Literature DB >> 31116764

Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan.

Muhammad Ashfaq1, Gergin Blagoev1, Hafiz Muhammad Tahir2, Arif M Khan3, Muhammad Khalid Mukhtar4, Saleem Akhtar5, Abida Butt6, Shahid Mansoor7, Paul D N Hebert1.   

Abstract

Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0-5.3% while congeneric distances varied from 2.8-23.2%. Excepting one species pair (Oxyopes azhari-Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.

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Mesh:

Year:  2019        PMID: 31116764      PMCID: PMC6530854          DOI: 10.1371/journal.pone.0217086

Source DB:  PubMed          Journal:  PLoS One        ISSN: 1932-6203            Impact factor:   3.240


Introduction

With nearly 48,000 known species in 117 families [1], spiders are a major component of terrestrial ecosystems with important practical applications as biocontrol agents [2] and as bio-indicators [3,4]. Prior studies have documented 4,300 spider species in Europe [5] and a similar number (3,800) in the Nearctic [6]. By contrast, just 2,300 species have been reported from South Asia [7], suggesting that many species await detection in this region. Although studies on the spider fauna of Pakistan began nearly a century ago [8], work has recently intensified, but most of these studies have produced regional checklists (S1 Table). Unfortunately, these publications often employ invalid or incorrect species names or only identify specimens to a family [9], compromising their value [10-12]. It is likely that many species reported as new discoveries from Pakistan [13] await description. For example, in her dissertation research on spiders of Punjab, Parveen [13] reported the discovery of 33 new species but only one has been formally described [9]. Examination of prior taxonomic work (S1 Table) indicates that just 400 species of spiders have been documented from Pakistan. Considering the country’s diverse ecosystems [14], this count must seriously underestimate the true diversity of its fauna given the much higher numbers reported for India (1686) [15] and Iran (528) [16]. The limited knowledge of the spider fauna of Pakistan is a particular example of the barrier to our general understanding of spider biodiversity in a global context, a factor compromising both scientific progress and conservation efforts [17]. The poor documentation of spider diversity of Pakistan reflects, in part, the paucity of taxonomic specialists working on the group [18]. Moreover, spiders pose a challenge for morphological approaches because cryptic species are common [19], and sexual dimorphism is often striking [20]. DNA barcoding [21] provides an alternate approach to identifications. It employs sequence diversity in a standard gene region (COI-5′) to discriminate both morphologically cryptic species and all life stages, even for species with sexual dimorphism [22,23]. Although concerns about the use of single marker [24,25] or discordance between the barcode and other gene regions [26] have been voiced [27], the advantages of employing a single standard gene region for DNA barcoding is now very well established [28]. Fifteen years after its introduction, this approach has demonstrated its effectiveness in discriminating species in diverse groups, including spiders [29-34]. The use of DNA barcoding for specimen identification and species discovery is greatly facilitated by BOLD, the Barcode of Life Data System (http://www.boldsystems.org). This informatics platform assembles specimen metadata and sequences and provides tools to facilitate data analysis and publication [35]. It also enables species discrimination by assigning each COI sequence cluster to a Barcode Index Number (BIN) [36], which is an analogue of Operational Taxonomic Unit (OTU). Because BINs have high congruence with species recognized through morphological analysis [37-40], they are now routinely used as a species proxy [41,42]. Consequently, they have gained wide adoption [41,43] for cryptic species recognition [40,43], species discovery [44], taxonomic revisions [45], and faunal assessments [46,47]. The DNA barcode reference libraries available for diverse animal groups [48-54] are helping to identify newly collected specimens [45,54] and to speed taxonomic progress [33]. By assigning sequences from unidentified specimens to a species proxy [44], the BIN system has greatly augmented the application of barcode data in groups where taxonomic knowledge is poor. These barcode libraries are, in effect, forming the foundation for a global “DNA library of life” [55]. At present, BOLD holds 6.8 million records derived from specimens representing 587,000 BINs (accessed 13 April, 2019). This total includes 117,000 records from spiders that have been assigned to more than 10,000 BINs. Past work on spiders has had varied motivations [39,56-60], but just two prior studies have aimed to construct a comprehensive DNA barcode library for a national fauna–Canada [61] and Germany [62]. The need for similar work in other regions is evident, particularly in south Asia. For example, barcode records are only available for 73 species of spiders from India [35,63] and for 41 species from Pakistan [64-66]. The current study aimed to develop a barcode library for the spider fauna of Pakistan and investigate the spider diversity overlap with other regions using BINs. The study addresses the gap for reference data in the country by expanding DNA barcode coverage for Pakistan to 202 species.

Materials and methods

Ethics statement

No specific permissions were required for this study. The study did not involve endangered or protected species.

Spider collection

From 2010 to 2016, 1,795 spiders were collected at 225 sites in Pakistan (Fig 1). Each spider was provisionally identified by collectors in Pakistan before it was sequenced for the barcode region of the mitochondrial COI gene [21]. GB subsequently validated and refined identifications by examining (including genitalic dissections) representative specimens from each barcode cluster. Generic and species assignments generally followed taxonomic publications on Asian spiders (S1 Table), but nomenclature was updated as required to follow the World Spider Catalog [1]. Collection data, a photograph, and a taxonomic assignment for each specimen are available in the public dataset, "DS-MASPD DNA barcoding spiders of Pakistan" (dx.doi.org/10.5883/DS-MASPD) on BOLD. The 1,795 specimens are held in four repositories: Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada (585); National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan (1126); University of Sargodha, Sargodha, Pakistan (84). The location of any particular specimen is reported in the dataset.
Fig 1

Map showing collection localities for the 1,795 spiders examined in this study.

