Advertisement
Browse Subject Areas
?

Click through the PLOS taxonomy to find articles in your field.

For more information about PLOS Subject Areas, click here.

  • Loading metrics

Further assessment of the Genus Neodon and the description of a new species from Nepal

  • Nelish Pradhan ,

    Roles Data curation, Formal analysis, Funding acquisition, Investigation, Project administration, Writing – original draft, Writing – review & editing

    ‡ These authors are joint senior authors on this work.

    Affiliation Department of Biology, University of Vermont, Burlington, Vermont, United States of America

  • Ajay N. Sharma,

    Roles Data curation, Investigation

    Affiliation Center for Molecular Dynamics–Nepal, Kathmandu, Nepal

  • Adarsh M. Sherchan,

    Roles Data curation, Investigation

    Affiliation Center for Molecular Dynamics–Nepal, Kathmandu, Nepal

  • Saurav Chhetri,

    Roles Investigation

    Affiliation Department of Biology, Trinity University, San Antonio, Texas, United States of America

  • Paliza Shrestha,

    Roles Investigation

    Affiliation Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, United States of America

  • C. William Kilpatrick

    Roles Data curation, Funding acquisition, Project administration, Supervision, Writing – original draft, Writing – review & editing

    wkilpatr@uvm.edu

    ‡ These authors are joint senior authors on this work.

    Affiliation Department of Biology, University of Vermont, Burlington, Vermont, United States of America

Further assessment of the Genus Neodon and the description of a new species from Nepal

  • Nelish Pradhan, 
  • Ajay N. Sharma, 
  • Adarsh M. Sherchan, 
  • Saurav Chhetri, 
  • Paliza Shrestha, 
  • C. William Kilpatrick
PLOS
x

Abstract

Recent molecular systematic studies of arvicoline voles of the genera Neodon, Lasiopodomys, Phaiomys, and Microtus from Central Asia suggest the inclusion of Phaiomys leucurus, Microtus clarkei, and Lasiopodomys fuscus into Neodon and moving Neodon juldaschi into Microtus (Blanfordimys). In addition, three new species of Neodon (N. linzhiensis, N. medogensis, and N. nyalamensis) have recently been described from Tibet. Analyses of concatenated mitochondrial (Cytb, COI) and nuclear (Ghr, Rbp3) genes recovered Neodon as a well-supported monophyletic clade including all the recently described and relocated species. Kimura-2-parameter distance between Neodon from western Nepal compared to N. sikimensis (K2P = 13.1) and N. irene (K2P = 13.4) was equivalent to genetic distances observed between recognized species of this genus. The specimens sampled from western Nepal were recovered sister to N. sikimensis in the concatenated analysis. However, analyses conducted exclusively with mitochondrial loci did not support this relationship. The occlusal patterns of the first lower (m1) and third upper (M3) molars were simpler in specimens from western Nepal in comparison to N. sikimensis from eastern Nepal and India. Twelve craniodental characters and four external field measurements were examined from specimens of N. sikimensis from eastern Nepal and India, N. irene, and Neodon from western Nepal. Neodon from western Nepal were significantly different from N. sikimensis from eastern Nepal and India in ten out of 16 characters measured and from N. irene for all characters except ear height. Specimens from western Nepal were smaller in size than N. sikimensis from Eastern Nepal and India and larger than N. irene. Together the results of the molecular and morphological analyses indicate that Neodon from western Nepal are distinct under the phylogenetic, genetic and morpho species concepts.

Introduction

The genus Neodon (Tribe Arvicolini, Subfamily Arvicolinae) was described by Horsfield [1] and was retained as a genus in early revisions [24]. Allen [5] recognized Neodon as a subgenus of Microtus whereas Ellerman and Morrison-Scott [6] included it in the genus Pitymys, a large and rather ill-defined genus with taxa occurring in the Palearctic and Nearctic. Gromov and Polyakov [7] considered Neodon a subgenus of Microtus whereas Corbet [8] followed the suggestion of Ellerman and Morrison-Scott [6] including Neodon in the genus Pitymys. Revisions in the 1990’s either recognized Neodon as a distinct genus [9, 10] or as a subgenus of Microtus [1113] whereas more recent revisions [14, 15] have recognized as a distinct genus. Central Asia voles including the genera Neodon, Blanfordimys, and Phaiomys have been hypothesized to be Pleistocene relicts due to their primitive molar occlusal patterns resembling the fossil genus Allophaiomys [16]. Additionally, N. juldaschi possesses a karyotype (2n = 54 or 56) thought to be ancestral to the Arvicolini [10, 17].

Musser and Carleton [14] recognized four species of Neodon (forresti, irene, juldaschi, sikimensis). Several molecular phylogenies have recovered Neodon as diphyletic [1822] with N. juldaschi in a clade with forms of Blanfordimys (recognized either as a distinct genus or as a subgenus of Microtus) and forms of Neodon other than N. juldaschi in a clade with Phaiomys leucurus [1822], Lasiopodomys fuscus [20], Microtus clarkei [18, 21, 22], or Volemys millicens [23]. Results from these phylogenetic analyses have led to further changes in the content of the genus with the recognition of P. leucurus as N. leucurus [20, 22], M. clarkei as N. clarkei [24], L. fuscus as N. fuscus [20, 22], and N. juldaschi as Microtus (Blanfordimys) juldaschi [19, 25]. Three additional species of Neodon have been described in recent years from China: N. linzhiensis [20] and N. nyalamensis and N. medogensis [22]. The most recent revision [15] recognized nine species of Neodon (clarkei, forresti, fuscus, irene, leucurus, linzhiensis, medogensis, nyalamensis, and sikimensis) while considering Blanfordimys as a subgenus of Microtus and recognizing N. juldaschi as Microtus (Blanfordimys) juldaschi.

Neodon sikimensis occurs on both the western and eastern sides of the Himalayas (Fig 1) with specimens reported from southern Tibet on the eastern side and in Nepal, India, and Bhutan on the western side [14]. In Nepal, the reported distribution of N. sikimensis extends well into western Nepal [26]. Several specimens from Nepal identified as N. irene reside at the American Museum of Natural History (AMNH) and the Natural History Museum in London (NHMUK). However, Pearch [26] reclassified specimens at the American Museum of Natural History identified as N. irene collected from Shey Gompa in western Nepal (AMNH 238055—AMNH 238058, AMNH 238060—AMNH 238063) as N. sikimensis citing the restricted distribution of N. irene to China [14, 27]. Specimens at the Natural History Museum in London identified as N. irene (cataloged as Pitymys irene forresti: NHMUK 1954.10.52–1954.10.77) collected from Saipal, Urai Lagna, Garanphu, and Seti in western Nepal could also be excluded from representing N. irene due to their distribution. Although N. irene has been included as a synonym of N. sikimensis by some authors [8, 28, 29], these two species have been distinguished based on differences in dentition and size [30, 31], leading others, including most recent reviews, to treat N. irene as a distinct species [6, 7, 14, 15]. Nadachowski and Zagorodnyuk [16] observed variation in dental characters among specimens from Nepal great enough to suggest that N. sikimensis may constitute a group of sibling species. Because of a lack of agreement of the number of species of Neodon that occur in Nepal a closer examination is needed.

thumbnail
Fig 1. Localities of specimens of Neodon examined.

Distributional boundaries of Neodon species novum (red), N. sikimensis (dotted), and N. irene (blue). Collecting localities of museum specimens of N. sikimensis (circles), N. irene (triangle), and N. species novum (squares) examined in the study, with the type locality of N. sikimensis indicated with a star. Localities of sequenced specimens of N. species novum (black squares), approximate location of specimens of N. sikimensis sequenced by Liu et al. [20, 22] (black circle), and N. irene misidentified as N. sikimensis in the FMNH (black triangle). Range shapefiles of N. sikimensis and N. irene acquired from Terrestrial Mammal dataset IUCN Red List (https://www.iucnredlist.org/resources/spatial-data-download). Shapefiles for Himalayan ecoregions acquired from The Nature Conservancy terrestrial ecoregion data set (http://maps.tnc.org/gis_data.html).

https://doi.org/10.1371/journal.pone.0219157.g001

We report on samples of Neodon collected from western Nepal and compare mitochondrial and nuclear DNA sequences obtained with existing sequences from Neodon and related species. The objectives of this study are: (1) to compare Cytb and other mitochondrial and nuclear sequence data from specimens of Neodon to determine if the samples from western Nepal represent a distinct species under the genetic and phylogenetic species concepts; (2) to determine if Neodon from western Nepal represent a distinct species under a morphospecies concept by comparison of craniodental measurements and external field measurements with N. sikimensis from eastern Nepal, India and Tibet, and with N. irene; and (3) to sample both mitochondrial and nuclear loci to provide better resolution of the phylogenetic relationships between Neodon and other genera and subgenera of the Arvicolini.

