A new species of Alticola (Mammalia, Rodentia, Arvicolinae) from southern Tibet, China

A new species of Alticola (Mammalia, Rodentia, Arvicolinae) from southern Tibet, China Ming Kun Tang1,2,3, Hong Qiu1,2,3, Bu Qing Peng1,2,3, Rui Liao1,2,3, Robert W. Murphy4, Xu Ming Wang1,2,3, Xuan Pan1,2,3, Xin Wang1,2,3, Shao Ying Liu1,2,3 1 Sichuan Key Laboratory of Ecological Restoration and Conservation for Forest and Wetland, Sichuan Academy of Forestry, Chengdu 610081, China 2 Sichuan Giant Panda National Park Observation and Research Station, Sichuan Academy of Forestry, Aba Tibetan and Qiang Autonomous Prefecture 623006, China 3 Wolong Forest Ecology Observation and Research Station of Sichuan, Sichuan Academy of Forestry, Aba Tibetan and Qiang Autonomous Prefecture 623006, China 4 Department of Natural History, Royal Ontario Museum, Toronto M5S 2C6, Canada https://zoobank.org/2AB54569-1546-43B1-9965-76503240F4A6 Corresponding author: Shao Ying Liu ([email protected]) Academic editor: M. T. R. Hawkins ♦ Received 1 September 2025 ♦ Accepted 19 November 2025 ♦ Published 3 December 2025 Abstract The complex topography and diverse habitats of the Qinghai-Tibet Plateau have made it a center of speciation and evolution for various taxa, including small mammals. Our surveys in 2008 and 2023 on the southern part of the plateau discovered a population of mountain voles (genus Alticola) not assignable to any known species. Specimens were collected from shrublands near streams (at elevations of 3,228–4,022 m) in Longzi and Lang counties, Tibet. Integrative taxonomic analyses, incorporating molecular phylogenetics and morphology, confirmed their distinct status. They form a well-supported clade that is sister to A. stoliczkanus, from which it diverged approximately 0.49 Mya (95% HPD interval: 0.20–0.77). Kimura-2-parameter distances for the complete cytochrome b gene between these individuals and other nominal species of Alticola range from 4.0% to 10.3%. Morphologically, this unique lineage is diagnosed by possessing the simplest M3 with a truncated posterior lobe, a slender tail, darker pelage, and distinctive bacular characteristics. We describe this lineage as Alticola yarlungia sp. nov. This discovery suggests that species diversity within genus Alticola remains underestimated and underscores the need for continued biodiversity exploration in the eastern Himalayan region. Key Words Morphology, mountain voles, penile morphology, phylogeny, species delimitation, Yarlung Zangbo River Introduction The rich biodiversity of rodents facilitates the identification of new species, and analyses of growing molecular and morphological data reveal their evolutionary relationships (Galewski et al. 2006; Cheng et al. 2017; Liu et al. 2019, 2022; Andreychev and Kuznetsov 2020; Wang et al. 2024). Mountain voles of the genus Alticola Blanford, 1881 (Rodentia, Arvicolinae) have a wide distribution in the mountains of Central Asia, living in steppe, rocky montane, and alpine habitats (Hinton 1926; Tang et al. 2018). The genus was first established with A. stoliczkanus Blanford, 1875 as the type species. Subsequent research throughout the 19th and 20th centuries led to the description of additional species and subspecies, as well as revisions of their taxonomic ranks based primarily on morphological traits (Hinton 1926; Allen 1940; Ellerman and Morrison-Scott 1951; Gromov and Polyakov 1977). This genus is closely related to Myodes, Craseomys, and Eothenomys according to morphological characteristics, such as palate structure and molars (Hinton 1926; Allen 1940), and molecular phylogenetic Zoosyst. Evol. 101 (4) 2025, 2387–2403|DOI 10.3897/zse.101.170704 Copyright Tang, M.K. et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. zse.pensoft.net Tang, M.K. et al.: A new species of Alticola from Tibet2388 analyses (Lebedev et al. 2007; Kohli et al. 2014; Tang et al. 2018). Species of Alticola are characterized by pale ash-brown fur and a narrow molar crown. Additionally, the third upper molar (M3) exhibits a shallow reentrant angle between the first two external angles and an extended posterior lobe (Luo et al. 2000; Smith et al. 2010; Tang et al. 2018). Most taxonomists have recognized Alticola as a valid genus (Hinton 1926; Allen 1940; Ellerman and Morrison-Scott 1951; Ognev 1962; Musser and Carleton 1993, 2005; Abramson and Lissovsky 2012; Holden et al. 2017; Wei et al. 2025). According to Musser and Carleton (2005), Alticola contains the following 12 species: A. albicaudus True, 1894; A. argentatus Severtzov, 1879; A. barakshin Bannikov, 1947; A. macrotis Radde, 1862; A. semicanus G. M. Allen, 1924; A. stoliczkanus; A. strelzowi Kastchenko, 1899; A. montosa True, 1894; A. lemminus Miller, 1898; A. olchonensis Litvinov, 1960; A. roylei Gray, 1842; and A. tuvinicus Ognev, 1950. The first seven species are distributed in China (Rossolimo et al. 1994; Musser and Carleton 2005; Liu et al. 2020; Wei et