The map was developed using www.simplemappr.net. The author of SimpleMapper has waived all copyrights and no permission is needed to use. GPS coordinates (Latitude, Longitude) for the collection localities were: 24.45, 70.8; 25.488, 67.821; 25.681, 67.781; 25.756, 67.739; 25.757, 67.732; 25.759, 67.737; 25.76, 67.732; 25.801, 67.733; 25.812, 67.739; 25.9, 69.85; 28.083, 70.283; 28.261, 70.647; 28.293, 70.115; 28.304, 70.134; 28.306, 70.128; 28.308, 70.132; 28.308, 70.134; 28.309, 70.13; 28.309, 70.131; 28.309, 70.133; 29.083, 69.083; 29.103, 70.324; 29.104, 70.324; 29.105, 70.328; 29.24, 71.415; 29.242, 71.413; 29.39, 71.68; 29.393, 71.688; 29.393, 71.684; 29.394, 71.682; 29.396, 71.683; 29.401, 71.627; 29.429, 71.548; 29.454, 71.161; 29.518, 71.645; 29.584, 71.439; 29.868, 71.291; 29.9167, 69.9667; 30, 70.6; 30.026, 71.381; 30.053, 71.385; 30.065, 71.363; 30.105, 71.417; 30.189, 71.455; 30.189, 71.458; 30.189, 71.457; 30.191, 71.457; 30.516, 72.583; 30.518, 72.624; 30.519, 72.606; 30.52, 72.624; 30.522, 72.635; 30.523, 72.629; 30.525, 72.624; 30.529, 72.63; 30.531, 72.655; 30.531, 72.632; 30.533, 72.63; 30.534, 72.633; 30.534, 72.606; 30.537, 72.638; 30.538, 72.641; 30.54, 72.608; 30.585, 72.993; 30.6, 73.0667; 30.65, 73.1; 30.66, 73.1; 30.6612, 73.1086; 30.791, 72.594; 30.8, 72.05; 30.832, 72.512; 30.85, 72.083; 30.85, 72.544; 30.854, 72.538; 30.855, 72.54; 30.855, 72.539; 30.856, 72.572; 30.857, 72.542; 30.859, 72.566; 30.862, 72.56; 30.862, 72.554; 30.866, 72.555; 30.875, 72.557; 30.959, 73.984; 31.024, 74.531; 31.033, 73; 31.0833, 73.95; 31.2167, 73.8667; 31.3333, 73.4167; 31.3833, 73.0167; 31.3833, 73; 31.393, 73.027; 31.394, 73.026; 31.4167, 73.05; 31.4167, 73.0667; 31.45, 73.7; 31.45, 73.6833; 31.45, 73.1333; 31.463, 74.436; 31.4667, 73.2; 31.496, 74.294; 31.5, 73.2667; 31.532, 73.063; 31.5333, 74.3333; 31.56, 72.54; 31.6167, 73.8667; 31.64, 74.13; 31.825, 72.541; 31.8424, 70.8952; 31.86, 73.276; 31.924, 72.863; 31.965, 72.867; 31.976, 72.328; 31.986, 72.832; 32.027, 72.653; 32.034, 72.703; 32.05, 73; 32.055, 72.946; 32.059, 73.011; 32.063, 73.042; 32.0667, 72.6667; 32.0667, 72.6833; 32.067, 73.05; 32.074, 72.684; 32.077, 72.671; 32.077, 72.67; 32.078, 72.672; 32.08, 72.9; 32.081, 72.667; 32.082, 72.675; 32.083, 73.067; 32.0837, 72.6719; 32.084, 72.68; 32.088, 72.673; 32.093, 72.684; 32.1, 73.067; 32.102, 72.957; 32.109, 72.846; 32.11, 72.655; 32.119, 72.679; 32.122, 72.681; 32.125, 72.693; 32.1333, 74.1833; 32.15, 74.1833; 32.17, 72.26; 32.19, 73.025; 32.267, 72.476; 32.275, 72.904; 32.287, 72.43; 32.3054, 72.3482; 32.5333, 69.85; 32.56, 72.02; 32.59, 72.999; 32.59, 72.008; 32.59, 73.049; 32.59, 73.999; 32.591, 73.008; 32.591, 72.999; 32.5916, 72.3446; 32.592, 73.011; 32.592, 72.999; 32.593, 72.999; 32.594, 73.02; 32.594, 72.999; 32.595, 72.999; 32.5964, 72.217; 32.597, 73.041; 32.601, 73.369; 32.601, 73.038; 32.603, 73.042; 32.624, 73; 32.629, 73.009; 32.63, 73.005; 32.632, 73.013; 32.637, 73.008; 32.637, 72.008; 32.652, 73; 32.656, 73.005; 32.657, 73.004; 32.658, 73.003; 32.6581, 73.0034; 32.659, 73.008; 32.6592, 72.2433; 32.755, 72.677; 33.686, 73.076; 33.714, 73.132; 33.714, 73.133; 33.714, 73.13; 33.715, 73.132; 33.716, 73.129; 33.7167, 73.0333; 33.7167, 73.05; 33.7667, 73.8833; 33.8, 72.9167; 33.8167, 73.8167; 33.9, 73.3833; 33.9167, 73.3833; 34.333, 73.204; 34.334, 73.201; 34.38, 73.52; 34.38, 73.54; 34.385, 73.544; 34.386, 73.546; 34.386, 73.545; 34.541, 73.348; 34.543, 73.348; 34.546, 73.349; 34.638, 73.461; 34.639, 73.461; 34.639, 73.462; 34.7333, 72.35; 34.7667, 72.35; 34.776, 73.527; 34.777, 73.526; 34.778, 73.528; 34.78, 73.53; 34.78, 73.531; 34.8167, 72.3333; 35.426, 74.098; 35.461, 72.588; 35.465, 72.584; 35.4667, 72.5833; 35.478, 72.588; 35.918, 74.29; 35.918, 74.289.

Map showing collection localities for the 1,795 spiders examined in this study.

The map was developed using www.simplemappr.net. The author of SimpleMapper has waived all copyrights and no permission is needed to use. GPS coordinates (Latitude, Longitude) for the collection localities were: 24.45, 70.8; 25.488, 67.821; 25.681, 67.781; 25.756, 67.739; 25.757, 67.732; 25.759, 67.737; 25.76, 67.732; 25.801, 67.733; 25.812, 67.739; 25.9, 69.85; 28.083, 70.283; 28.261, 70.647; 28.293, 70.115; 28.304, 70.134; 28.306, 70.128; 28.308, 70.132; 28.308, 70.134; 28.309, 70.13; 28.309, 70.131; 28.309, 70.133; 29.083, 69.083; 29.103, 70.324; 29.104, 70.324; 29.105, 70.328; 29.24, 71.415; 29.242, 71.413; 29.39, 71.68; 29.393, 71.688; 29.393, 71.684; 29.394, 71.682; 29.396, 71.683; 29.401, 71.627; 29.429, 71.548; 29.454, 71.161; 29.518, 71.645; 29.584, 71.439; 29.868, 71.291; 29.9167, 69.9667; 30, 70.6; 30.026, 71.381; 30.053, 71.385; 30.065, 71.363; 30.105, 71.417; 30.189, 71.455; 30.189, 71.458; 30.189, 71.457; 30.191, 71.457; 30.516, 72.583; 30.518, 72.624; 30.519, 72.606; 30.52, 72.624; 30.522, 72.635; 30.523, 72.629; 30.525, 72.624; 30.529, 72.63; 30.531, 72.655; 30.531, 72.632; 30.533, 72.63; 30.534, 72.633; 30.534, 72.606; 30.537, 72.638; 30.538, 72.641; 30.54, 72.608; 30.585, 72.993; 30.6, 73.0667; 30.65, 73.1; 30.66, 73.1; 30.6612, 73.1086; 30.791, 72.594; 30.8, 72.05; 30.832, 72.512; 30.85, 72.083; 30.85, 72.544; 30.854, 72.538; 30.855, 72.54; 30.855, 72.539; 30.856, 72.572; 30.857, 72.542; 30.859, 72.566; 30.862, 72.56; 30.862, 72.554; 30.866, 72.555; 30.875, 72.557; 30.959, 73.984; 31.024, 74.531; 31.033, 73; 31.0833, 73.95; 31.2167, 73.8667; 31.3333, 73.4167; 31.3833, 73.0167; 31.3833, 73; 31.393, 73.027; 31.394, 73.026; 31.4167, 73.05; 31.4167, 73.0667; 31.45, 73.7; 31.45, 73.6833; 31.45, 73.1333; 31.463, 74.436; 31.4667, 73.2; 31.496, 74.294; 31.5, 73.2667; 31.532, 73.063; 31.5333, 74.3333; 31.56, 72.54; 31.6167, 73.8667; 31.64, 74.13; 31.825, 72.541; 31.8424, 70.8952; 31.86, 73.276; 31.924, 72.863; 31.965, 72.867; 31.976, 72.328; 31.986, 72.832; 32.027, 72.653; 32.034, 72.703; 32.05, 73; 32.055, 72.946; 32.059, 73.011; 32.063, 73.042; 32.0667, 72.6667; 32.0667, 72.6833; 32.067, 73.05; 32.074, 72.684; 32.077, 72.671; 32.077, 72.67; 32.078, 72.672; 32.08, 72.9; 32.081, 72.667; 32.082, 72.675; 32.083, 73.067; 32.0837, 72.6719; 32.084, 72.68; 32.088, 72.673; 32.093, 72.684; 32.1, 73.067; 32.102, 72.957; 32.109, 72.846; 32.11, 72.655; 32.119, 72.679; 32.122, 72.681; 32.125, 72.693; 32.1333, 74.1833; 32.15, 74.1833; 32.17, 72.26; 32.19, 73.025; 32.267, 72.476; 32.275, 72.904; 32.287, 72.43; 32.3054, 72.3482; 32.5333, 69.85; 32.56, 72.02; 32.59, 72.999; 32.59, 72.008; 32.59, 73.049; 32.59, 73.999; 32.591, 73.008; 32.591, 72.999; 32.5916, 72.3446; 32.592, 73.011; 32.592, 72.999; 32.593, 72.999; 32.594, 73.02; 32.594, 72.999; 32.595, 72.999; 32.5964, 72.217; 32.597, 73.041; 32.601, 73.369; 32.601, 73.038; 32.603, 73.042; 32.624, 73; 32.629, 73.009; 32.63, 73.005; 32.632, 73.013; 32.637, 73.008; 32.637, 72.008; 32.652, 73; 32.656, 73.005; 32.657, 73.004; 32.658, 73.003; 32.6581, 73.0034; 32.659, 73.008; 32.6592, 72.2433; 32.755, 72.677; 33.686, 73.076; 33.714, 73.132; 33.714, 73.133; 33.714, 73.13; 33.715, 73.132; 33.716, 73.129; 33.7167, 73.0333; 33.7167, 73.05; 33.7667, 73.8833; 33.8, 72.9167; 33.8167, 73.8167; 33.9, 73.3833; 33.9167, 73.3833; 34.333, 73.204; 34.334, 73.201; 34.38, 73.52; 34.38, 73.54; 34.385, 73.544; 34.386, 73.546; 34.386, 73.545; 34.541, 73.348; 34.543, 73.348; 34.546, 73.349; 34.638, 73.461; 34.639, 73.461; 34.639, 73.462; 34.7333, 72.35; 34.7667, 72.35; 34.776, 73.527; 34.777, 73.526; 34.778, 73.528; 34.78, 73.53; 34.78, 73.531; 34.8167, 72.3333; 35.426, 74.098; 35.461, 72.588; 35.465, 72.584; 35.4667, 72.5833; 35.478, 72.588; 35.918, 74.29; 35.918, 74.289.