Materials and methods

Specimens and taxonomic sampling

Tissues (ear punches) of Neodon specimens (n = 6) from the Myagdi District (Permit no.– 10/070/071) and the Dolpo District (Permit no.– 1/2071/72) of western Nepal were collected in 2013 and 2015 respectively (Table 1). Permits were secured from the Department of National Parks and Wildlife Conservation in Nepal to collect samples from the Nepalese field mouse (Apodemus gurkha), at the time considered an endangered species, hence specimens were to be released following the collection of ear punches under the permit conditions. Voucher specimens were prepared for all individuals that perished in the traps overnight (Table 1). Specimens were collected following methods outlined in the American Society of Mammalogists Guidelines [32]. Mitochondrial (Cytb and COI) and nuclear (Rbp3 and Ghr) sequences for select Arvicolinae and outgroup taxa (Mesocricetus auratus, Subfamily Cricetinae) were obtained from GenBank (S1 and S2 Appendices).

thumbnail
Table 1. Localities of specimens collected from Nepal with accession numbers of sequences obtained in this study.

https://doi.org/10.1371/journal.pone.0219157.t001

A total of 170 specimens cataloged as N. sikimensis from the Field Museum of Natural History (FMNH; n = 168, including a juvenile) and the National Museum of Natural History (NMNH; n = 2), were measured and examined for molar occlusal patterns (S3 Appendix). In addition, 6 specimens cataloged as N. sikimensis from Sichuan and Yunnan [outside the reported range of N. sikimensis] provinces in China (east of Tibet) in the FMNH (n = 4) and the NMNH (n = 2) were examined. Measurements were also taken from 8 specimens of N. irene in the FMNH (n = 2) and the NMNH (n = 6) and from 3 new specimens of Neodon collected from western Nepal (S3 Appendix).

DNA extraction, sequencing, and alignment

DNA extraction and sequencing for Neodon sampled in Nepal was carried out at the Center for Molecular Dynamics, Nepal (CMDN). Approximately 25 mg of ear tissue stored in 95% ethanol was used for DNA extractions that were conducted using DNeasy Blood and Tissue Kit (Qiagen, Germany). Tissue samples were air dried for 30 min prior to extraction. Each tissue sample was cut into small pieces (approx. 20) and incubated at 56°C in 180 μl of ATL (Tissue Lysis Buffer) and Proteinase K in a shaking incubator until the tissue samples were completely lysed. DNA was finally eluted in 50 μl of Elution buffer and the quantity and quality of the extracted DNA was assessed on a NanoVue Plus (GE Healthcare Life Sciences) spectrophotometer.

Cytochrome b (Cytb), cytochrome oxidase I (COI), interphotoreceptor retinoid binding protein (Rbp3), and growth hormone receptor (Ghr) were amplified with the primer pairs: L14274/H15915 [33], COIF/COIR [34], Rbp3217/Rbp31531 [35], and Ghr5/Ghr4 [36] respectively. Amplification of Cytb was performed with initial denaturation at 94°C for 5 min followed by 31 cycles of denaturation at 95°C for 1 min, annealing at 50°C for 1 min and extension at 68°C for 1 min and final extension at 68°C for 10 min. Attempts to amplify Cytb from “crusties” from six museum specimens included in the morphological analyses were unsuccessful. Amplification of Rbp3 was carried out with initial denaturation at 94°C for 5 min followed by 35 cycles of denaturation at 94°C for 1 min, annealing at 50°C for 1 min and extension at 68°C for 1.5 min and final extension at 68°C for 10 min. Cycling parameters specified in Galewski et al. [36] were used to amplify Ghr whereas COI was amplified following the cycling parameters from Zeng et al. [34]. Amplification reactions were conducted in 25 µl volumes (H2O – 16.9 μl; 5X PCR buffer+ MgCl2−5 μl; 5000 U Taq Polymerase– 0.125 μl; 10 pMol/µl Forward Primer– 0.75 μl; 10 pMol/µl Reverse Primer– 0.75 μl; 10 mM dNTPs– 0.50 μl; DNA template– 1 μl) using OneTaq DNA Polymerase (NEB, Ipswich, MA, USA). PCR products were visualized with ethidium bromide after gel electrophoresis on 2% agarose gels. ExoSAP (Exonuclease and Shrimp Alkaline Phosphatase) (ThermoFisher Scientific) was used to purify the PCR products following manufacturer’s protocol prior to sequencing reactions. Sequencing reactions (10 µl) were conducted with 1 μl of ExoSAP product, 3 µl primer (5 µM/µl), 2 µl nuclease free water and 4 µl of Ready reaction mix containing fluorescent tagged terminator (BigDye v3.1; Applied Biosystems Foster City, CA). The sequencing reaction was further purified using Big Dye X-Terminator Purification Kit (ThermoFisher Scientific) (45 µl SAM solution + 10 µl Big Dye X-terminator solution along with all sequencing PCR product (10 µl) in a 0.5 ml tube. The reactions were optimally diluted in ABI 310 Sequencing Strip tubes for running the final sequencing reaction on ABI 310 avoiding the formation of any air bubbles in the strip tubes.

Chromatograms outputted from the sequencers were visualized and edited in Chromas 2.6.2 (Technelysium: http://technelysium.com.au/wp/chromas/). Sequences from two mitochondrial genes, Cytb (1140 bp) and COI (1542 bp) and two nuclear genes Rbp3 (1227 bp) and Ghr (869 bp) were aligned using ClustalW [37] in Mesquite 3.50 [38]. The codon positions for each locus were assigned and the alignments of the genes were concatenated in Mesquite. Concatenations for species of Neodon were compiled based on sequences from the same specimen or specimens from the same locality when possible (S1 Appendix).

Genetic distance and phylogenetic analyses

Kimura 2-parameter [39] genetic distances between and within genera were determined from Cytb sequences of Neodon (S2 Appendix) to compare levels of differentiation observed with values reported for other mammals that have been used to characterize species differentiation under the genetic species concept [40,41]. These measures of genetic differentiation were estimated with MEGA6.0 [42] based on the Cytb alignment of the individuals in Table 1 and Neodon sequences from GenBank (S2 Appendix).

The concatenated data set was divided into 12 individual partitions a priori with each gene (Cytb, COI, Rbp3, and Ghr) divided by codon positions. Partition finder 2.1.1 [43] was used to determine the best partitioning scheme and best model for each partition based on the AIC criterion (Table 2) under a likelihood framework using PhyML [44] and the greedy algorithm [45].

thumbnail
Table 2. Partitioning scheme and best molecular evolution models selected by PartitionFinder [43].

https://doi.org/10.1371/journal.pone.0219157.t002

Maximum Likelihood (ML) analysis was conducted with RAxML [46] for the concatenated sequences with 1000 bootstrap replicates using the GTR+I+G model on all partitions shown in Table 2. The majority rule consensus (MRC) tree of the bootstrapped analysis was constructed in Mesquite. A partitioned Bayesian analysis was conducted on the CIPRES portal [47] using the 11 partitions and models in Table 2 for the concatenated dataset in MrBayes 3.2.3 [48]. Two simultaneous runs of 10,000,000 generations with sampling every 1000 generations was carried out. The MrBayes log files for both runs were examined in Tracer 1.6 [49] and a burnin of 2,500,000 generations was set for each run. The runs were combined after discarding the burnin and the MRC tree with posterior probability values was constructed in Mesquite. In addition, partitioned Bayesian analyses of mitochondrial genes (Cytb and COI), nuclear genes (Rbp3 and Ghr) and each gene were also carried out separately using the models from Table 2 and same parameters as mentioned above.

Morphometric analyses

From examination of photos (S1 Fig) of the dentition of the specimens used by Nadachowski and Zagorodnyuk (see Fig 2 [16]) to illustrate the variation observed in the occlusal pattern of the first lower molar (m1) and third upper (M3) molar among specimens of N. sikimensis, diagrams of the discrete patterns of the m1 and M3 were constructed (Fig 2). The numerical designations of the original illustration (see Fig 2 [16]) were used as code for the patterns observed. The occlusal patterns of the first lower molar varied from a tooth with an anterior loop followed by one pair of confluent triangles followed by three alternating closed triangles and a posterior loop resulting in four lingual and three labial folds (Fig 2, pattern 7) to a tooth with an anterior loop followed by two pairs of confluent triangles followed by three alternating closed triangles and a posterior loop resulting in five lingual and four labial folds (Fig 2, pattern 11). Patterns 8–10 (Fig 2) vary in the degree of development of the second pair of confluent triangles. The upper third molar varied from a tooth with an anterior loop followed by three alternating triangles, the first two which were closed and a third which was either opened or closed, and a posterior loop without a medially inflected end resulting in two lingual folds (Fig 2, pattern 12) to a tooth with and anterior loop followed by three alternating closed triangles and a posterior loop with a clearly defined medially inflected end resulting in three lingual folds (Fig 2, pattern 14). Pattern 13 (Fig 2) has three closed triangles and a weakly defined medially inflected end of the posterior loop.

thumbnail
Fig 2. Illustration of occlusal patterns of m1 (top) and M3 (bottom) molars of Neodon.

Illustrations derived from photos of the dentition of specimens (S1 Fig) examined by Nadachowski and Zagorodnyuk following their numbering system (see Fig 2 [16]).

https://doi.org/10.1371/journal.pone.0219157.g002

Discrete numerical codes were assigned to the m1 and M3 molar patterns of 177 specimens of Neodon examined (S3 Appendix). Variation in the distribution of occlusal patterns was examined from a geographic prospective.

