasystems (BOLD) Barcode Index Numbers (BIN). Site codes and unique BOLD Process IDs are also provided for each specimen

Order Family Genus species MOTU (BIN) Site BOLD ID
Amphipoda Paracrangonyctidae Paracrangonyx sp. BOLD:ADL2540 WM6 NZGDW023‐18
NZGDW028‐18
WM7 NZGDW024‐18
NZGDW036‐18
NZGDW039‐18
BOLD:ADL3783 MT7 NZGDW029‐18
NZGDW038‐18
NZGDW040‐18
BOLD:ADL5568 WA5 NZGDW079‐18
NZGDW083‐18
Paraleptamphopidae Paraleptamphopus sp. BOLD:AAB2704 CP3 NZGDW308‐18
NZGDW311‐18
NZGDW314‐18
NZGDW315‐18
NZGDW322‐18
NZGDW324‐18
CP5 NZGDW052‐18
NZGDW068‐18
NZGDW380‐18
RL1 NZGDW001‐18
NZGDW002‐18
NZGDW013‐18
NZGDW017‐18
RL6 NZGDW215‐18
WA8 NZGDW351‐18
Ringanui sp. BOLD:ADL2688 RL1 NZGDW008‐18
RL3 NZGDW362‐18
BOLD:ADL5144 WM6 NZGDW033‐18
BOLD:ADL5178 WM6 NZGDW032‐18
NZGDW035‐18
Indeterminate BOLD:ADL3023 WM7 NZGDW031‐18
BOLD:ADL3150 WM6 NZGDW044‐18
NZGDW057‐18
NZGDW063‐18
NZGDW067‐18
NZGDW070‐18
WM7 NZGDW043‐18
NZGDW046‐18
NZGDW047‐18
NZGDW054‐18
BOLD:ADL3507 MT7 NZGDW045‐18
NZGDW050‐18
BOLD:ADL3923 WA11 NZGDW003‐18
NZGDW004‐18
NZGDW010‐18
NZGDW011‐18
NZGDW012‐18
NZGDW018‐18
NZGDW089‐18
WA3 NZGDW074‐18
WA5 NZGDW075‐18
NZGDW088‐18
BOLD:ADL5343 CP4 NZGDW301‐18
NZGDW303‐18
CP5 NZGDW065‐18
BOLD:ADO8356 CP3 NZGDW319‐18
NZGDW331‐18
BOLD:ADO8751 CP3 NZGDW313‐18
NZGDW317‐18
CP5 NZGDW058‐18
NZGDW061‐18
NZGDW066‐18
NZGDW212‐18
NZGDW294‐18
CPC NZGDW363‐18
WA3 NZGDW073‐18
NZGDW090‐18
WA4 NZGDW198‐18
NZGDW206‐18
NZGDW208‐18
NZGDW209‐18
NZGDW217‐18
WA5 NZGDW078‐18
NZGDW080‐18
NZGDW082‐18
NZGDW087‐18
BOLD:ADO9995 RL4 NZGDW199‐18
NZGDW202‐18
NZGDW210‐18
NZGDW369‐18
BOLD:ADP0945 CP4 NZGDW307‐18
BOLD:ADP2782 CP3 NZGDW291‐18
NZGDW305‐18
NZGDW312‐18
NZGDW316‐18
NZGDW323‐18
NZGDW325‐18
NZGDW328‐18
NZGDW329‐18
CP4 NZGDW296‐18
CP5 NZGDW216‐18
NZGDW286‐18
NZGDW297‐18
NZGDW300‐18
WA6 NZGDW337‐18
BOLD:ADR4302 WM6 NZGDW041‐18
WM7 NZGDW042‐18
WM7 NZGDW049‐18
BOLD:ADR9818 CP4 NZGDW288‐18
WA3 NZGDW072‐18
NZGDW081‐18
NZGDW086‐18
BOLD:ADS1859 MA1 NZGDW357‐18
NZGDW358‐18
NZGDW359‐18
MA2 NZGDW356‐18
Phreatogammaridae Indeterminate BOLD:AAC7108 CPB NZGDW355‐18
BOLD:AAC7110 RL1 NZGDW016‐18