Molecular analysis

DNA extraction, PCR, and Sanger sequencing were performed at the Canadian Centre for DNA Barcoding (CCDB) (http://ccdb.ca/resources/) using standard protocols. A single leg was removed from each specimen with a sterile forceps and transferred into a well in a 96-well microplate pre-filled with 30 μl of 95% EtOH. DNA was subsequently extracted by tissue lysis at 56°C overnight followed by a column-based protocol [67]. PCR amplification of the COI-5′ barcode region employed the primer pair C_LepFolF and C_LepFolR (http://ccdb.ca/site/wp-content/uploads/2016/09/CCDB_PrimerSets.pdf). This primer cocktail includes equal volume of LepF1 [68] /LCO1490 [69] and LepR1 [68] /HCO2198 [69], respectively. The target COI region was amplified using 2 μL of DNA template in a 12.5 μL reaction containing standard PCR ingredients [30] employing the following PCR regime: 94°C (1 min), 5 cycles of 94°C (40 s), 45°C (40 s), 72°C (1 min); 35 cycles of 94°C (40 s), 51°C (40 s), 72°C (1 min) and final extension of 72°C (5 min). Amplicons were analyzed on a 2% agarose E-gel 96 system (Invitrogen Inc.) and were sequenced bidirectionally using the BigDye Terminator Cycle Sequencing Kit (v3.1) on an Applied Biosystems 3730XL DNA Analyzer. Sequences were assembled, aligned, and edited using CodonCode Aligner (CodonCode Corporation, USA) and validated in MEGA5 [70] to ensure they lacked a stop codon.

Data analysis

All sequences were submitted to BOLD (DS-MASPD) where those meeting required quality criteria (>507 bp, <1% Ns, no stop codon or contamination flag) were assigned to a BIN [36]. An accumulation curve, BIN discordance, genetic distance analysis, barcode gap analysis (BGA), and geo-distance correlation were determined using analytical tools on BOLD. The Accumulation Curve plots the rise in the number of BINs with increased sampling effort making it possible to ascertain if asymptotic diversity has been reached. The BGA determines if the maximum sequence divergence within members of a species or BIN is less than the distance to its Nearest-Neighbor (NN) species or BIN, a condition required for unambiguous identification [71,72]. The geo-distance correlation ascertains the correlation between geographic distance and genetic distance in each species or BIN employing two methods. The Mantel Test [73] examines the relationship between the geographic distance (km) and genetic divergence (K2P) matrices. The second approach compares the spread of the minimum spanning tree of collection sites and maximum intra-specific divergence [61]. The relationship between geographic and intraspecific distances was analyzed for each species with at least one individual from three or more sites. The analysis included all the conspecific records public on BOLD. A neighbor-joining (NJ) tree was generated in MEGA5 using the Kimura-2-Parameter (K2P) [74] distance model along with pairwise deletion of missing sites. Nodal support on the NJ tree was estimated by 1000 bootstrap replicates. Bayesian inference (BI) was calculated by MrBayes v3.2.0 [75] using representative sequences of the 221 BINs and employing Phalangium opilio (Arachnida: Opiliones) and Galeodes sp. (Arachnida: Solifugae) as outgroups. The data was partitioned in two ways; i) a single partition with parameters estimated across all codon positions, ii) a codon-partition in which each codon position was allowed different parameter estimates. Sequence evolution was modelled by the GTR+Γ model independently for the two partitions using the ‘‘unlink” command in MrBayes. Analyses were run for 10 million generations using four chains with sampling every 1000 generations and the BI trees were obtained using the Markov Chain Monte Carlo (MCMC) technique. Posterior probabilities were calculated from the sample points once the MCMC algorithm converged. Convergence was determined when the standard deviation of split frequencies was less than 0.022 and the PSRF (potential scale reduction factor) approached 1, and both runs converged to a stationary distribution after the burn-in stage (the first 25% of samples were discarded by default). The resultant trees were visualized in FigTree v1.4.0. The NJ and Bayesian analyses were employed to assess support for the BINs detected in this study, not to reconstruct the phylogeny of Araneae.

Results

Coupling of the DNA sequence results with detailed morphological analysis made it possible to assign 1,574 of the 1,795 barcoded specimens to one of 109 species, but the other 221 specimens could only be placed into one of 93 interim species. Collectively, these specimens included representatives of 27 families, 113 genera, and 202 species (Table 1). Most species were only represented by a single sex, usually females. Two-thirds (1,256) of the specimens were immatures that lacked the diagnostic characters required for species assignment. However, their DNA barcodes allowed them to be linked to adults whose identification was established through morphology. Four families (Amaurobiidae, Atypidae, Ctenidae, Segestriidae), 43 genera, and 74 species identified here represent first records for Pakistan (Tables 1 and S1). As adults from 12 of the 93 interim species possessed clear morphological differences from any known species in their genus, they are likely new to science (Table 1).
Table 1

Species, maximum barcode divergence (K2P), nearest neighbor distance (NN), and BIN assignment of 1,795 spiders collected in Pakistan.