Eight cranial characters were measured (±0.01 mm) with dial calipers including: skull greatest length (SGL), skull basal length (SBL), condylobasal length (CBL), zygomatic breadth (ZB), mastoidal breadth (MB), least interorbital width (IOW), skull height (SH), and auditory bullae length (ABL). In addition, four dental characters were also measured including: length of maxillary tooth-row (LMxT), greatest width across upper molars (MM), length of the mandibular tooth-row (LMbT), and breadth across the two upper incisors (TUIB). External measurements (in mm) including total body length (TBL), tail length (TL), length of hind foot (HF), and ear length (EL) were obtained from skin tags on the specimens. Measurements for the three voucher specimens housed in Nepal are provided in S1 Table.

Estimation of descriptive statistics (mean, range, and standard error) of all measurements for each species (S3 Appendix) and one-way ANOVA with pairwise (t-test) comparisons between N. species novum (n = 15), N. sikimensis (n = 157 excluding the juvenile FMNH 142100), and N. irene (n = 14) were conducted on JMP Pro 13.0. Individuals of N. irene examined include specimens FMNH 33939–33942, NMNH 240368 and NMNH 259931 which are cataloged as N. sikimensis but were collected outside of the currently recognized range of N. sikimensis and displayed molar occlusal patterns characteristic of N. irene. Individuals with missing measurements (S3 Appendix) and FMNH 142100 (juvenile) were excluded from the dataset and measurements were log transformed before conducting multivariate analyses. Statistical significance of differences between N. species novum (n = 12), N. sikimensis (n = 74), and N. irene (n = 8) were tested using multivariate analysis of variance (MANOVA) with Hotelling's pairwise comparisons on the log transformed measurements where p-values are reported as Bonferroni-corrected p-values. Canonical variate analysis (CVA) of N. species novum (n = 12), N. sikimensis (n = 74), and N. irene (n = 8) was performed to visualize separation among the species. Variable loadings used in the CVA were based on the product of correlated coefficients of principal components of the log transformed measurements. A scatter plot displaying the first two canonical axes was plotted along with convex hulls, where the axes represent linear combinations of the original variables in a Principal Component Analysis. Both the MANOVA and CVA were performed in the statistical package PAST [50].

Nomenclatural acts

The electronic edition of this article conforms with the requirements of the amended Code of Zoological Nomenclature, and hence the new name contained herein are available under that Code from the electronic edition of this article. This published work and the nomenclatural acts it contains have been registered in ZooBank, the online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix http://zoobank.org/. The LSID for this publication is urn:lsid:zoobank.org:pub: E296Ø27B-E533-4DF7-9720-BFFDBC5FB48D. The electronic edition of this work was published in a journal with an ISSN and has been archived and is available from the following digital repositories: PubMed and LOCKSS.

Results

Cytochrome b divergence within Neodon

Kimura 2-parameter (K2P) genetic distances between specimens of Neodon sequenced from wester Nepal and N. sikimensis (mean = 13.1) or N. irene (mean = 13.4) were comparable to the K2P distances between recognized species of Neodon (mean = 11.1–14.4) (Table 3). Large genetic distances between the western Nepal Neodon sampled from Dolpo and Myagdi Districts, Nepal were also observed (mean = 7.8; range = 7.6–8.0) (Table 4).

thumbnail
Table 3. Mean cytochrome b Kimura 2-parameter distance (percent) within and between species of Neodon.

https://doi.org/10.1371/journal.pone.0219157.t003

thumbnail
Table 4. Cytochrome b Kimura 2-parameter distances (percent) between samples from western Nepal.

https://doi.org/10.1371/journal.pone.0219157.t004

Phylogenetic analyses

Neodon formed a strongly supported clade in both the Maximum Likelihood (ML = 99) and Bayesian analyses (PP = 1.00) using the concatenated dataset of four genes (Fig 3). Monophyly of Neodon was supported by all loci: concatenated analyses of mitochondrial (PP = 1.00; S2 Fig) and nuclear loci (PP = 1.00; S3 Fig) as well as Cytb (PP = 1.00; S4 Fig), COI (PP = 1.00; S5 Fig), Rbp3 (PP = 1.00; S6 Fig), and Ghr (PP = 1.00; S7 Fig) gene trees. Neodon was recovered sister to a clade containing Microtus and Alexandromys (ML<50; PP = 0.78) with the four-gene concatenated dataset.

thumbnail
Fig 3. Arvicolinae phylogenetic tree.

Bayesian tree of concatenated Cytb, COI, Rbp3, and Ghr genes with nodal support as Maximum Likelihood bootstraps (1000 replicates) and Bayesian posterior probability values (ML/PP; only if >50%) where an asterisk (*) refers to ML = 100 and PP = 1.00.

https://doi.org/10.1371/journal.pone.0219157.g003

Specimens of Neodon from western Nepal (N. species novum) formed a well-supported clade in the concatenated analyses (ML = 100; PP = 1.00; Fig 3), mitochondrial loci (PP = 1.00; S2 Fig), nuclear loci (PP = 1.00; S3 Fig), and all individual gene trees (PP = 1.00; S4S7 Figs). The N. species novum clade was sister to N. sikimensis (ML<50; PP = 0.92) with the four-gene concatenated dataset, however this relationship was not recovered in trees built with only mitochondrial loci, nuclear loci alone, or individual genes. Neodon species novum, N. leucurus, and N. fuscus formed a weakly supported clade with the concatenated mitochondrial loci (PP = 0.66; S2 Fig). Sister species relationships between irene/linzhiensis (ML = 82; PP = 0.98), leucurus/fuscus (ML = 52; PP = 0.97), were recovered with both likelihood and Bayesian analyses, whereas medogensis/clarkei was supported only in the Bayesian analyses (PP = 0.99) (Fig 3). The species novum/sikimensis clade recovered in the analysis of the concatenated dataset was sister to a clade containing the other 7 species of Neodon examined in this study (Fig 3).

The taxon, previously recognized as N. juldaschi, was recovered in a clade with taxa of Microtus of the subgenus Blanfordimys (ML = 100; PP = 1.00; Fig 3) with the four-gene concatenated dataset. This relationship was well supported in trees built with individual genes (S4, S6 and S7 Figs) other than COI (S5 Fig) for which no sequence data are available for juldaschi. A sister taxon relationship was recovered between the well supported subgenus Blanfordimys clade and Microtus (Agricola) agrestis from the four-gene concatenated dataset (ML = 54; PP = 0.84; Fig 3) and the Cytb data (PP = 0.99; S4 Fig). However, the subgenus Blanfordimys clade was recovered as sister to the Neodon clade in the analysis of the Ghr data (PP = 0.88; S7 Fig).

Neodon was recovered as the sister taxon to a clade containing the genera Microtus and Alexandromys from analysis of the four-gene concatenated dataset, however, this relationship was poorly supported (ML<50; PP = 0.70; Fig 3). Other sister taxon relationships recovered include a Microtus clade from analysis of only mitochondrial genes (PP = 0.57; S2 Fig), an Alexandromys clade from analysis of only Cytb data (PP = 0.90; S4 Fig), and a Blanfordimys clade from the analysis of the Rbp3 data (PP = 0.88; S6 Fig).

Molar occlusal patterns

The new specimens of Neodon collected from western Nepal had occlusal patterns of their m1 (S8 Fig) that were best characterized as discrete pattern 9 (Fig 2) and of their M3 that were best characterized as patterns 13 (n = 1) or 14 (n = 2). These patterns were simpler than the patterns observed in a paratype of N. sikimensis and specimens from N. sikimensis reported from Tibet [20] or examined from Sikkim (Table 5). Occlusal patterns were more variable among specimens cataloged as N. sikimensis from Nepal with both the m1 and M3 varying across the range of patterns identified by Nadachowski and Zagorodnyuk [16]. However, more complex patterns (m1 –patterns 10 & 11 and M3 –patterns 13 & 14) were observed in specimens in eastern Nepal whereas simpler patterns (m1 –patterns 7–9 and M3 –patterns 12 &13) were characteristic of specimens from western Nepal (Table 5). Based on the observed geographic variation of occlusal patterns in specimens from Nepal, we hypothesize that the specimens from western Nepal, including the newly collected material that are genetically distinct from N. sikimensis, represent a distinct species based on morphological species concept.

thumbnail
Table 5. Occlusal patterns of m1 and M3 in specimens of Neodon examined.

https://doi.org/10.1371/journal.pone.0219157.t005

Specimens from Sichuan and Yunnan catalogued as N. sikimensis had m1 occlusal patterns assigned to pattern 7 (Fig 2) and M3 occlusal patterns assigned to pattern 12, identical to some of the patterns reported for N. irene from Sichuan [16]. A few populations of Neodon examined from northeastern Nepal, Khumjung, Num and Balutar (S9 Fig), were observed to have molar with rather simple occlusal patterns (m1 –patterns 8–10; M3 –pattern 12).

Morphometric analyses

Pairwise t-tests showed that specimens in the FMNH from Sichuan and Yunnan catalogued as N. sikimensis were only significantly differenty from N. irene for two characters (LMxT and LMbT), whereas they differed from N. sikimensis by all characters except MB. The specimens catalogued as N. sikimensis from Sichuan and Yunnan were pooled with N. irene for all subsequent statistical analyses.