BOLD:ADL2601 MT7 NZGDW048‐18
BOLD:ADL2933 CPC NZGDW361‐18
RL7 NZGDW338‐18
NZGDW353‐18
WA3 NZGDW085‐18
BOLD:ADL3480 WM7 NZGDW053‐18
NZGDW064‐18
NZGDW069‐18
Indeterminate Indeterminate BOLD:ADL2934 WA5 NZGDW076‐18
BOLD:ADL3262 RU6 NZGDW077‐18
BOLD:ADL3398 MT7 NZGDW060‐18
BOLD:ADL5342 WM6 NZGDW059‐18
BOLD:ADO7909 CP5 NZGDW302‐18
BOLD:ADO7917 CP3 NZGDW320‐18
CP4 NZGDW287‐18
NZGDW293‐18
BOLD:ADP0919 WM5 NZGDW341‐18
BOLD:ADP1876 WA6 NZGDW333‐18
BOLD:ADR2136 WM6 NZGDW056‐18
BOLD:ADS6423 CP3 NZGDW330‐18
BOLD:ADV1824 RL3 NZGDW332‐18
Isopoda Janiridae Indeterminate BOLD:ADP3141 WA6 NZGDW342‐18
Paranthuridae Cruregens fontanus BOLD:ADL2602 RL1 NZGDW006‐18
NZGDW009‐18
RL6 NZGDW200‐18
BOLD:ADL3149 WM6 NZGDW022‐18
NZGDW030‐18
NZGDW034‐18
NZGDW037‐18
WM7 NZGDW027‐18
BOLD:ADL3492 CP5 NZGDW051‐18
NZGDW367‐18
NZGDW371‐18
NZGDW374‐18
NZGDW376‐18
WA8 NZGDW345‐18
NZGDW349‐18
BOLD:ADP0923 MT4 NZGDW348‐18
BOLD:ADP4594 CP3 NZGDW310‐18
CP6 NZGDW204‐18
Tylidae Phreatoicus orarii BOLD:ADO9117 CP5 NZGDW194‐18
NZGDW197‐18
NZGDW379‐18
BOLD:ADP4302 CP5 NZGDW195‐18
Phreatoicus typicus BOLD:ADP4667 CP4 NZGDW292‐18
NZGDW304‐18
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Fenwick, G. D. , Greenwood, M. J. , Hogg, I. D. , & Meyer, S. J. (2021). High diversity and local endemism in Aotearoa New Zealand's groundwater crustacean fauna. Ecology and Evolution, 11, 15664–15682. 10.1002/ece3.8220

DATA AVAILABILITY STATEMENT

Residual cuticular material after DNA extraction for each specimen was deposited with the NIWA (National Institute of Water and Atmospheric Research Ltd, Wellington) Invertebrate Collection (NIC) as museum vouchers available for morphological study. Specimen images, collection data, raw trace files, and edited sequences were all uploaded to and are available on the Barcode of Life Datasystems (BOLD) database (https://doi.org/10.5883/DS‐GDWMS) and cross‐referenced to GenBank (accession numbers OK072722‐OK072875). All data associated with the paper are also available from the NZ Biological Heritage National Science Challenge data repository at https://doi.org/10.34721/qk3f‐6y64.