No.TaxaNK2PNNBINs
Agelenidae C. L. Koch,1837
1Draconarius sp. 1GAB_PAK208.8BOLD:AAO2052
2Draconarius sp. 2GAB_PAK208.8BOLD:AAO2053
*NP3Tegenaria domestica (Clerck, 1757)1N/A19BOLD:AAF1312
NPAmaurobiidae Thorell,1870
*NS4Himalmartensus cf. martensi Wang & Zhu, 20081N/A14BOLD:ACB2928
Araneidae Clerck, 1757
NP5Araneus affinis Zhu, Tu & Hu, 198820.612BOLD:AAV7611
6Araneus mitificus (Simon, 1886)201.713BOLD:AAV1598
7Araniella sp. 1GAB_PAK40.810BOLD:AAV1625
8Argiope aemula (Walckenaer, 1841)81.410BOLD:ACG0732
9Argiope anasuja Thorell, 18871N/A9.5BOLD:ACB2926
NP10Argiope lobata (Pallas, 1772)20.512BOLD:ACI8559
NP11Argiope pulchella Thorell, 188160.89.5BOLD:ACG0576
12Argiope trifasciata (Forsskål, 1775)151.110BOLD:AAQ2634
NP13Chorizopes wulingensis Yin, Wang & Xie, 199420.512BOLD:ABX7347
U14Cyclosa confraga (Thorell, 1892)80.818BOLD:ADF2726
15Cyclosa hexatuberculata Tikader, 19824011BOLD:ADD8756
NP16Cyclosa moonduensis Tikader, 196391.111BOLD:ACZ2455
17Cyrtophora citricola (Forsskål, 1775)661.613BOLD:AAO2032
18Eriovixia excelsa (Simon, 1889)401.116BOLD:AAQ0105
19Gea subarmata Thorell, 18901N/A10BOLD:ACG0733
*NS20Hypsosinga cf. alboria Yin, Wang, Xie & Peng, 19904010BOLD:ABX7344
*NP21Hypsosinga wanica Song, Qian & Gao, 1996171.610BOLD:AAQ0134
22Larinia phthisica (L. Koch, 1871)50.910BOLD:AAO2160
23Larinia sp. 1GAB_PAK1N/A11BOLD:ABX7407
*24Leviellus sp. 1GAB_PAK2014BOLD:AAV1590
NP25Neoscona polyspinipes Yin, Wang, Xie & Peng, 1990200.84.9BOLD:AAO1983
NP26aNeoscona scylla (Karsch, 1879)131.97.8BOLD:ACI8762
26bNeoscona scylla (Karsch, 1879)16BOLD:AAO1997
27Neoscona sp. 1BAG_PAK1N/A7.6BOLD:ACI2573
28Neoscona sp. 2BAG_PAK1N/A9BOLD:ADD4537
NP29Neoscona subfusca (C. L. Koch, 1837)1N/A8.6BOLD:AAV3851
30Neoscona theisi (Walckenaer, 1841)1602.57.6BOLD:ACM3489
31Neoscona vigilans (Blackwall, 1865)381.54.9BOLD:AAO2202
32Plebs himalayaensis (Tikader, 1975)2017BOLD:ACI8675
NPAtypidae Thorell, 1870
*NS33Calommata sp. 1GAB_PAK1N/A21BOLD:ACP9624
Cheiracanthiidae Wagner, 1887
NP34Cheiracanthium inornatum O. Pickard-Cambridge, 187452.37.4BOLD:ACC4872
NP35Cheiracanthium insulanum (Thorell, 1878)203.36.9BOLD:AAQ0110
36Cheiracanthium sp. 1GAB_PAK20.211BOLD:ACA7676
37Cheiracanthium sp. 2GAB_PAK21.14.9BOLD:ABW2880
38Cheiracanthium sp. 3GAB_PAK20.24.9BOLD:AAU6055
Clubionidae Wagner, 1887
39Clubiona drassodes O. Pickard-Cambridge, 1874280.913BOLD:AAV1620
40Clubiona filicata O. Pickard-Cambridge, 1874180.913BOLD:AAV1603
41Clubiona sp. 1GAB_PAK1N/A8.8BOLD:AAV1602
42Clubiona sp. 2GAB_PAK1N/A8.8BOLD:AAO2055
Corinnidae Karsch, 1880
43Castianeira sp. 1GAB_PAK1N/A16BOLD:ACP7698
NPCtenidae Keyserling, 1877
*44Anahita sp. 1GAB_PAK1N/A12BOLD:ADF5307
*45Ctenus sp. 1GAB_PAK1N/A9BOLD:AAV1591
*46Ctenus sp. 2GAB_PAK1N/A9BOLD:ABW2888
Filistatidae Ausserer, 1867
47Kukulcania sp. 1GAB_PAK1N/A22BOLD:ABX7408
Gnaphosidae Pocock, 1898
48Berlandina afghana Denis, 19581N/A14BOLD:AAV1613
49Drassodes sp. 1GAB_PAK1N/A12BOLD:AAV1404
*NP50Drassyllus coreanus Paik, 19862014BOLD:AAV0899
51Gnaphosa jodhpurensis Tikader & Gajbe, 197721.215BOLD:ACR0656
*NP52Haplodrassus signifer (C. L. Koch, 1839)1N/A13BOLD:ACB2432
53Micaria sp. 1GAB_PAK1N/A13BOLD:ACP3811
*54Phaeocedus sp. 1GAB_PAK21.214BOLD:AAV1605
*NP55Scopoides maitraiae (Tikader & Gajbe, 1977)2016BOLD:ACZ1655
*NP56Trachyzelotes kulczynskii (Bösenberg, 1902)1N/A13BOLD:AAQ2633
NS57Zelotes cf. puritanus Chamberlin, 192220.812BOLD:AAQ0137
NP58Zelotes shantae Tikader, 19821N/A12BOLD:ADD7482
59Zelotes sp. 1GAB_PAK1N/A12BOLD:ACZ4032
*NP60Zimiris diffusa Platnick & Penney, 20041N/A14BOLD:AAV1616
Hersiliidae Thorell, 1870
61Hersilia savignyi Lucas, 1836161.117BOLD:AAP4789
Linyphiidae Blackwall, 1859
62Gnathonarium dentatum (Wider, 1834)5014BOLD:AAQ0150
*63Mermessus sp. 1GAB_PAK1N/A14BOLD:ACP3810
*NP64Neriene emphana (Walckenaer, 1841)30.814BOLD:ACI8558
Lycosidae Sundevall, 1833
*65Alopecosa sp. 1GAB_PAK1N/A9.2BOLD:AAV1615
NS66Arctosa cf. serrulata Mao & Song, 19851N/A9.4BOLD:ACB2931
67Arctosa sp. 1GAB_PAK1N/A13BOLD:AAV1608
68Draposa oakleyi (Gravely, 1924)191.65.8BOLD:ABX7398
NS69Evippa sp. 1GAB_PAK51.48.3BOLD:ABX7397
70Evippa sp. 2GAB_PAK1N/A8.3BOLD:ABW2890
71aHippasa pisaurina Pocock, 1900164.15.8BOLD:AAO2058
71bHippasa pisaurina Pocock, 19001BOLD:ADF3448
72Hippasa sp. 1GAB_PAK1N/A5.8BOLD:ADE8277
*73Hogna sp. 1GAB_PAK50.610BOLD:AAQ0158
*74Hogna sp. 2GAB_PAK1N/A11BOLD:ADF5080
75Lycosa poonaensis Tikader & Malhotra, 198050.610BOLD:ABW2889
76Lycosa sp. 1GAB_PAK1N/A10BOLD:AAO2168
E77Lycosa terrestris Butt, Anwar & Tahir, 2006450.94.3BOLD:AAO2150
NP78Pardosa mionebulosa Yin, Peng, Xie, Bao & Wang, 199731.65.3BOLD:ACZ3882
79Pardosa pseudoannulata (Bösenberg & Strand, 1906)50.65.9BOLD:AAO2149
80Pardosa sp. 1GAB_PAK30.25.9BOLD:AAO2146
81Pardosa sp. 2GAB_PAK1N/A4.9BOLD:AAO2148
82Pardosa sp. 3GAB_PAK1N/A5.2BOLD:AAV1588
83Pardosa sp. 4GAB_PAK132.44.6BOLD:AAO2147
84Pardosa sp. 5GAB_PAK40.85.2BOLD:AAV1589
NP85Pardosa sutherlandi (Gravely, 1924)70.24.6BOLD:ABX7411
NP86Trochosa aquatica Tanaka, 1985170.65.9BOLD:AAV3200
87Trochosa sp. 1GAB_PAK30.35.9BOLD:ADF4175
*NP88Wadicosa fidelis (O. Pickard-Cambridge, 1872)751.97.2BOLD:AAG7456
Oecobiidae Blackwall, 1862
89Oecobius putus O. Pickard-Cambridge, 1876100.414BOLD:AAV1624
Oxyopidae Thorell, 1870
E90Oxyopes azhari Butt & Beg, 20011123.63.6BOLD:AAO1991
E91Oxyopes chenabensis Mukhtar, 201750.96.4BOLD:ABX7410
NP92Oxyopes heterophthalmus (Latreille, 1804)80.34.9BOLD:AAD0599
93Oxyopes hindostanicus Pocock, 190112335.6BOLD:AAO1990
NP94Oxyopes macilentus L. Koch, 187881.51.3BOLD:AAF9665
NP95aOxyopes matiensis Barrion & Litsinger, 199532.11.3BOLD:ACX5149
95bOxyopes matiensis Barrion & Litsinger, 19955BOLD:ABX7414
E96Oxyopes oryzae Mushtaq & Qadar, 1999521.93.6BOLD:AAO1989
97Oxyopes sp. 1GAB_PAK1N/A6.7BOLD:ACZ2323
NS98Oxyopes sp. 2GAB_PAK31.25.7BOLD:ACZ4097
99Oxyopes sp. 3GAB_PAK1N/A11BOLD:ACP4193
NP100Peucetia ranganathani Biswas & Roy, 2005140.811BOLD:ACB4190
101Peucetia sp. 1GAB_PAK1N/A13BOLD:ACB4188
Philodromidae Thorell, 1870
102Philodromus sp. 1GAB_PAK1N/A12BOLD:ADD8987
103Philodromus sp. 2GAB_PAK3213BOLD:ABX7412
*NP104Pulchellodromus mainlingensis (Hu & Li, 1987)2012BOLD:ACB4189
NS105Rhysodromus cf. xinjiangensis (Tang & Song, 1987)4013BOLD:AAO2159
NP106Thanatus vulgaris Simon, 187020.315BOLD:AAQ0111
Pholcidae C. L. Koch, 1850