One-way ANOVA comparing Neodon species novum, N. sikimensis, and N. irene resulted in statistically significant (p<0.0001) differences between the species for all measurements (Table 6). Neodon species novum from western Nepal were significantly smaller than N. sikimensis and larger than N. irene (Fig 4 and Table 6). ANOVA indicated significant differences among the three species (N. species novum, N. sikimensis, and N. irene) for all observed characters (p<0.0001: Table 6). Post hoc pairwise comparisons using a t-test between the species revealed that N. species novum differed from N. sikimensis and N. irene with 10 and 15 characters out of 16 respectively (Table 6).

thumbnail
Fig 4. Box plots of morphometric characters.

Box plots for eight cranial, four dental, and four external field measurements comparing specimens of Neodon species novum (n = 15), N. sikimensis (n = 146), and N. irene (n = 14). Mean±SEM in red and median denoted by thick black horizontal bar. SGL = skull greatest length, SBL = skull basal length, CBL = condylobasal length, ZB = zygomatic breadth, MB = mastoid breadth, IOW = least interorbital width, SH = skull height, ABL = auditory bullae length, LMxT = length of maxillary tooth row, LMbT = length of mandibular tooth row, MM = width across upper molars, TUIB = breath across upper incisors, TBL = total body length, TL = tail length, HF = length of hind foot, and EL = length of ear.

https://doi.org/10.1371/journal.pone.0219157.g004

thumbnail
Table 6. Summary of one-way ANOVA and pairwise t-test comparison between Neodon species novum (Nsn), N. sikimensis (Ns), and N. irene (Ni).

https://doi.org/10.1371/journal.pone.0219157.t006

MANOVA results found the three species differed significantly from each other (Wilks’ λ = 0.02794; F = 23.67; p < 0.0001). Hotelling’s P indicated that N. sikimensis differed significantly from N. species novum (p = 4.63E-13) and N. irene (p = 1.27E-29), whereas N. species novum and N. irene did not (p = 0.27). MANOVA comparing just N. species novum and N. irene, however, showed significant difference between the two groups (Wilks’ λ = 0.00327; F = 57.2; p = 0.0033). Discriminant analysis or CVA clearly separated N. irene from N. species novum and N. sikimensis with CV1 separating N. irene from N. sikimensis and N. species novum, while CV2 separated N. sikimensis and N. species novum (Fig 5). Specimens classified with the discriminant analysis based on the Mahalanobis distance and cross-validated with a jackknifing procedure confirmed species were correctly identified in 97.87% of cases, incorrectly classifying 2 out 74 N. sikimensis specimens (FMNH 104299 and FMNH 142098) as N. species novum.

thumbnail
Fig 5. Projection of canonical variates from discriminant analyses.

Includes analysis of 8 cranial (SGL, SBL, CBL, ZB, MB, IOW, SH, and ABL), 4 dental (LMxT, LMbT, M-M, and TUIB) and 4 external field measurements (TBL, TL, HF, and EL) for Neodon species novum (n = 12), N. sikimensis (n = 74), and N. irene (n = 8).

https://doi.org/10.1371/journal.pone.0219157.g005

Discussion

Neodon of Western Nepal

Presently two species of Neodon are recognized as occurring in Nepal, N. sikimensis and N. leucurus [26], though the molar patterns of two specimens (NHML 541076 & NHML 662583) referred to as N. irene were illustrated by Nadachowski and Zagorodnyuk [16]. In addition, specimens cataloged as N. irene collected from locations in Nepal are housed in the American Museum of Natural History and the Natural History Museum of London. Pearch [26] included some of these specimens reported as N. irene as N. sikimensis based on the range of N. irene being restricted to China [14, 27] rather than examination of these specimens. The molar occlusal patterns of the specimens N. irene from Nepal illustrated by Nadachowski and Zagorodnyuk (see Fig 3 [16]) are very similar to the m1 pattern 9 and the M3 patterns 12 and 13 presented for N. sikimensis (see Fig 2 [16]).

Sequence data obtained from specimens on Neodon from western Nepal demonstrated considerable genetic differentiation (Cytb K2P) from N. sikimensis, N. irene, N. leucurus, and other species of Neodon. Mean genetic distance (K2P) of Cytb between N. sikimensis and the N. species novum (13.1) exceeds the K2P values calculated between N. sikimensis and all other species of Neodon (range = 11.1–12.5) except for N. fuscus (14.4) and is comparable to genetic distances between recognized species of Neodon (range = 11.1–14.9) (Table 3). Moreover, the mean genetic distance derived between N. sikimensis and N. species novum (K2P = 13.1) is larger than the K2P distances reported within Rodentia for sister species (mean K2P = 7.3, range = 1.3–13.0) and comparable to intrageneric distances (mean K2P = 10.9, range = 4.9–16.9) for species of rodents [41]. In a comparable “genus”, Microtus, the reported mean K2P distances of Cytb was 6.8 (range = 4.3–11.1) between sister species and 10.9 (range = 5.1–12.8) for congeneric species [41], both of which are smaller than what was observed between N. sikimensis and the Neodon from western Nepal. Hence, N. species novum should be considered a distinct species under the genetic species concept based of the large genetic distances (Cytb K2P) between it and other species of the genus.

Systematics of Neodon

Hinton [2] provided a description of the essential features of the genus Neodon and commented on the presence of three closed triangles on the m1 as in Pitymys, instead of the five, characteristic of Microtus. Neodon is not as highly modified for subterranean habits as Pitymys, with moderately long ears clearly visible above the fur [2].

Our molecular analyses support the conclusion of other recent studies [2022] and revisions [14, 15] in the recognition of Neodon as a distinct genus of the Arvicolini. Unlike previous molecular studies where the Neodon clade was recovered as a monophyletic clade within the Microtus clade [2022], it was recovered in our phylogenetic analysis as the sister group to a Microtus-Alexandromys clade though with rather low support. Furthermore, our molecular phylogeny supports the conclusion regarding the taxonomic treatment of M. (Blanfordimys) juldashi [15, 19, 25] rather than retaining it in the genus Neodon [14].

Several misplaced sequences were initially detected in our phylogeny, including sequences identified as M. clarkei (AY641526) from Luo et al. [51] and N. leucurus (AM392371 and AM392394) from Galewski et al. [36] which appear to represent misidentified specimens of N. irene and N. fuscus respectively (represented as N. irene 12 and N. fuscus 9 in Fig 3). The Cytb sequence AY641526 was originally placed in GenBank by Luo et al. [51] as from M. clarkei but identified as N. irene (though included in their appendix as M. clarkei) by Liu et al. [20, 22]. This sequence (AY641526) has a 95% identity with Cytb sequences from N. irene and only an 88% identity with sequences from M. clarkei, thus we conclude this sequence is representative of N. irene. Similarly, Cytb sequence (AM392371 and Ghr sequence AM392394 were submitted to GenBank by Galewski et al. [36] as sequences from N. leucurus but changed to Lemmus leucurus in Chen et al. [23] and to N. fuscus in Liu et al. [22]. The Cytb sequence AM392371 has a 99% identity with Cytb sequences from N. fuscus and an 89% identity with N. leucurus sequences. In addition, the Rbp3 sequence AY163593 submitted by Weksler [52] as from a N. sikimensis was derived from specimen USNM449126 which is cataloged as N. irene from Qinghai, China. This sequence (AY163593) was concatenated with the Ghr sequence AY294924 from a specimen (USNM449173) of N. irene collected from the same location in our analysis (N. irene 6). The Rbp3 sequence AM919400 was excluded from our concatenated analyses due to uncertainty as whether it was derived from N. fuscus or N. irene but was included in the Rbp3 gene tree (S6 Fig). Arvicolines are often difficult to distinguish morphologically, subsequently leading to misidentification of the taxon that was the source of molecular data. Unfortunately, no voucher specimens are associated with these sequences from misidentified specimens other than AY163593. This further demonstrates the importance of voucher specimens and the identification of those vouchers in association with sequences in GenBank and in the publications reporting new sequence data. In addition, once these misidentifications are recognized the database (GenBank) needs to be corrected. Without correction of the taxon misidentification in the database the use of these misidentified sequences will continue to cause confusion in the literature and contribute further to the confusion in resolving the phylogeny of an already problematic group.