REFERENCES

  1. Booker, D. J. , & Whitehead, A. L. (2017). NZ River Maps: An interactive online tool for mapping predicted freshwater variables across New Zealand. (https://shiny.niwa.co.nz/nzrivermaps/): NIWA. [Google Scholar]
  2. Boulton, A. J. (2020). Editorial: Conservation of groundwaters and their dependent ecosystems: Integrating molecular taxonomy, systematic reserve planning and cultural values. Aquatic Conservation‐Marine and Freshwater Ecosystems, 30, 1–7. 10.1002/aqc.3268 [DOI] [Google Scholar]
  3. Bradford, T. , Adams, M. , Humphreys, W. F. , Austin, A. D. , & Cooper, S. J. B. (2010). DNA barcoding of stygofauna uncovers cryptic amphipod diversity in a calcrete aquifer in Western Australia’s arid zone. Molecular Ecology Resources, 10, 41–50. 10.1111/j.1755-0998.2009.02706.x [DOI] [PubMed] [Google Scholar]
  4. Bradshaw, M. , & Soons, J. M. (2008). The lie of the land. In Winterbourn M. J., Knox G. A., Burrows C. J., & Marsden I. (Eds.), The natural history of Canterbury (pp. 13–36). Canterbury University Press and Manaaki Whenua Press. [Google Scholar]
  5. Brown, L. J. (2001). Canterbury. In Rosen M. R., & White P. A. (Eds.), Groundwaters of New Zealand (pp. 441–459). New Zealand hydrological Society Inc. [Google Scholar]
  6. Chilton, C. (1894). The subterranean Crustacea of New Zealand with some general remarks on the fauna of caves and wells. Transactions of the Linnean Society of London (2nd Series Zoology) 6:163–284, pls 116‐123. [Google Scholar]
  7. Close, M. E. , Stanton, G. J. , & Pang, L. (2002). Use of rhodamine WT with XAD‐7 resin for determining groundwater flow paths. Hydrogeology Journal, 10, 368–376. 10.1007/s10040-002-0202-z [DOI] [Google Scholar]
  8. Collins, G. E. , Hogg, I. D. , Baxter, J. R. , Maggs‐Kölling, G. , & Cowan, D. A. (2019). Ancient landscapes of the Namib Desert harbor high levels of genetic variability and deeply divergent lineages for Collembola. Ecology and Evolution, 9, 4969–4979. 10.1002/ece3.5103 [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cooper, S. J. B. , Bradbury, J. H. , Saint, K. M. , Leys, R. , Austin, A. D. , & Humphreys, W. F. (2007). Subterranean archipelago in the Australian arid zone: mitochondrial DNA phylogeography of amphipods from central Western Australia. Molecular Ecology, 16, 1533–1544. 10.1111/j.1365-294X.2007.03261.x [DOI] [PubMed] [Google Scholar]
  10. Costa, F. O. , deWaard, J. R. , Boutillier, J. , Ratnasingham, S. , Dooh, R. T. , Hajibabaei, M. , & Hebert, P. D. N. (2007). Biological identifications through DNA barcodes: The case of the Crustacea. Canadian Journal of Fisheries and Aquatic Sciences, 64, 272–295. 10.1139/f07-008 [DOI] [Google Scholar]
  11. Cox, S. C. , Rutter, H. K. , Sims, A. , Manga, M. , Weir, J. J. , Ezzy, T. , White, P. A. , Horton, T. W. , & Scott, D. (2012). Hydrological effects of the M W 7.1 Darfield (Canterbury) earthquake, 4 September 2010, New Zealand. New Zealand Journal of Geology and Geophysics, 55, 231–247. [Google Scholar]
  12. Craw, D. , & Waters, J. (2007). Geological and biological evidence for regional drainage reversal during lateral tectonic transport, Marlborough, New Zealand. Journal of the Geological Society, 164, 785–793. 10.1144/0016-76492006-064 [DOI] [Google Scholar]
  13. Culver, D. C. , Master, L. L. , Christman, M. C. , & Hobbs, H. H. III (2000). Obligate Cave Fauna of the 48 contiguous United States. Conservation Biology, 14, 386–401. 10.1046/j.1523-1739.2000.99026.x [DOI] [Google Scholar]