107Artema sp. 1GAB_PAK1N/A19BOLD:ABW2886
NP108Artema transcaspica Spassky, 19342119-
109Crossopriza lyoni (Blackwall, 1867)20.316BOLD:AAG2795
110aCrossopriza maculipes (Spassky, 1934)45.316BOLD:ACN4846
110bCrossopriza maculipes (Spassky, 1934)7BOLD:AAU5412
110cCrossopriza maculipes (Spassky, 1934)1BOLD:ACB2929
Pisauridae Simon, 1890
*NP111Pisaura mirabilis (Clerck, 1757)40.510BOLD:AAE4245
112Pisaura sp. 1GAB_PAK1N/A12BOLD:AAO2059
Salticidae Blackwall, 1841
NP113Bianor albobimaculatus (Lucas, 1846)210.712BOLD:AAP4728
114Bianor sp. 1GAB_PAK1N/A13BOLD:ACI8750
NP115Epocilla sirohi Caleb, Chatterjee, Tyagi, Kundu, Kumar, 201871.911BOLD:ADD4346
116Euophrys sp. 1GAB_PAK1N/A13BOLD:ADD1307
*NS117Evarcha sp. 1GAB_PAK30.89BOLD:AAV1614
118Hasarius adansoni (Audouin, 1826)2013BOLD:AAW0165
NP119Hyllus dotatus (Peckham & Peckham, 1903)30.711BOLD:AAV1597
NP120Menemerus brevibulbis (Thorell, 1887)31.47.7BOLD:AAO2155
121Menemerus marginatus (Kroneberg, 1875)1N/A11BOLD:AAV1611
122Menemerus nigli Wesolowska & Freudenschuss, 2012121.17.7BOLD:AAQ0156
*NP123Modunda staintoni (O. Pickard-Cambridge, 1872)30.814BOLD:AAV0387
NP124Mogrus cognatus Wesolowska & van Harten, 1994121.48.1BOLD:AAV1599
125Mogrus sp. 1GAB_PAK1N/A8.1BOLD:ACZ1977
126Mogrus sp. 2GAB_PAK60.810BOLD:AAQ2635
127Myrmarachne melanocephala MacLeay, 18391N/A6.7BOLD:AAV1609
128Myrmarachne robusta (Peckham & Peckham, 1892)51.46.7BOLD:ACS0377
*NP129Philaeus chrysops (Poda, 1761)1N/A9.8BOLD:ACE4347
*130Philaeus sp. 1GAB_PAK1N/A9.8BOLD:AAV0574
131Phintella vittata (C. L. Koch, 1846)1109.9BOLD:ACR1776
132aPlexippus paykulli (Audouin, 1826)3458.8BOLD:AAO2152
132bPlexippus paykulli (Audouin, 1826)4BOLD:AAO2151
132cPlexippus paykulli (Audouin, 1826)1BOLD:ACU8433
132dPlexippus paykulli (Audouin, 1826)1BOLD:ABX7409
132ePlexippus paykulli (Audouin, 1826)1BOLD:ACZ4027
133Plexippus sp. 1GAB_PAK20.28.8BOLD:AAV1604
134aPseudicius admirandus Logunov, 200781.49.4BOLD:AAQ0115
134bPseudicius admirandus Logunov, 20072BOLD:ADD4534
NP135Rhene albigera (C. L. Koch, 1846)1N/A5.9BOLD:AAV5815
NP136Rhene flavigera (C. L. Koch, 1846)405.4BOLD:ADD7823
137Rhene sp. 1GAB_PAK1N/A5.4BOLD:ACU6737
*NS138Sonoita cf. lightfooti Peckham & Peckham, 19031N/A13BOLD:ADD9560
139Stenaelurillus arambagensis (Biswas & Biswas, 1992)30.311BOLD:ABX7343
*140Talavera sp. 1GAB_PAK1N/A12BOLD:ACZ2472
141Telamonia dimidiata (Simon, 1899)171.410BOLD:ACG1123
142Thyene imperialis (Rossi, 1846)563.59BOLD:AAO2153
143Thyene sp. 1GAB_PAK1N/A11BOLD:AAV1607
*NS144Trite sp. 1GAB_PAK130.511BOLD:AAO2154
NPSegestriidae Simon, 1893
*145Ariadna sp. 1GAB_PAK1N/A20BOLD:AAO2054
Sparassidae Bertkau, 1872
NP146Heteropoda maxima Jäger, 2001200.34.3BOLD:ACB5077
147aHeteropoda sp. 3GAB_PAK12.35.4BOLD:ABW2881
147bHeteropoda sp. 3GAB_PAK1BOLD:AAO2057
148Heteropoda sp. 4GAB_PAK1N/A4.3BOLD:ACB5549
149Olios sp. 1GAB_PAK1N/A3.9BOLD:ADD6859
150Olios sp. 2GAB_PAK100.53.9BOLD:ADD7417
151Olios sp. 3GAB_PAK40.34.1BOLD:ACB4191
152Olios sp. 4GAB_PAK41.17.2BOLD:AAQ0159
153Olios sp. 5GAB_PAK152.27.2BOLD:AAQ0157
154aOlios tener (Thorell, 1891)41.911BOLD:AAQ0107
154bOlios tener (Thorell, 1891)1BOLD:ADK3497
154cOlios tener (Thorell, 1891)1BOLD:ADJ7965
155Pseudopoda prompta (O. Pickard-Cambridge, 1885)40.913BOLD:AAO2056
156aSpariolenus tigris Simon, 188014.112BOLD:ADF5077
156bSpariolenus tigris Simon, 18801BOLD:ABW2878
Tetragnathidae Menge, 1866
*NP157Glenognatha tangi (Zhu, Song & Zhang, 2003)31.218BOLD:AAQ0147
158Guizygiella indica (Tikader & Bal, 1980)81.114BOLD:ABX7345
159Leucauge celebesiana (Walckenaer, 1841)70.211BOLD:AAO2068
160Leucauge decorata (Blackwall, 1864)300.511BOLD:AAG8516
*161Metleucauge sp. 1GAB_PAK1N/A19BOLD:AAV1600
NP162Tetragnatha boydi O. Pickard-Cambridge, 18983015BOLD:ACB2930
NP163Tetragnatha cavaleriei Schenkel, 196320.516BOLD:AAT8904
164Tetragnatha javana (Thorell, 1890)432.817BOLD:AAO2174
165Tetragnatha mandibulata Walckenaer, 18411N/A15BOLD:AAK2567
NP166Tetragnatha maxillosa Thorell, 189540.315BOLD:AAK2560
NP167Tetragnatha nitens (Audouin, 1826)60.815BOLD:AAD3790
168Tetragnatha sp. 1GAB_PAK1N/A16BOLD:ABW2885
Theraphosidae Thorell, 1869
*169Chilobrachys sp. 1GAB_PAK1N/A4.3BOLD:ADD5278
*170Chilobrachys sp. 2GAB_PAK1N/A4.3BOLD:AAQ0160
Theridiidae Sundevall, 1833
*NP171Emertonella taczanowskii (Keyserling, 1886)1N/A12BOLD:AAV1610
172Enoplognatha sp. 1GAB_PAK1N/A12BOLD:ACI8909
173Enoplognatha sp. 2GAB_PAK1N/A15BOLD:ACP4208
*174Euryopis sp. 1GAB_PAK1N/A12BOLD:AAQ0155
175Latrodectus sp. 1GAB_PAK1N/A19BOLD:AAV1732
176Latrodectus sp. 2GAB_PAK1N/A16BOLD:AAO3347
*177Meotipa sp. 1GAB_PAK2212BOLD:AAQ0152
178Phylloneta sp. 1GAB_PAK110.311BOLD:AAV3043
*NP179Steatoda cingulata (Thorell, 1890)2014BOLD:ABW2877
NP180Theridion melanostictum O. Pickard-Cambridge, 18761N/A11BOLD:AAV1617
181Theridion sp. 1GAB_PAK1N/A11BOLD:ACB2932
182Theridion sp. 3GAB_PAK1N/A12BOLD:AAV1623
Thomisidae Sundevall, 1833
*NP183Coriarachne melancholica Simon, 18801N/A7.9BOLD:ACI8639
*NP184Ebelingia kumadai (Ono, 1985)3012BOLD:AAV1619
185Henriksenia hilaris (Thorell, 1877)1N/A11BOLD:AAV1618
NP186Lysiteles kunmingensis Song & Zhao, 1994309.9BOLD:ACI8899
*187Misumenoides sp. 1GAB_PAK1N/A11BOLD:AAV1594
*188Misumenops sp. 1GAB_PAK21.911BOLD:AAV1596
*189Ozyptila sp. 1GAB_PAK1N/A11BOLD:ADF5201
190aRuncinia insecta (L. Koch, 1875)404.911BOLD:AAI0997
190bRuncinia insecta (L. Koch, 1875)2BOLD:AAQ0108
*NP191Tharpyna indica Tikader & Biswas, 19791N/A12BOLD:AAV1606
NP192Thomisus onustus Walckenaer, 18051N/A8.6BOLD:AAD7031
E193aThomisus zaheeri Parveen, Khan, Mushtaq, Ahmad & Rana, 2008304.311BOLD:AAP4819
193bThomisus zaheeri Parveen, Khan, Mushtaq, Ahmad & Rana, 20081BOLD:AAQ0153
194Tmarus dostinikus Barrion & Litsinger, 1995130.211BOLD:ABX7413
NS195aTmarus sp. 1GAB_PAK32.911BOLD:ABX7346
195bTmarus sp. 1GAB_PAK5BOLD:ADJ6297
195cTmarus sp. 1GAB_PAK4BOLD:ADK4624
195dTmarus sp. 1GAB_PAK1BOLD:ADK4625
NP196Xysticus joyantius Tikader, 19661N/A13BOLD:ADF4849
197Xysticus sp. 1GAB_PAK30.67.9BOLD:ACI8898
198Xysticus sp. 2GAB_PAK1N/A12BOLD:ADF4647
Uloboridae Thorell, 1869
*199Hyptiotes sp. 1GAB_PAK1N/A15BOLD:AAQ2632
200aUloborus sp. 1GAB_PAK4414BOLD:AAW8359
200bUloborus sp. 1GAB_PAK1BOLD:ABW2879
Zodariidae Thorell, 1881
*201Zodarion sp. 1GAB_PAK1N/A14BOLD:AAV1621
*202Zodarion sp. 2GAB_PAK1N/A14BOLD:ACG0983
Total1795221