All species of Neodon, including N. species novum, form strong supported clades (ML = 100; PP = 1.00) that are reciprocally monophyletic with other Neodon clades. This well support reciprocal monophyly with other clades of Neodon, supports the recognition of N. species novum as a distinct species under a phylogenetic species concept [53, 54]. The phylogeny (Fig 2) supports the currently recognized content of the genus [15] with the addition of N. species novum and presents greater resolution of the relationships among Neodon species (excluding N. forresti for which no data are available). However, there are discrepancies among relationships recovered within Neodon between mitochondrial and nuclear loci. All phylogenies show a distant relationship between N. irene and either N. species novum or N. sikimensis. Phylogenies recovered from different concatenation of genes (mitochondrial+nuclear or mitochondrial and nuclear separately) differ in the placement of Neodon specimens from western Nepal. Use of concatenated mitochondrial+nuclear loci recovers N. species novum sister to N. sikimensis, whereas use of just mitochondrial loci recovers N. species novum in a weakly supported clade containing N. leucurus, and N. fuscus and the use of nuclear loci exclusively does not resolve the N. species novum/N. sikimensis relationship. The use of mitochondrial loci to construct phylogenies for arvicolines has been shown to yield low support values and polytomies among the deeper nodes [36, 55]. Most Neodon species (N. clarkei, N. leucurus, N. linzhiensis, N. medogensis, and N. nyalamensis) have only sequence from mitochondrial loci available. However, well supported sister taxa relationships were recovered between N. clarkei and N. medogensis, N. leucurus and N. fuscus, and N. irene and N. linzhiensis. Our analyses support the need for both mitochondrial and nuclear loci to resolve species relationships among arvicolines, as addition of just a few nuclear loci markedly improved the support values.

Molar occlusal patterns

Among the samples of Neodon from western Nepal for which sequence data were obtained, three specimens were vouchered (Table 1). These three N. species novum had molar occlusal pattern (S8 Fig) more complex than observed in N. irene and less complex than observed in specimens of N. sikimensis from Sikkim, reported from Tibet [20] and observed in most specimens of Neodon from eastern Nepal. The molar patterns were most similar with those observed in other specimens of Neodon from western Nepal. We combined all of the Neodon from western Nepal into N. species novum based on their simpler m1 and M3 occlusal patterns (S9 Fig). Population sampled from western Nepal, N. species novum, and N. sikimensis from eastern Nepal and Sikkim have marked differences in the predominant occlusal patterns of their m1 and M3 molars (Fig 6).

thumbnail
Fig 6. Pie chart of variation of molar occlusal patterns.

Comparison of first lower molar (m1) and third upper molar (M3) of Neodon species novum (n = 15) and Neodon sikimensis (n = 156).

https://doi.org/10.1371/journal.pone.0219157.g006

Morphometrics

Neodon species novum was significantly smaller than N. sikimensis in four cranial, three dental and three external measurements, but was significantly larger in breadth across the upper incisors. Compared with N. irene, N. species novum was significantly larger in all measurements examined other than ear height. Although N. species novum was significantly larger than N. irene in all measurements, the MANOVA failed to differentiate N. nepalensis and N. irene based on the non-significant Bonferroni-corrected p-value in the pairwise comparisons when all three species were included but yielded a highly significant p-value differentiating the two species when N. sikimensis was excluded. The pairwise comparisons conducted in PAST for MANOVA use within-group covariance matrix pooled over all groups, which could lead to discrepancies in p-values if groups are included/excluded.

In the two-dimensional plot in multivariate space N. species novum was more similar to N. sikimensis, though all three species were clearly differentiated. Measurements reported for N. sikimensis from Tibet included only mean, maximum, and minimum values [20] and without standard error or deviation being reported, limited statistical analyses could be conducted. A CVA including the mean, maximum, and minimum values of Tibet specimens [20] cluster with the N. sikimensis specimens.

All three species were clearly separated by canonical variance analysis and the discriminant analysis correctly identified over 97% of the specimens with only two specimens of N. sikimensis being identified as N. species novum. Specimens from western Nepal, N. species novum, are morphologically distinct from both N. sikimensis and N. irene.

Neodon sikimensis Horsfield, 1851 –Sikkim Vole

One of the problems in trying to address the variation observed among Neodon occurring in Nepal is the lack of a good description of N. sikimensis. Not only is this taxon poorly described [7] but there is some confusion about the author and date of the limited description that is available. Kaneko and Smeenk [56] clarified that the author and date of the publication of the Sikkim vole N. sikimensis is Horsfield (1851) [1] rather than Hodgson (1849). The paper of 1849 was a letter published in the Annals and Magazine of Natural History written by Horsfield [57] commenting on a specimen that Hodgson considered to be a new species and pointing out that the molars had some unique feature that would be described in detail later by Hodgson. Hodgson’s expected description never appeared and Horsfield (1851:145–146) [1] formally described the genus Neodon and N. sikimensis based on characteristics of a single specimen from Sikkim. Kaneko and Smeenk [56] concluded that specimen BM 79.11.21.395 in the British Museum is the holotype and reported that there is no skull for this specimen.

Horsfield [1] described N. sikimensis as having very soft and silky uniform pelage that was deep brownish black, with a slight rusty shade dorsally, with the chin, breast, and abdomen being a deep bluish gray, with a slightly ferruginous shade. The ears were described as moderate in size and hairy externally. The tail was described as short (1½ inches) and a head and body of 5 inches. Jerdon [58] provided a similar description of the external morphology and reported measurements of the head and body as 4¾ inches, tail length 1½ inches, and hind foot ¾ of an inch of an individual collected in Sikkim, near Darjeeling.

Three specimens on N. sikimensis all collected by B. H. Hodgson from Sikkim were donated to the British Museum of Natural History in 1879 by the Museum of the East-India Company (P. Jenkins, pers. com.). In addition to the holotype (1879.11.21.395) specimen 1879.11.21.397 (skin only) and 1879.11.21.396 (skin with a damaged skull) were collected from the type locality. Specimen 1879.11.21.396 displays complex occlusal patterns of the m1 and M3 (S10 Fig) characteristic of the descriptions provided by Hinton [3] and Agrawal [59] with an anterior loop followed by two pairs of confluent triangles, three closed triangles and a posterior loop in the m1 (pattern 11, Fig 2) while the M3 possesses a long posterior loop with a well-developed third inner angle (pattern 14, Fig 2). Variation in the occlusal patterns of the m1 and M3 has been reported [16] and variation within and between populations was observed in our examination of additional specimens (S9 Fig). In general, specimens from eastern Nepal, had more complex m1 and M3 occlusal patterns characteristic of N. sikimensis from Sikkim and Tibet.

The Sikkim vole has been characterized by its large size (hind foot 20 mm and condyle-basal length of skull 28 mm) [3] and more complex cheek teeth [3, 59]. Eight cranial characters were examined from a single specimen collected in 1915 from Lachen, Sikkim [3] and standard external and six cranial characters were examined from 12 and 16 specimens from India [59], respectively. In addition, standard external and 11cranial characters were examined in 13–16 specimens from Tibet [20]. Unfortunately, there is limited overlap in the cranial measurements reported among these three studies [3, 20, 59] but there would appear to be differences in several characters between populations sampled from Tibet and India. For example, the head and body to tail ratio is 2.14 for specimens from eastern Nepal and India compared to 2.55 for specimens from Tibet.

The holotype of N. sikimensis (BM 79.11.21.395) identifies the type locality only as Sikkim, India [1, 56]. Jerdon [58] stated “it [N. sikimensis] had only been procured in Sikkim, near Darjeeling, at heights varying from 7,000 to 15,000 feet.” Thus, we propose to restrict the type locality to Sikkim, near Darjeeling. The distribution of the Sikkim vole extends from eastern Nepal into northern India and southern Tibet [1, 16, 20, 30, 58] and has not been verified to occur in either Sichuan or Yunnan [27].

Together, the results from the DNA sequence data, the and molecular phylogenetic analyses, the geographic distribution of the variation in molar occlusal patterns, and the morphometric analyses supports the hypothesis that the individuals (previously referred to as N. sikimensis) from western Nepal represent an undescribed species of Neodon. Below, these populations of Neodon from western Nepal are formally described as a new species.

Neodon nepalensis, species novum

Holotype.

Field Museum of Natural History (FMNH) 142081; adult female; skin and skull (S11 Fig). Original number R. M. Mitchell 2112.

Type locality.

Nepal, Dolpo District, Dhorpatan, 8,950 ft (UTM R44-703810-3159902; N 28o33’ E 83o05’), collected 3 February 1969.

Paratypes.

Skins and skulls of four males (FMNH142080, FMNH142082, FMNH142083, NMNH142084 and one female FMNH142079) deposited in the Field Museum of Natural History.

Diagnosis.

A species of Neodon with the following characteristics: size medium for the genus; tail about one-third the length of the head and body; hind foot medium; ear small; dorsal coloration dark (Buffy Brown at tips, Deep Mouse Gray at base, with guard hairs projecting 3–5 mm above pelage with lighter Cream Color tips; color nomenclature following Ridgeway [60]; sides Clay Color; venter Clay Color tips, Mouse Gray base, and lighter Cream Color middle band; tail bicolored, Buffy Brown above and Clay Color below; feet Cream Color with claws about 2.5 mm in length; ears Mummy brown; vibrissae black, 10–15 mm in length, some with white tips; cranium square, 1.7 times as long as wide; rostrum short, NL 85.6% of RL and RL 32.7% of SGL; molar tooth row 26.1% of SGL; incisors proodont; m1 with only one complete anterior confluent loop; M3 without or with very small third labial angle.

Distribution.

West of the Trisuli River in western Nepal at elevations between 2400 and 4200 m. Recorded from Ghorepani (2800 m), Apoon Hill (3200 m), Tukche (~2800 m), Dhorpatani (~2800 m), Shey Gompa (~4200 m), Renchi (3030 m), Ringmo (3750 m), Jumla (2400 m), Mugu (~2900 m) and Rara Lake (2975 m).