  14. Culver, D. C. , Pipan, T. , & Schneider, K. (2009). Vicariance, dispersal and scale in the aquatic subterranean fauna of karst regions. Freshwater Biology, 54, 918–929. 10.1111/j.1365-2427.2007.01856.x [DOI] [Google Scholar]
  15. Culver, D. C. , & Sket, B. (2000). Hotspots of subterranean biodiversity in caves and wells. Journal of Cave and Karst Studies, 62, 11–17. [Google Scholar]
  16. Culver, D. C. , Trontelj, P. , Zagmajster, M. , & Pipan, T. (2012). Paving the way for standardized and comparable subterranean biodiversity studies. Subterranean Biology, 10, 43–50. [Google Scholar]
  17. Danielopol, D. L. , Griebler, C. , Gunatilaka, A. , & Notenboom, J. (2003). Present state and future prospects for groundwater ecosystems. Environmental Conservation, 30, 104–130. 10.1017/S0376892903000109 [DOI] [Google Scholar]
  18. Danielopol, D. L. , & Pospisil, P. (2001). Hidden biodiversity in the groundwater of the Danube Flood Plain National Park (Austria). Biodiversity and Conservation, 10, 1711–1721. [Google Scholar]
  19. Danielopol, D. , Pospisil, P. , & Rouch, R. (2000). Biodiversity in groundwater: A large‐scale view. Trends in Ecology & Evolution, 15, 223–224. 10.1016/S0169-5347(00)01868-1 [DOI] [PubMed] [Google Scholar]
  20. Davey, G. (2006). A contribution to the understanding of Canterbury Plains aquifers. Environment Canterbury, Christchurch, New Zealand.
  21. Deharveng, L. , Stoch, F. , Gibert, J. , Bedos, A. , Galassi, D. , Zagmajster, M. , Brancelj, A. , Camacho, A. , Fiers, F. , Martin, P. , Giani, N. , Magniez, G. , & Marmonier, P. (2009). Groundwater biodiversity in Europe. Freshwater Biology, 54, 709–726. 10.1111/j.1365-2427.2008.01972.x [DOI] [Google Scholar]
  22. Delić, T. , Trontelj, P. , Rendoš, M. , & Fišer, C. (2017). The importance of naming cryptic species and the conservation of endemic subterranean amphipods. Scientific Reports, 7, 3391. 10.1038/s41598-017-02938-z [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Eberhard, S. M. , Halse, S. A. , Williams, M. R. , Scanlon, M. D. , Cocking, J. , & Barron, H. J. (2009). Exploring the relationship between sampling efficiency and short‐range endemism for groundwater fauna in the Pilbara region, Western Australia. Freshwater Biology, 54, 885–901. 10.1111/j.1365-2427.2007.01863.x [DOI] [Google Scholar]
  24. Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Eme, D. , Zagmajster, M. , Delić, T. , Fišer, C. , Flot, J.‐F. , Konecny‐Dupré, L. , Pálsson, S. , Stoch, F. , Zakšek, V. , Douady, C. , & Malard, F. (2018). Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants. Ecography, 41, 424–436. 10.1111/ecog.02683 [DOI] [Google Scholar]
  26. Fenwick, G. D. (2000). Collections of New Zealand groundwater amphipods. NIWA technical report 95, 21. [Google Scholar]
  27. Fenwick, G. D. (2001). The freshwater Amphipoda (Crustacea) of New Zealand: a review. Journal of the Royal Society of New Zealand, 31, 341–363. 10.1080/03014223.2001.9517658 [DOI] [Google Scholar]
  28. Fenwick, G. D. (2006). Ringanui, a new genus of stygobitic amphipod from New Zealand (Amphipoda: Gammaridea: Paraleptamphopidae). Zootaxa, 1148, 1–25. 10.11646/zootaxa.1148.1.1 [DOI] [Google Scholar]
  29. Ferreira, D. , Malard, F. , Dole‐Olivier, M.‐J. , & Gibert, J. (2007). Obligate groundwater fauna of France: Diversity patterns and conservation implications. Biodiversity and Conservation, 16, 567. 10.1007/s10531-005-0305-7 [DOI] [Google Scholar]