N = number of individuals; K2P = maximum Kimura 2-parameter distance; NN = distance to Nearest Neighbor species; BIN = Barcode Index Number; NP = new species or family to Pakistan; * = new genus to Pakistan; E = endemic species to Pakistan; U = undescribed opposite sex; NS = putative new species to science.

N = number of individuals; K2P = maximum Kimura 2-parameter distance; NN = distance to Nearest Neighbor species; BIN = Barcode Index Number; NP = new species or family to Pakistan; * = new genus to Pakistan; E = endemic species to Pakistan; U = undescribed opposite sex; NS = putative new species to science. As the accumulation curve failed to approach an asymptote (Fig 2), it is certain that more species await detection. Although one species (Artema transcaspica) failed to qualify for a BIN assignment because its only sequence was too short, the other 108 morphological species were assigned to 123 BINs with 10 species showing a split to two or more BINs (Table 1 and Fig 3). The 93 interim species were allocated to 98 BINs with three showing BIN splits (Table 1), making the total BIN count 221 –with 94 of them singletons. NJ clustering (Fig 3) and Bayesian inference (Fig 4), supported the monophyly of all 221 BINs. Barcode distances (K2P) varied for differing taxonomic ranks with conspecific values ranging from 0.0–5.3% (mean = 0.8%), congenerics from 2.8–23.2% (mean = 8.8%), and confamilials from 4.3–26.7% (mean = 15.1%) (Table 2). Excepting 14 species, maximum intraspecific divergences did not exceed 2% in the 90 species that were represented by two or more specimens (Table 1). The barcode gap analysis showed that maximum intraspecific distance for all but one of the 90 species with two or more records was less than its NN distance (Oxyopes azhari was the exception, overlapping with Oxyopes oryzae) (Fig 5). The Mantel test was non-significant (P>0.01) for 60 of the 69 species and the regression line for all species showed a weak positive relationship (R2 = 0.08; y = 0.0003x + 2.62) (Fig 6).
Fig 2

Accumulation curve for morphological species and barcode index numbers (BINs) for 1,795 spiders from Pakistan.