Measurements.

External measurements of the holotype as taken in the field (in mm) are: total length, 130.5; tail length, 31; hindfoot, 19.9; and ear, 12.7. Cranial measurements were obtained using dial calipers (in mm) and are as follows: SGL, 25.6; ZB, 14.8; IOW, 3.55; MB, 12.04; SH, 9.12; ABL, 6.79; LMxT, 6.69; LMbT, 6.19; MM, 5.46; and TUIB, 2.61. Mean measurements and standard errors for the five paratypes are as follows: TBL, 134±1.85; TL, 33.65±1.38; HF, 19.93±0.18; EL, 12.68±0.19; SGL, 25.9±0.17; ZB, 15.15±0.13; IOW, 3.78±0.08; MB, 11.92±0.06; SH, 9.11±0.06; ABL, 6.73±0.1; LMxT, 6.66±0.05; LMbT, 6.36±0.07; MM, 5.48±0.05; and TUIB, 2.74±0.12. Measurements of the three specimens in the private collection in Nepal are presented in S1 Table and the mean measurements and standard errors for these and additional specimens are presented in Table 6.

Comparisons.

A species of Neodon resembling N. sikimensis and N. irene but is smaller than N. sikimensis and larger than N. irene. Tail shorter but with a higher head and body to tail ratio (2.99) than N. sikimensis (2.14–2.55) and longer than in N. irene but with lower head and body to tail ratio (3.13). Much smaller but with a longer tail than N. leucurus which has a head and body to tail ratio of 3.33 or greater. The ventral pelage of N. nepalensis is brown (Clay colored tips) compared with the lighter venters of N. sikimensis (Cream Buff tips) and N. irene (Slaty washed with gray white). Neodon nepalensis is significantly smaller than N. sikimensis in total body length, tail length, ear height, and 6 cranial measurements including greatest length of the skull, condylobasal length, mastoid breadth, skull height, length of the mandibular tooth row, width across molars but is significantly larger in breath of incisors. This newly described taxon is significantly larger than N. irene in all measurements other than ear height.

The molar patterns of the m1 and M3 observed in N. nepalensis are simpler than those observed in N. sikimensis and are more similar to those observed in N. irene. A m1 with an anterior loop followed by a single pair of confluent triangles, three alternating closed triangles, and a posterior loop resulting in four lingual and three labial folds is characteristic of N. nepalensis (Fig 2, pattern 8) though some individuals showed an unpaired addition confluent triangle following the anterior loop (Fig 2, pattern 9). The m1 of N. sikimensis contained two pairs of confluent triangles following the anterior loop (Fig 2, pattern11), though specimens with only one triangle of the second pair were observed (Fig 2, pattern 10). Specimens of N. irene examined also displayed a m1 with a single pair of confluent triangles (Fig 2, pattern 7) as has been previously reported [16, 19, 30]. The m1 of N. sikimensis contained five lingual and four labial folds whereas four lingual and three labial folds were observed of the m1 of N. nepalensis and N. irene.

A third upper molar with an anterior loop followed by two alternating closed triangles and an open triangle that was confluent with a posterior loop without a medially inflected end was characteristic of N. nepalensis (Fig 2, pattern 12), though some individuals had either a weakly defined medially inflected end of the posterior loop or an additoional medial triangle that was not closed (Fig 2, pattern 13). The more complex M3 of N. sikimensis had a clearly defined medially inflected end of the posterior loop (Fig 2, pattern 14, though this was weakly defined in some specimens (Fig 2, pattern 13). No medial inflection was observed of the posterior loop of the M3 of N. irene and this tooth had only 2 lingual folds (Fig 2, pattern 12). The M3 of N. nepalensis contained either two lingual folds or two with a hint of a third fold whereas N. sikimensis usually contained a M3 with three lingual folds and rarely two with a hint of a third.

Neodon nepalensis demonstrates differentiation from other species of Neodon, including Neodon sikimensis from Tibet in both of the mitochondrial genes examined (Cytb and COI). Although sequence data are not available from N. sikimensis from eastern Nepal or India, N. nepalensis is morphologically distinct from samples examined from those regions.

Habitat.

Inhabits edges of rhododendron (Rhododendron sp.) forest, coniferous (Abies sp., Cedrus sp., Picea sp., Pinus sp.) forests, scrub habitat with peashrub (Caragana sp,) and honeysuckle (Lonicera sp.) and ecotones between scrub and forest at elevations between 2400 and 4200 m. Also reported from areas with clumps of ephedra (Ephedra sp.) and stunted junipers (Juniperus sp.) [61]. Restricted to the western Himalayan broadleaf and coniferous forest, whereas N. sikimensis occurs in the eastern Himalayan broadleaf and coniferous forest in Nepal.

Remarks.

Results from the phylogenetic, genetic distance and morphological analyses support the recognition of Neodon nepalensis as a distinct species under phylogenetic, genetic and morpho species concepts.

Etymology.

This species is named to recognize its endemic distribution to Nepal. The common name Nepalese vole is recommended.

Nomenclatural statement.

A life science identifier (LSID) number was obtained for the new species Neodon nepalensis: urn:lsid:zoobank.org:act: 881FFC1FF-4Ø2Ø-4533-B98D-E93C8ØC4FC22.

Specimens examined.

Additional material, including specimens examined, are identified in S3 Appendix.

Other potentially unidentified cryptic species of Neodon in Nepal

Genetic distances between N. nepalensis sampled from Myagdi District (GPN16 and GPN25) and Dolpo District (RCH4, RGM4, RGM6, and RGM11) were between 7.6 to 8.0, which are comparable to the reported mean between sister species of Microtus [41]. The topography between these regions where these specimens were collected in western Nepal are separated by deep river valleys created by the Kali Gandaki River and numerous high mountains which may act as barriers to gene flow. However, the current sampling represents two populations without any intermediate sampling of localities and the divergence observed may be an effect of isolation by distance. The current sampling does not provide data to exclude either of these alternative hypotheses. Hence, more intensive sampling of N. nepalensis is need, especially in the areas between the localities from which sequence data were obtained, to determine if additional cryptic species of Neodon occur in western Nepal.

Specimens (BMNH 1922.3.2.20 and 1922.3.2.21) collected in 1921 from East Everest at 17,000 ft in elevation were recognized as Phaiomys everesti [62] and the type locality for this taxon has been reported as northern Nepal [7, 63]. The original description of P. everesti [62] indicated that it resembled P. waltoni but was considerable smaller and P. waltoni [64] was described as smaller than P. blythi. Since its description [62] this small taxon has been considered as a subspecies of Microtus (Neodon) leucurus [7], a synonym of M. leucurus waltoni [65], a synonym of M. leucurus [11], or a synonym of P. leucurus [7]. Phaiomys leucurus now recognized as N. leucurus [20] has also been reported to occur in the Mustang District of northcentral Nepal [26, 61, 66]. A few specimens examined, currently recognized as N. sikimensis from northeastern Nepal (Solukhumbu and Sankhuwasabha Districts) collected by the Arun Valley Wildlife Expedition (1972–1973) and by Mitchell [61], have simple molar patterns (m1 and M3) not characteristic of the Sikkim vole (S9 Fig). The localities from which these voles with simpler molars were collected include Khumjung (FMNH 142092–1420940 and Num (FMNH 114333 and 114336), sites approximately 10 mi SW and 35 mi SE of the type locality of P. everesti, respectively. Additional research is needed to determine if a population of Neodon occurring in northeastern Nepal near Mount Everest represent a population of N. leucurus or if this material represents an additional cryptic species.

Supporting information

S1 Appendix. Sequences used in phylogenetic analyses.

GenBank accession numbers of mitochondrial (Cytb, COI) and nuclear (Ghr, Rbp3) genes of select taxa of Arvicolinae and outgroup taxa included in this study.

https://doi.org/10.1371/journal.pone.0219157.s001

(PDF)

S2 Appendix. Neodon Cytochrome b sequences.

GenBank accession numbers of sequence used to calculate K2P genetic distances.

https://doi.org/10.1371/journal.pone.0219157.s002

(PDF)

S3 Appendix. Material of N. species novum, N. sikimensis and N. irene examined.

Museums designation: PC = private collection Nelish Pradhan, FMNH = Field Museum of Natural History, ZFMK = Zoological Research Museum Alexander Koenig, SAF = Sichuan Academy of Forestry, SNU = Sichuan Normal University, BMNH = British Museum of Natural History, GNHM = Guangxi Natural History Museum. Other appreciations: ‡ = specimen examined, ‡md = specimen with missing measurements and excluded from multivariant analyses, A = molar patterns shown in Fig 2 in Liu et al. [20], B = mean and range of measurements including these specimens provided by Liu et al. [20].

https://doi.org/10.1371/journal.pone.0219157.s003

(PDF)

S1 Table. Measurements of three voucher specimen in collection of Nelish Pradhan.