  30. Ficetola, G. F. , Canedoli, C. , & Stoch, F. (2019). The Racovitzan impediment and the hidden biodiversity of unexplored environments. Conservation Biology, 33, 214–216. 10.1111/cobi.13179 [DOI] [PubMed] [Google Scholar]
  31. Finston, T. L. , Johnson, M. S. , Humphreys, W. F. , Eberhard, S. M. , & Halse, S. A. (2007). Cryptic speciation in two widespread subterranean amphipod genera reflects historical drainage patterns in an ancient landscape. Molecular Ecology, 16, 355–365. 10.1111/j.1365-294X.2006.03123.x [DOI] [PubMed] [Google Scholar]
  32. Folmer, B. , Hoeh, W. , Lutz, R. , & Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3(5), 294–299. [PubMed] [Google Scholar]
  33. Gibert, J. , & Culver, D. C. (2009). Assessing and conserving groundwater biodiversity: an introduction. Freshwater Biology, 54, 639–648. 10.1111/j.1365-2427.2009.02202.x [DOI] [Google Scholar]
  34. Gibert, J. , Culver, D. C. , Dole‐Olivier, M.‐J. , Malard, F. , Christman, M. C. , & Deharveng, L. (2009). Assessing and conserving groundwater biodiversity: Synthesis and perspectives. Freshwater Biology, 54, 930–941. 10.1111/j.1365-2427.2009.02201.x [DOI] [Google Scholar]
  35. Gibert, J. , & Deharveng, L. (2002). Subterranean ecosystems: a truncated functional biodiversity. BioScience, 52, 573–481. 10.1641/0006-3568(2002)052[0473:SEATFB]2.0.CO;2 [DOI] [Google Scholar]
  36. Gladstone, N. S. , Niemiller, M. L. , Hutchins, B. , Schwartz, B. , Czaja, A. , Slay, M. E. , & Whelan, N. V. (2021). Subterranean freshwater gastropod biodiversity and conservation in the United States and Mexico. Conservation Biology (online early). 10.1111/cobi.13722 [DOI] [PubMed] [Google Scholar]
  37. Griebler, C. , Avramov, M. , & Hose, G. (2019). Groundwater ecosystems and their services: current status and potential risks. In Schröter M., Bonn A., Klotz S., Seppelt R., & Baessler C. (Eds.), Atlas of ecosystem services (pp. 197–203). Springer. [Google Scholar]
  38. Haase, M. (2008). The radiation of hydrobiid gastropods in New Zealand: a revision including the description of new species based on morphology and mtDNA sequence information. Systematics and Biodiversity, 6, 99–159. 10.1017/S1477200007002630 [DOI] [Google Scholar]
  39. Hancock, P. J. , & Boulton, A. J. (2008). Stygofauna biodiversity and endemism in four alluvial aquifers in eastern Australia. Invertebrate Systematics, 22, 117–126. 10.1071/IS07023 [DOI] [Google Scholar]
  40. Hancock, P. J. , & Boulton, A. J. (2009). Sampling groundwater fauna: efficiency of rapid assessment methods tested in bores in eastern Australia. Freshwater Biology, 54, 902–917. [Google Scholar]
  41. Harvey, M. S. (2002). Short‐range endemism amongst the Australian fauna: some examples from non‐marine environments. Invertebrate Systematics, 16, 555–570. [Google Scholar]
  42. Harvey, M. S. , Rix, M. G. , Framenau, V. W. , Hamilton, Z. R. , Johnson, M. S. , Teale, R. J. , Humphreys, G. , & Humphreys, W. F. (2011). Protecting the innocent: studying short‐range endemic taxa enhances conservation outcomes. Invertebrate Systematics, 25, 1–10. 10.1071/IS11011 [DOI] [Google Scholar]