Fig 3

NJ analysis of spider species based on the analysis of 1,782 COI sequences.

Bootstrap values (50% or higher; 1000 replicates) are shown above the branches. The scale bar shows K2P distances. The node for each species with multiple specimens is collapsed to a vertical line or triangle, with the horizontal depth indicating the level of intraspecific divergence. Species assigned to multiple BINs are indicated in bold. The tree is presented in two parts.

Fig 4

Bayesian phylogenetic analysis of spiders from Pakistan based on COI sequences.

Posterior probabilities are indicated at the nodes. Taxa are followed by the BINs. Phalangium opilio (Arachnida: Opiliones) and Galeodes sp. (Arachnida: Solifugae) were employed as outgroups. Due to its large size, the tree is presented in two parts.

Table 2

Sequence divergences (K2P) for differing levels of taxonomic affinity for the COI-5′ gene region for the spiders from Pakistan.

Analysis was restricted to sequences >400 bp.

Distance classnTaxaComparisonsMin (%)Mean (%)Max (%)
Intraspecific17021224434700.85.3
Congeners133844567922.88.823.2
Confamilial1662151371644.315.126.7
Fig 5

Barcode gap analysis for spider species represented by three or more records.

Points that fall above the 1:1 line (blue) indicate the presence of a local barcode gap. NN = Nearest-Neighbor species.

Fig 6

Intraspecific sequence divergence (K2P) for the COI gene (blue dots) versus geographic distance (km) for spider species from Pakistan with data from other regions.

The relationship between genetic and geographic distances is indicated by a regression line. P-values for the Mantel Test are indicated by red vertical lines.

NJ analysis of spider species based on the analysis of 1,782 COI sequences.

Bootstrap values (50% or higher; 1000 replicates) are shown above the branches. The scale bar shows K2P distances. The node for each species with multiple specimens is collapsed to a vertical line or triangle, with the horizontal depth indicating the level of intraspecific divergence. Species assigned to multiple BINs are indicated in bold. The tree is presented in two parts.

Bayesian phylogenetic analysis of spiders from Pakistan based on COI sequences.

Posterior probabilities are indicated at the nodes. Taxa are followed by the BINs. Phalangium opilio (Arachnida: Opiliones) and Galeodes sp. (Arachnida: Solifugae) were employed as outgroups. Due to its large size, the tree is presented in two parts.

Barcode gap analysis for spider species represented by three or more records.

Points that fall above the 1:1 line (blue) indicate the presence of a local barcode gap. NN = Nearest-Neighbor species.

Intraspecific sequence divergence (K2P) for the COI gene (blue dots) versus geographic distance (km) for spider species from Pakistan with data from other regions.

The relationship between genetic and geographic distances is indicated by a regression line. P-values for the Mantel Test are indicated by red vertical lines.

Sequence divergences (K2P) for differing levels of taxonomic affinity for the COI-5′ gene region for the spiders from Pakistan.

Analysis was restricted to sequences >400 bp. The similarity between the spider fauna in Pakistan and that of other nations was calculated by examining BIN overlap. Less than a quarter (52/221) of the BINs from Pakistan were represented among the 10,229 spider BINs reported in prior studies. As expected, the highest overlap (23%) was with India, but the proportion of shared BINs was far lower for the other 43 countries (Fig 7).
Fig 7

Percentage of spider BINs shared between Pakistan and 41 other nations.

Discussion

Most prior work on the spider fauna of Pakistan has had a regional focus and only employed morphological approaches. For example, 157 species were reported from the province of Punjab [9], 56 from the district of Sargodha [76], 23 from Peshawar [11], and 13 from Buner [77]. A recent checklist for the spiders of Pakistan [10] included records for 239 species, but the present study has substantially increased this total by adding first records for 84 described species and another 93 that could not be assigned to a known taxon. Most importantly, this study generated a DNA barcode reference library for 202 species, facilitating their future identification. Because the spider fauna of Pakistan has seen such limited study, the discovery of new species was not unexpected, and follows a pattern seen for spiders in other regions. For example, the analysis of 80 species of Salticidae from Papua New Guinea revealed 34 species and five genera new to the country [78]. Likewise, 6% of the 136 spider species recovered from the Northern Cape Province, South Africa were new [79]. This study employed a mix of methods for spider collection, including beating, sweeping, and pitfalls. The choice of sampling method impacts species detection [80] and extensive sampling is critical to generate comprehensive species coverage [81]. Although the present study involved collections at 225 sites, the resultant species accumulation curve did not reach an asymptote, indicating that many more species await detection. The present study revealed a close correspondence (93%) between BINs and morphospecies as 188 of the 202 species were assigned to a unique BIN, reinforcing a pattern seen in other groups [37,38,40]. For example, the concordance between BINs and species was 78% in a study that examined 30,000 Canadian spiders representing 1,018 species [61] with most discordances reflecting BIN splits suggestive of overlooked species. Stronger species-BIN correspondence has been reported in several insect groups; 96% for Erebidae (Lepidoptera) from the Iberian Peninsula [38], 94% for tiger moths from Brazil [82] and 92% for beetles from central Europe [40]. However, some arthropod groups have shown relatively low level of species-BIN concordance; for example, orthopterans in Central Europe (76%) [83], waterstriders in Germany (82%) [84] and katydids in China (75%) [85]. Thirteen (6%) species in this study were assigned to two or more BINs (BIN splits), and one species (Plexippus paykulli) was assigned to five. BIN splits often indicate the presence of a species complex [43]. For example, 13% of 1,018 species of Canadian spiders [61], 13% of 1,541 Canadian Noctuoidea [86], 5.7% of 1,872 Finnish beetles [87], and 20% of 62 global mealybugs [88] possessed BIN splits. Although in most cases the subsequent morphological investigation has revealed overlooked species [89], other factors can cause BIN splits/mergers, such as hybridization [90], incomplete lineage sorting [83], or rapid speciation [91]. K2P divergences >2% were found in 14 of the 202 spider species from Pakistan with a maximum value of 5.3%. There was, however, no significant relationship between intraspecific divergence and the number of specimens analyzed. For example, 12 specimens of Crossopriza maculipes (3 BINs) showed 5.3% divergence and were assigned to three BINs while 160 specimens of Neoscona theisi possessed a maximum divergence of 2.5%. High COI divergence is not uncommon in spiders. For example, the maximum intraspecific divergence in 561 spider species from Germany was 10.1%, but it was below 2.5% in 95% of the cases with an arithmetic mean of 0.7% [62]. The divergence could depend on several factors such as the number of specimens analyzed, the number of localities, the geographic distance between them and the dispersal capabilities of the particular species [92,93]. With the exception of a single species (Oxyopes azhari), high conspecific distances did not impede the capacity of DNA barcodes to discriminate the species encountered in our study. However, species with BIN splits and high divergences are likely to represent a cryptic species complex. Preliminary morphological analyses including genitalic dissections of specimens from taxa with BIN splits in this study reinforced this conclusion. Correlation analysis revealed only a weak relationship between the geographic range of the species examined in this study and their intraspecific divergence value. The Mantel test was significant for a few (13%) species, but species identification was not impeded as maximum intraspecific distances were nearly always less than NN distances. Similar results have been reported for Lepidoptera from Europe [94], Pakistan [32] and Central Asia [95]. Although a study that examined a single tribe, Agabini, of aquatic beetles in Europe [96] argued that regional divergences were so great as to obscure species assignments, this result is clearly not the rule [72]. Because BINs are generally an effective species proxy [41], we used them to assess faunal overlap. This work revealed that most (76%) BINs detected in this study were first records. Just 52 BINs have records from other nations and 13 of these were shared only with India. The BIN overlap with other nations was considerably lower for the spiders (24%) of Pakistan than for its Lepidoptera (42%) [42], but this difference almost certainly reflects the intensive barcode studies on the latter group. Although DNA barcoding has been used to assess regional biodiversity [41,47] and to ascertain species connections [42], the limited data availability complicates interpretation. Although further sampling will add new BINs, it is also likely to raise BIN overlap with other regions, improving our understanding of faunal overlap. Such efforts to better document local biodiversity are also certain to reveal new species as evidenced by the discovery of 93 taxa in this study that could not be assigned to a known species.