SGL = skull greatest length, SBL = skull basal length, CBL = condylobasal length, ZB = zygomatic breadth, MB = mastoid breadth, IOW = least interorbital width, SH = skull height, ABL = auditory bullae length, LMxT = length of maxillary tooth row, LMbT = length of mandibular tooth row, MM = width across upper molars, TUIB = breath across upper incisors, TBL = total body length, TL = tail length, HF = length of hind foot, and EL = length of ear.

https://doi.org/10.1371/journal.pone.0219157.s004

(PDF)

S1 Fig. Molar types.

Neodon specimens from Nepal examined by Nadachowski and Zagorodnyuk [16] to illustrate the variation in lower (m1: 7–11) and upper (M3: 12–14) molar. ZFMK 84.347 –Tukche; ZFMK 84.918 –Dhorpatan; ZFMK 84.905 –Thakkhola, Tukche; ZFMK 84.910 –Khumbu, Phulung; ZFMK 84.915 –Thodung, Ramechap.

https://doi.org/10.1371/journal.pone.0219157.s005

(TIF)

S2 Fig. Bayesian majority rule consensus tree for Arvicolinae and outgroup taxa based on concatenated mitochondrial loci (Cytb and COI).

Nodal support provided as Bayesian posterior probability values.

https://doi.org/10.1371/journal.pone.0219157.s006

(TIF)

S3 Fig. Bayesian majority rule consensus tree for Arvicolinae and outgroup taxa based on concatenated nuclear loci (Rbp3 and Ghr).

Nodal support provided as Bayesian posterior probability values.

https://doi.org/10.1371/journal.pone.0219157.s007

(TIF)

S4 Fig. Bayesian majority rule consensus tree for Arvicolinae and outgroup taxa based on Cytb gene.

Nodal support provided as Bayesian posterior probability values.

https://doi.org/10.1371/journal.pone.0219157.s008

(TIF)

S5 Fig. Bayesian majority rule consensus tree for Arvicolinae and outgroup taxa based on COI gene.

Nodal support provided as Bayesian posterior probability values.

https://doi.org/10.1371/journal.pone.0219157.s009

(TIF)

S6 Fig. Bayesian majority rule consensus tree for Arvicolinae and outgroup taxa based on Rbp3 gene.

Nodal support provided as Bayesian posterior probability values.

https://doi.org/10.1371/journal.pone.0219157.s010

(TIF)

S7 Fig. Bayesian majority rule consensus tree for Arvicolinae and outgroup taxa based on Ghr gene.

Nodal support provided as Bayesian posterior probability values.

https://doi.org/10.1371/journal.pone.0219157.s011

(TIF)

S8 Fig. Photos of skulls and mandibles showing molar occlusal patterns of three voucher specimen in collection of Nelish Pradhan.

https://doi.org/10.1371/journal.pone.0219157.s012

(TIF)

S9 Fig. Localities examined and observed molar patterns (m1/M3) in Neodon species novum (red) and N. sikimensis (yellow).

1. Rara Lake, Mugu (8/12); 2. Maharigaon, Jumla (8/12, 8/13); 3. Ringmo, Dolpa (9/12); 4. Dhorpatan, Dolpa (7/12, 8/12, 8/13); 5. Ghorepani, Myagdi (9/12, 9/13); 6. Phulung Ghyang, Nawakot (11/13, 11/14); 7. Gosenkunde, Nawakot (11/13, 11/14); 8. Langtang Village, Rasuwa (11/13); 9. Uring Ghyang, Sindhu (10/14); 10. Dhukphu, Sindhu (10/13); 11. Tserping, Ramechap (11/14); 12. Thodung, Ramechap (11/14); 13. Lukla Airport, Solukhumbu (10/14, 11/14); 14. Khumjung, Solukhumbu (8/12, 10/12); 15. Kasua Khola, Sankhuwasabha (11/14); 16. Num, Sankhuwasabha (10/13, 10/14, 11/14); 17. Balutar, Sankhuwasabha (9/14, 10/14, 11/14); 18. Chainpur, Sankhuwasabha (10/14); 19. Jamnagaon, Ilam(11/14); 20. Thangu, Sikkim (11/13, 11/14); 21. Lachen, Sikkim (11/13, 11/14); 22. Tibet (11/14 see Fig 2 [20]).

https://doi.org/10.1371/journal.pone.0219157.s013

(TIF)

S10 Fig. Upper and lower molars of Neodon sikimensis.

Paratype specimen NHMUK 1879.11.21.39 from Sikkim.

https://doi.org/10.1371/journal.pone.0219157.s014

(TIF)

S11 Fig. Skull, mandible, and skin of holotype FMNH 142081.

https://doi.org/10.1371/journal.pone.0219157.s015

(TIF)

Acknowledgments

The Department of National Parks and Wildlife Conservation, Nepal provided collection permits. We are grateful to the staff at the Center for Molecular Dynamics Nepal especially Jyoti Joshi and Priya Joshi for providing high quality sequences. We also thank Dr. Bruce Patterson, Dr. Adam Ferguson, and John Phelps at the Field Museum and Darrin Lunde and Nicole Edmison at the Smithsonian National Museum of Natural History, for providing access to the specimens in their research collections. Dr. Jan Decher of the Zoological Research Museum Alexander Koenig kindly provided photos of skulls previously examined by Nadachowski and Zagorodnyuk [16] and Dr. Paula Jenkins of the Natural History Museum in London kindly provided clarification of the status and source of the type series of N. sikimensis. We greatly appreciate the constructive comments and suggestions provided by two anonymous reviewers.