  43. Hebert, P. D. N. , Penton, E. H. , Burns, J. M. , Janzen, D. H. , & Hallwachs, W. (2004). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator . Proceedings of the National Academy of Sciences of the United States of America, 101, 14812–14817. 10.1073/pnas.0406166101 [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Hogg, I. D. , Stevens, M. I. , Schnabel, K. E. , & Chapman, M. A. (2006). Deeply divergent lineages of the widespread New Zealand amphipod Paracalliope fluviatilis revealed using allozyme and mitochondrial DNA analyses. Freshwater Biology, 51, 236–248. 10.1111/j.1365-2427.2005.01491.x [DOI] [Google Scholar]
  45. Ivanova, N. V. , deWaard, J. R. , & Hebert, P. D. N. (2006). An inexpensive, automation‐friendly protocol for recovering high‐quality DNA. Molecular Ecology Notes, 6, 998–1002. [Google Scholar]
  46. Ivanova, N. V. , deWaard, J. R. , & Hebert, P. D. N. (2007). CCDB protocols, glass fiber plate DNA extraction. ccdb.ca/site/wp‐content/uploads/2016/09/CCDB_DNA_Extraction.pdf
  47. Ivanova, N. V. , & Grainger, C. M. (2007). CCDB protocols, COI amplification. ccdb.ca/site/wp‐content/uploads/2016/09/CCDB_Amplification.pdf
  48. Kearse, M. , Moir, R. , Wilson, A. , Stones‐Havas, S. , Cheung, M. , Sturrock, S. , Buxton, S. , Cooper, A. , Markowitz, S. , Duran, C. , Thierer, T. , Ashton, B. , Meintjes, P. , & Drummond, A. (2012). Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England), 28(12), 1647–1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. King, R. A. , & Leys, R. (2014). Molecular evidence for mid‐Pleistocene divergence of populations of three freshwater amphipod species (Talitroidea: Chiltoniidae) on Kangaroo Island, South Australia, with a new spring‐associated genus and species. Australian Journal of Zoology, 62, 137–156. [Google Scholar]
  50. Korbel, K. , Chariton, A. , Stephenson, S. , Greenfield, P. , & Hose, G. C. (2017). Wells provide a distorted view of life in the aquifer: implications for sampling, monitoring and assessment of groundwater ecosystems. Scientific Reports, 7, 40702. 10.1038/srep40702 [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Kumar, S. , Stecher, G. , & Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874. 10.1093/molbev/msw054 [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Larned, S. T. (2012). Phreatic groundwater ecosystems: Research frontiers for freshwater ecology. Freshwater Biology, 57, 885–906. 10.1111/j.1365-2427.2012.02769.x [DOI] [Google Scholar]
  53. Larned, S. T. , Unwin, M. J. , & Boustead, N. C. (2014). Ecological dynamics in the riverine aquifers of a gaining and losing river. Freshwater Science, 34, 1–19. [Google Scholar]
  54. Lefébure, T. , Douady, C. J. , Gouy, M. , Trontelj, P. , Briolay, J. , & Gibert, J. (2006). Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments. Molecular Ecology, 15, 1797–1806. 10.1111/j.1365-294X.2006.02888.x [DOI] [PubMed] [Google Scholar]
  55. Lefébure, T. , Douady, C. J. , Malard, F. , & Gibert, J. (2007). Testing dispersal and cryptic diversity in a widely distributed groundwater amphipod (Niphargus rhenorhodanensis). Molecular Phylogenetics and Evolution, 42, 676–686. 10.1016/j.ympev.2006.08.020 [DOI] [PubMed] [Google Scholar]
  56. Malard, F. , Dole‐Olivier, M.‐J. , Mathieu, J. , Stoch, F. , Boutin, C. , Brancelj, A. , Camacho, A. I. , Fiers, F. , Galassi, D. , Gibert, J. , Lefebure, T. , Martin, P. , Sket, B. , & Valdecasas, A. G. (2002). Sampling manual for the assessment of regional groundwater biodiversity. Protocols for the Assessment and Conservation of Aquatic Life In the Subsurface. EU.