Taxonomic publications consulted for this study.

(DOCX) Click here for additional data file.
  60 in total

1.  DNA barcoding will often fail to discover new animal species over broad parameter space.

Authors:  Michael J Hickerson; Christopher P Meyer; Craig Moritz
Journal:  Syst Biol       Date:  2006-10       Impact factor: 15.683

Review 2.  Multi-locus species delimitation in closely related animals and fungi: one marker is not enough.

Authors:  Julian R Dupuis; Amanda D Roe; Felix A H Sperling
Journal:  Mol Ecol       Date:  2012-08-14       Impact factor: 6.185

3.  DNA barcoding Central Asian butterflies: increasing geographical dimension does not significantly reduce the success of species identification.

Authors:  Vladimir A Lukhtanov; Andrei Sourakov; Evgeny V Zakharov; Paul D N Hebert
Journal:  Mol Ecol Resour       Date:  2009-02-25       Impact factor: 7.090

Review 4.  DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests.

Authors:  Muhammad Ashfaq; Paul D N Hebert
Journal:  Genome       Date:  2016-08-30       Impact factor: 2.166

5.  A spider species complex revealed high cryptic diversity in South China caves.

Authors:  Yuanyuan Zhang; Shuqiang Li
Journal:  Mol Phylogenet Evol       Date:  2014-06-30       Impact factor: 4.286

6.  DNA barcoding: error rates based on comprehensive sampling.

Authors:  Christopher P Meyer; Gustav Paulay
Journal:  PLoS Biol       Date:  2005-11-29       Impact factor: 8.029

7.  Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve.

Authors:  Angela C Telfer; Monica R Young; Jenna Quinn; Kate Perez; Crystal N Sobel; Jayme E Sones; Valerie Levesque-Beaudin; Rachael Derbyshire; Jose Fernandez-Triana; Rodolphe Rougerie; Abinah Thevanayagam; Adrian Boskovic; Alex V Borisenko; Alex Cadel; Allison Brown; Anais Pages; Anibal H Castillo; Annegret Nicolai; Barb Mockford Glenn Mockford; Belén Bukowski; Bill Wilson; Brock Trojahn; Carole Ann Lacroix; Chris Brimblecombe; Christoper Hay; Christmas Ho; Claudia Steinke; Connor P Warne; Cristina Garrido Cortes; Daniel Engelking; Danielle Wright; Dario A Lijtmaer; David Gascoigne; David Hernandez Martich; Derek Morningstar; Dirk Neumann; Dirk Steinke; Donna DeBruin Marco DeBruin; Dylan Dobias; Elizabeth Sears; Ellen Richard; Emily Damstra; Evgeny V Zakharov; Frederic Laberge; Gemma E Collins; Gergin A Blagoev; Gerrie Grainge; Graham Ansell; Greg Meredith; Ian Hogg; Jaclyn McKeown; Janet Topan; Jason Bracey; Jerry Guenther; Jesse Sills-Gilligan; Joseph Addesi; Joshua Persi; Kara K S Layton; Kareina D'Souza; Kencho Dorji; Kevin Grundy; Kirsti Nghidinwa; Kylee Ronnenberg; Kyung Min Lee; Linxi Xie; Liuqiong Lu; Lyubomir Penev; Mailyn Gonzalez; Margaret E Rosati; Mari Kekkonen; Maria Kuzmina; Marianne Iskandar; Marko Mutanen; Maryam Fatahi; Mikko Pentinsaari; Miriam Bauman; Nadya Nikolova; Natalia V Ivanova; Nathaniel Jones; Nimalka Weerasuriya; Norman Monkhouse; Pablo D Lavinia; Paul Jannetta; Priscila E Hanisch; R Troy McMullin; Rafael Ojeda Flores; Raphaëlle Mouttet; Reid Vender; Renee N Labbee; Robert Forsyth; Rob Lauder; Ross Dickson; Ruth Kroft; Scott E Miller; Shannon MacDonald; Sishir Panthi; Stephanie Pedersen; Stephanie Sobek-Swant; Suresh Naik; Tatsiana Lipinskaya; Thanushi Eagalle; Thibaud Decaëns; Thibault Kosuth; Thomas Braukmann; Tom Woodcock; Tomas Roslin; Tony Zammit; Victoria Campbell; Vlad Dinca; Vlada Peneva; Paul D N Hebert; Jeremy R deWaard
Journal:  Biodivers Data J       Date:  2015-08-30

8.  Testing DNA barcode performance in 1000 species of European lepidoptera: large geographic distances have small genetic impacts.

Authors:  Peter Huemer; Marko Mutanen; Kristina M Sefc; Paul D N Hebert
Journal:  PLoS One       Date:  2014-12-26       Impact factor: 3.240

9.  Mapping global biodiversity connections with DNA barcodes: Lepidoptera of Pakistan.

Authors:  Muhammad Ashfaq; Saleem Akhtar; Muhammad Athar Rafi; Shahid Mansoor; Paul D N Hebert
Journal:  PLoS One       Date:  2017-03-24       Impact factor: 3.240

10.  Plutella australiana (Lepidoptera, Plutellidae), an overlooked diamondback moth revealed by DNA barcodes.

Authors:  Jean-François Landry; Paul Dn Hebert
Journal:  Zookeys       Date:  2013-08-29       Impact factor: 1.546

View more
  5 in total

1.  Complete mitochondrial genomes and phylogenetic relationships of the genera Nephila and Trichonephila (Araneae, Araneoidea).

Authors:  Hoi-Sen Yong; Sze-Looi Song; Kah-Ooi Chua; I Wayan Suana; Praphathip Eamsobhana; Ji Tan; Phaik-Eem Lim; Kok-Gan Chan
Journal:  Sci Rep       Date:  2021-05-21       Impact factor: 4.379

2.  DNA barcodes reveal population-dependent cryptic diversity and various cases of sympatry of Korean leptonetid spiders (Araneae: Leptonetidae).

Authors:  Jong-Hwa Oh; Sora Kim; Seunghwan Lee
Journal:  Sci Rep       Date:  2022-09-15       Impact factor: 4.996

3.  High genetic diversity of spider species in a mosaic montane grassland landscape.

Authors:  Jason L Botham; Charles R Haddad; Marieka Gryzenhout; Vaughn R Swart; Emile Bredenhand
Journal:  PLoS One       Date:  2020-06-08       Impact factor: 3.240

4.  BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae).

Authors:  Muhammad Tayyib Naseem; Muhammad Ashfaq; Arif Muhammad Khan; Akhtar Rasool; Muhammad Asif; Paul D N Hebert
Journal:  PLoS One       Date:  2019-12-10       Impact factor: 3.240

5.  First Report of the Ash Sawfly, Tomostethus nigritus, Established on Fraxinus excelsior in the Republic of Ireland.

Authors:  Erika Soldi; Emma Fuller; Anna M M Tiley; Archie K Murchie; Trevor R Hodkinson
Journal:  Insects       Date:  2021-12-21       Impact factor: 2.769

  5 in total

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