References

  1. 1. Horsfield Th. A Catalogue of the Mammalia in the Museum of the Hon. East-India Company. London: The Honourable East-India Company; 1851.
  2. 2. Hinton MAC. On the voles collected by Mr. G. Forrest in Yunnan; with remarks upon the genera Eothenomys and Neodon and upon their allies. Ann Mag Nat Hist 1923; ser 9, 11,145–162.
  3. 3. Hinton MAC. Monograph on the voles and lemmings (Microtinae) living and extinct. Volume 1. London: British Museum (Natural History); 1926.
  4. 4. Ellerman JR. The families and genera of living rodents. Vol. II. Family Muridae. London: British Museum (Natural History); 1941.
  5. 5. Allen GM. The mammals of China and Mongolia. In: Granger W, editor. Natural history of Central Asia. New York: Central Asiatic Expeditions of the American Museum of Natural History; Vol 2, 1940.
  6. 6. Ellerman JR, Morrison-Scott TCS. Checklist of Palaearctic and Indian mammals 1758 to 1946. London: Trustees of the British Museum (Natural History); 1951.
  7. 7. Gromov IM, Polyakov IYa. Fauna of the USSSR, mammals, Vol. 3, No. 8. Voles (Microtinae). New Delhi: Smithsonian Inst. Libraries and the National Science Foundation; 1977.
  8. 8. Corbet GB. The mammals of the Palaearctic region: a taxonomic review. London: British Museum (Natural History); 1978.
  9. 9. Zagorodnyuk IV. Kariotipicheskaya izmenchivost' i sistematika serykh polevok (Rodentia, Arvicolini). Soobshchenie 1. Vidovoi sostav i khromosomnye chisla [Karyotypic variability and systematics of the gray voles (Rodentia, Arvicolini). Comunication 1. Species composition and chromosomal numbers]. Vestn Zool 1990; 2: 26–37 (in Russian).
  10. 10. Zagorodnyuk IV. [Karyotypic variability and systematics of the Arvicolini (Rodentia). Communication 2. Correlation pattern of chromosomal numbers.] Vestn Zool 1992; 5: 36–45 (in Russian).
  11. 11. Musser GG, Carleton MD. Family Muridae. In: Wilson DE, Reeder DM, editors. Mammal species of the world, a taxonomic and geographic reference. 2nd ed. Washington DC: Smithsonian Institution Press; 1993.
  12. 12. Gromov IM, Erbajeva MA. [The mammals of Russia and adjacent territories. Lagomorphs and Rodents.] St. Petersburg: Russian Academy of Sciences, Zoological Institut; 1995 (in Russian).
  13. 13. Pavlinov IYa, Yakhontov EL, Agadzhanyan AK. [Mammals of Eurasia. I. Rodentia. Taxonomic and geographic guide.] Archives of the Zoological Museum, Moscow State University 1995; 32: 1–289 (in Russian).
  14. 14. Musser GG, Carleton MD. Superfamily Muroidea. In: Wilson DE, Reeder DM, editors. Mammal species of the world–a taxonomic and geographic reference. 3rd ed. Baltimore: Johns Hopkins University Press; 2005, 894–1531.
  15. 15. Pardiñas UFJ, Myers P, León-Paniagus L, Ordóñez Garza N, Cook JA, Kryštufek B, Haslauer R, Bradley RD, Shenbrot GI, Patton JL. Family Cricetidae (true hamsters, voles, lemmings and New World rats and mice). In: Wilson DE, Lacher TE Jr, Mittermeier RA, editor. Handbook of mammals of the world. Vol. 7. rodents II. Barcelona: Lynx Edicions; 2017.
  16. 16. Nadachowski A, Zagorodnyuk I. Recent Allophaiomys-like species in the Palaearctic:Pleistocene relicts or a return to an initial type. Acta Zool Cracov 1996; 39: 387–394.
  17. 17. Chaline J, Matthey R. Hypotheses relatives a la formule chromosomique d’Allophaiomys pliocaenicus (Rodentia, Arvicolidae) et a la diversification de cette espece. C R Acad Sci, ser D 1971; 272: 1071–1074.
  18. 18. Robovský J, Řičánková V, Zrzavý J. Phylogeny of Arvicolinae (Mammalia, Cricetidae): Utility of morphological and molecular data sets in a recently radiating clade. Zool Scr 2008; 37: 571–590.
  19. 19. Bannikova AA, Lebedev VS, Lissovsky AA, Matrosova V, Abramson NI, Obolenskaya EV, Tesakov AS. Molecular phylogeny and evolution of the Asian lineage of vole genus Microtus (Rodentia: Arvicolinae) inferred from mitochondrial cytochrome b sequence. Biol J Linn Soc 2010; 99: 595–613.
  20. 20. Liu SY, Sun ZY, Liu Y, Wang H, Guo P, Murphy RW. A new vole from Xizang, China and the molecular phylogeny of the genus Neodon (Cricetidae: Arvicolinae). Zootaxa. 2012; 3235: 1–22.
  21. 21. Martínková N, Moravec J. Multilocus phylogeny of arvicoline voles (Arvicolini, Rodentia) shows small tree terrace size. Folia Zool 2012; 61: 254–267.
  22. 22. Liu SY, Jin W, Liu Y, Murphy RW, Lv B, Hao H, Liao R, Sun Z, Tang M, Chen W, Fu J. (2016). Taxonomic position of Chinese voles of the tribe Arvicolini and the description of 2 new species from Xizang, China. J Mammal 2016; 98: 166–182. pmid:29674783
  23. 23. Chen W-C, Hao H-B, Sun Z-Y, Liu Y, Liu S-Y, Yue B-S. Phylogenetic position of the genus Proedromys (Arvicolinae, Rodentia): Evidence from nuclear and mitochondrial DNA. Biochem Syst Ecol 2012; 42: 59–68.
  24. 24. Haslauer R. Clarke’s vole Neodon clarkei. In: Wilson DE, Lacher TE Jr, Mittermeier RA, editor. Handbook of mammals of the world. Vol. 7. rodents II. Barcelona: Lynx Edicions; 2017.
  25. 25. Bannikova AA, Lebedev VS, Golenishchev FN. Taxonomic position of Afghan vole (Subgenus Blanfordimys) by the sequence of the mitochondrial Cytb gene. Russ J Genet 2009; 45: 91–97.
  26. 26. Pearch ML.A review of the biological diversity and distribution of small mammal taxa in the terrestrial ecoregions and protected areas on Nepal. Zootaxa. 2011; 3072: 1–286.
  27. 27. Smith AT, Xie Y. A guide to the mammals of China. Princeton University Press; 2008.
  28. 28. Weigel I. Systematische Ubersicht uber die Insektenfresser und Nager Nepals nebst Bemerkungen zur Tiergeographie. In: Hellmich W, editor. Khumbu Himal. Ergebnisse des Forschungsunternehmens Nepal Himalaya, 3(2),149–312. Universitatsverlag Wagner Ges MBH, Innsbruck-Munchen;1969. pp149-1–96 (English summary).
  29. 29. Honacki JH, Kinman KE, Koeppl JW, editors. Mammal species of the world a taxonomic and geographic reference. 1st ed. Lawrence: Allen Press and Association of Systematics Collections; 1982.
  30. 30. Ellerman JR. A key to the Rodentia inhabiting India, Ceylon, and Burma, based on collections in the British Museum. Journal of Mammalogy. 1947; 28: 249–278. pmid:20258869
  31. 31. Ellerman JR. The fauna of India including Pakistan, Burma, and Ceylon, Mammalia 2nd ed. Calcutta: Baptist Mission Press; Vol 3, Part 1, 1961.
  32. 32. Sikes RS, The Animal Care and Use Committee of the American Society of Mammalogists. Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education. J Mammal 2016; 97: 663–688. pmid:29692469
  33. 33. Irwin DM, Kocher TD, Wilson AC. Evolution of the cytochrome-b gene of mammals. J Mol Evol 1991; 32 128–144. pmid:1901092
  34. 34. Zeng T, Jin W, Sun ZY, Liu Y, Murphy RW, Fu JR, et al. Taxonomic position of Eothenomys wardi (Arvicolinae: Cricetidae) based on morphological and molecular analyses with a detailed description of the species. Zootaxa 2013; 3682: 85–104. pmid:25243276
  35. 35. Stanhope MJJ, Czelusniak J, Si S, Mickerson J, Goodman M. A molecular perspective of mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly. Mol Phylogenet Evol 1992; 1: 148–160. pmid:1342928
  36. 36. Galewski T, Tilak M, Sanchez S, Chevret P, Paradis E, Douzery EJP. The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies. BMC Evol Biol 2006; 6, 80. pmid:17029633
  37. 37. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22: 4673–4680. pmid:7984417
  38. 38. Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. Version 3.51; 2018. http://mesquiteproject.org
  39. 39. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16: 111–120. pmid:7463489
  40. 40. Bradley RD, Baker RJ. A test of the genetic species concept: Cytochrome-b sequences and mammals. J Mamm 2001; 82: 960–973.
  41. 41. Baker RJ, Bradley RD. Speciation in mammals and the genetic species concept. J Mammal 2006; 87: 643–662. pmid:19890476
  42. 42. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30: 2725–2729. pmid:24132122
  43. 43. Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol 2016; 34: 772–773.
  44. 44. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59: 307–321. pmid:20525638
  45. 45. Lanfear R, Calcott B, Ho SY, Guindon S. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol 2012; 29: 1695–1701. pmid:22319168
  46. 46. Stamatakis A. RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30: 1312–1313. pmid:24451623
  47. 47. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES science gateway for inference of large phylogenetic trees. In: Proceedings of the gateway computing environments workshop (GCE), 14 November 2010, New Orleans.
  48. 48. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2013; 19: 1572–1574.
  49. 49. Rambaut A, Suchard MA, Xie D, Drummond AJ. Tracer v1.6. 2014; http://beast.bio.ed.ac.uk/Tracer
  50. 50. Hammer O, Harper DAT, Ryan PD. PAST: paleontological statistics software package for education and data analysis. Palaeontologia Electronica 2001; 4: 1–9.
  51. 51. Luo J, Yanga D, Suzuki H, Wang Y. Chen W-J, Campbell KL, Zhang Y. Molecular phylogeny and biogeography of Oriental voles: genus Eothenomys (Muridae, Mammalia). Mol Phylogenet Evol 2004; 33: 349–362. pmid:15336670
  52. 52. Weksler M. Phylogeny of Neotropical Oryzomyine rodents (Muridae: Sigmodontinae) based on nuclear IRBP exon. Mol Phylogenet Evol 2003; 29: 331–349. pmid:13678688
  53. 53. Eldredge N, Cracraft J, Phylogenetic patterns and the evolutionary process, New York: Columbia University Press; 1980.
  54. 54. Nelson G, Platnick NI. Systematics and biogeography: Cladistics and vicariance. New York: Columbia University Press; 1981.
  55. 55. Conroy CJ, Cook JA. MtDNA evidence for repeated pulses of speciation within arvicoline and murid rodents. J Mammal Evol 1999; 6: 221–245.
  56. 56. Kaneko Y, Smeenk C. The author and date of publication of the Sikkim vole Microtus sikimensis. Mammal Study 1996; 21: 161–164.
  57. 57. Th Horsfield. Brief notice of several Mammalia and birds discovered by B. H. Hodgson, Esq., in Upper India. Annals and Magazine of Natural History, London 1849; ser 2, 3: 202–203.
  58. 58. Jerdon TC. The mammals of India; a natural history of all the animals known to inhabit continental India. London: John Wheldon, 1874.
  59. 59. Agrawal VC. Taxonomic studies on Indian Muridae and Hystricidae (Mammalia: Rodentia). Records Zool Surv India, Occas Pap 180; 2000.
  60. 60. Ridgeway R. Color standards and color nomenclature. Washington DC: Privately Published; 1912.
  61. 61. Mitchell RM. Accounts of Nepalese mammals and analysis of the host-ectoparasite data by computer techniques. Ph.D. Dissertation, Iowa State University. 1977. Available from: https://lib.dr.iastate.edu/rtd/7626/
  62. 62. Thomas O, Hinton MAC. The mammals of the 1921 Mount Everest Expedition. Ann Mag Nat Hist 1922; ser 9, 9: 178–186.
  63. 63. Hoffmann RS. Noteworthy shrews from the Xizang-Qinghai Plateau. In Genoways HH, Baker RJ, editors. Contributions to Mammalogy: a memorial volume honoring Dr. J. Knox Jones. Museum Texas Tech University; 1996, pp. 155–168.
  64. 64. Bonhote JL. On a collection of mammals brought home by the Tibet Frontier Commission. Proc Zool Soc London 1905; 2: 302–308.
  65. 65. Zheng C-L, Wang S. [On the taxonomic status of Pitymys leucurus Blyth. Acta Zootax Sinica 1980; 5: 106–112 (in Chinese).
  66. 66. Mitchell RM, Derksen DV. Additional new mammal records from Nepal. Mammalia 1976; 40: 55–61.