  57. Mammola, S. , Amorim, I. R. , Bichette, M. E. , Borges, P. A. V. , Cheeptham, N. , Cooper, S. J. B. , Culver, D. C. , Deharveng, L. , Eme, D. , Ferreira, R. L. , Fišer, C. , Fišer, Ž. , Fong, D. W. , Griebler, C. , Jeffery, W. R. , Jugovic, J. , Kowalko, J. E. , Lilley, T. M. , Malard, F. , … Cardoso, P. (2020). Fundamental research questions in subterranean biology. Biological Reviews, 95, 1855–1872. 10.1111/brv.12642 [DOI] [PubMed] [Google Scholar]
  58. Mammola, S. , Cardoso, P. , Culver, D. C. , Deharveng, L. , Ferreira, R. L. , Fišer, C. , Galassi, D. M. P. , Griebler, C. , Halse, S. , Humphreys, W. F. , Isaia, M. , Malard, F. , Martinez, A. , Moldovan, O. T. , Niemiller, M. L. , Pavlek, M. , Reboleira, A. P. S. , Souza‐Silva, M. , Teeling, E. C. , … Zagmajster, M. (2019). Scientists’ warning on the conservation of subterranean ecosystems. BioScience, 69, 641–650. 10.1093/biosci/biz064 [DOI] [Google Scholar]
  59. Marmonier, P. , Vervier, P. , Gibert, J. , & Dole‐Olivier, M.‐J. (1993). Biodiversity in ground waters. Trends in Ecology and Evolution, 8, 392–395. 10.1016/0169-5347(93)90039-R [DOI] [PubMed] [Google Scholar]
  60. Milton, M. , Pierossi, P. , & Ratnasingham, S. (2013). Barcode of life data systems handbook. Barcode of Life Data Systems; [Google Scholar]
  61. Ministry for the Environment . (2015). Location and extent of New Zealand's aquifers New Zealand's Environmental Reporting Series: The Ministry for the Environment and Statistics New Zealand.
  62. Moreau, M. , & Bekele, M. (2015). Groundwater component of the Water Physical Stock Account (WPSA). GNS Science. [Google Scholar]
  63. Moreau, M. , White, P. A. , Mourot, F. , Rawlinson, Z. J. , Tschritter, C. , Cameron, S. G. , & Westerhoff, R. S. (2019). Classification of New Zealand hydrogeological systems. GNS Science. [Google Scholar]
  64. Murphy, N. P. , Adams, M. , Guzik, M. T. , & Austin, A. D. (2013). Extraordinary micro‐endemism in Australian desert spring amphipods. Molecular Phylogenetics and Evolution, 66, 645–653. 10.1016/j.ympev.2012.10.013 [DOI] [PubMed] [Google Scholar]
  65. Pang, L. , Close, M. , & Noonan, M. (1998). Rhodamine WT and Bacillus subtilis transport through an alluvial gravel aquifer. Groundwater, 36, 112–122. 10.1111/j.1745-6584.1998.tb01071.x [DOI] [Google Scholar]
  66. R Development Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing. Retrieved from http://www.R‐project.org. [Google Scholar]
  67. Ratnasingham, S. , & Hebert, P. D. N. (2007). BOLD: the barcode of life data system (www.barcodinglife.org). Molecular Ecology Notes, 7, 355–364. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Ratnasingham, S. , & Hebert, P. D. N. (2013). A DNA‐based registry for all animal species: The Barcode Index Number (BIN) System. PLoS One, 8, e66213. 10.1371/journal.pone.0066213 [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Rutter, H. K. , Cox, S. C. , Dudley Ward, N. F. , & Weir, J. J. (2016). Aquifer permeability change caused by a near‐field earthquake, Canterbury, New Zealand. Water Resources Research, 52, 8861–8878. 10.1002/2015WR018524 [DOI] [Google Scholar]
  70. Scarsbrook, M. R. , & Fenwick, G. D. (2003). Preliminary assessment of crustacean distribution patterns in New Zealand groundwater aquifers. New Zealand Journal of Marine and Freshwater Research, 37, 405–413. 10.1080/00288330.2003.9517176 [DOI] [Google Scholar]
  71. Scarsbrook, M. R. , Fenwick, G. D. , Duggan, I. C. , & Haase, M. (2003). A guide to the groundwater invertebrates of New Zealand. New Zealand Publication. [Google Scholar]
  72. Trontelj, P. , Douady, C. J. , Fiser, C. , Gibrt, J. , Goricki, Š. , Lefebure, T. , Sket, B. , & Zaksek, V. (2009). A molecular test for cryptic diversity in ground water: how large are the ranges of macro‐stygobionts? Freshwater Biology, 54, 727–744. 10.1111/j.1365-2427.2007.01877.x [DOI] [Google Scholar]
  73. Tschritter, C. , Westerhoff, R. S. , Rawlinson, Z. J. , & White, P. A. (2017). Aquifer classification and mapping at the national scale ‐ Phase 1: identification of hydrogeological units. GNS Science, Te Pū Ao, New Zealand. [Google Scholar]
  74. Watson, N. T. N. , Duggan, I. C. , & Hogg, I. D. (2015). Assessing the diversity of New Zealand freshwater harpacticoid copepods (Crustacea: Copepoda) using mitochondrial DNA (COI) barcodes. New Zealand Journal of Zoology, 42, 57–67. 10.1080/03014223.2015.1011592 [DOI] [Google Scholar]
  75. Wattier, R. , Mamos, T. , Copilaş‐Ciocianu, D. , Jelić, M. , Ollivier, A. , Chaumot, A. , Danger, M. , Felten, V. , Piscart, C. , Žganec, K. , Rewicz, T. , Wysocka, A. , Rigaud, T. , & Grabowski, M. (2020). Continental‐scale patterns of hyper‐cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda). Scientific Reports, 10, 16536. 10.1038/s41598-020-73739-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
  76. Westram, A. M. , Jokela, J. , Baumgartner, C. , & Keller, I. (2011). Spatial distribution of cryptic species diversity in European freshwater amphipods (Gammarus fossarum) as revealed by pyrosequencing. PLoS One, 6, e23879. 10.1371/journal.pone.0023879 [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. White, P. A. (2001). Groundwater resources in New Zealand. In Rosen M. R., & White P. A. (Eds.), Groundwater of New Zealand (pp. 45–75). New Zealand Hydrological Society. [Google Scholar]
  78. White, P. A. , Moreau, M. , Mourot, F. , & Rawlinson, Z. J. (2019). New Zealand Groundwater Atlas: Hydrogeological‐Unit Map of New Zealand. GNS consultancy report 2019/144.
  79. White, P. A. , & Rosen, M. R. (2001). Introduction. In Rosen M. R., & White P. A. (Eds.), Groundwaters of New Zealand (pp. 1–3). New Zealand Hydrological Society Inc. [Google Scholar]
  80. Wilson, G. D. F. , & Fenwick, G. D. (1999). Taxonomy and ecology of Phreatoicus typicus Chilton, 1883 (Crustacea, Isopoda, Phreatoicidae). Journal of the Royal Society of New Zealand, 29, 41–64. [Google Scholar]
  81. Witt, J. D. S. , Threloff, D. L. , & Hebert, P. D. N. (2006). DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Molecular Ecology, 15, 3073–3082. 10.1111/j.1365-294X.2006.02999.x [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

Residual cuticular material after DNA extraction for each specimen was deposited with the NIWA (National Institute of Water and Atmospheric Research Ltd, Wellington) Invertebrate Collection (NIC) as museum vouchers available for morphological study. Specimen images, collection data, raw trace files, and edited sequences were all uploaded to and are available on the Barcode of Life Datasystems (BOLD) database (https://doi.org/10.5883/DS‐GDWMS) and cross‐referenced to GenBank (accession numbers OK072722‐OK072875). All data associated with the paper are also available from the NZ Biological Heritage National Science Challenge data repository at https://doi.org/10.34721/qk3f‐6y64.

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