al. 2025), with most inhabiting rocky desert environments at high latitudes and elevations. Their occurrence in remote and extreme habitats has resulted in a dearth of comprehensive sampling and systematic research (Bolshakov et al. 2012), a situation that is particularly pronounced for Chinese populations. The Qinghai-Tibet Plateau’s complex topography and climatic history have made it a significant center for rodent diversity, harboring numerous endemic species (Zhang et al. 2022). The Yarlung Zangbo River, which drains its southern region, is a key component of this biodiversity hotspot. Despite this, the river basin remains under-surveyed due to its challenging terrain and poor transportation infrastructure (Wang et al. 2024; Gu and Zhu 2025). For over 20 years, we have collected an extensive series of specimens to investigate phylogenetic relationships within Alticola (Tang et al. 2018). Discoveries involved the first documentation of A. albicauda from Xinjiang (Liu et al. 2020). In 2008, we collected a morphologically distinctive specimen (Field number GB828002, catalog number SAF 081053) from Lang County, located on the right bank of the middle reaches of the Yarlung Zangbo River in southern Tibet. This specimen was initially identified as A. stracheyi by Liu et al. (2012). A subsequent taxonomic revision by Tang et al. (2018) formally synonymized A. stracheyi under A. stoliczkanus, thereby re-identifying this specimen as A. stoliczkanus. Furthermore, Tang et al. (2018) documented at least five distinct molar patterns within A. stoliczkanus and reported substantial genetic divergence (K2P distance of 4.3% for CYTB) between populations from Lang and Pulan counties. In 2023, we collected eight additional specimens from Lang and Longzi counties morphologically similar to GB828002 and which form a monophyletic clade with it. These collective findings indicate that the identification of these specimens as A. stoliczkanus is untenable, leading us to hypothesize that they represent a previously unrecognized species. To test this hypothesis, we integrate morphological and genetic analyses to determine the taxonomic status of these specimens. Given that the characters of the male genitalia are important in mammalian systematics and provide useful clues to species identification of microtines (Hooper 1958; Hooper and Hart 1962), we evaluate and compare penis morphology among some closely related taxa of Alticola. Based on this integrative evidence, we formally describe the population from the Yarlung Zangbo River basin as a new species, Alticola yarlungia sp. nov. Materials and methods Ethics statement All specimens were obtained following the American Society of Mammalogists guidelines and the laws and regulations of China concerning the protection of wild terrestrial animals (State Council Order of the People’s Republic of China 1992; Sikes and the Animal Care and Use Committee of the American Society of Mammalogists 2016). Field collecting protocols were approved by the Ethics Committee of the Sichuan Academy of Forestry (permit number: SAF2023001). Voucher specimens are deposited at the Sichuan Academy of Forestry (SAF), Chengdu, China. Sampling and sequencing Tissue samples for sequencing were collected from across much of the distributional range of the genus Alticola, including localities in Russia, Mongolia, Pakistan, Kazakhstan, and northwestern China. In total, 93 specimens were used in our phylogenetic analyses: 42 newly collected and 51 represented by approximately 116 sequences obtained from GenBank. Six specimens, comprising Neodon irene and Volemys millicens, were included as outgroups to root the phylogeny. Detailed information is provided in Suppl. material 2: appendix 1. The mitochondrial genome sequence of one sample (Field ID: 27253) was aligned using BLASTn against homologous genes from the reference mitogenome of Alticola stoliczkanus (XZ16N120), including CYTB (GenBank: KY968270), CO1 (KY968258) and ND2 (PV614058). We assembled and annotated the mitogenomes from whole-genome shotgun sequencing data for two additional samples (Field ID: 3124 and ZMMU:voucher 4445) using MitoZ v2.3 (Meng et al. 2019) with the --data_size_for_mt_assembly 3,0 parameter. Total DNA was extracted from 95% alcohol-preserved liver or muscle tissue with the Animal Tissue Genomic DNA Rapid Extraction Kit (Chengdu Fuji Biotechnology Co., Ltd., Sichuan, China). Three mitochondrial genes (mtDNA, cytochrome b [CYTB, 1,143 bp], cytochrome c oxidase subunit I [CO1, 1,545 bp], and NADH dehydrogenase subunit 2 [ND2, 1,036 bp]) and four nuclear genes (nuDNA, growth hormone receptor [GHR, 883 bp], lecithin cholesterol acyl transferase [LCAT, 628 bp], breast Zoosyst. Evol. 101 (4) 2025, 2387–2403 zse.pensoft.net 2389 cancer protein 1 [BRCA1, 1,022 bp], and interphotoreceptor retinoid-binding protein [IRBP, 1,286 bp]) were sequenced for phylogenetic analysis. Primer sets were taken from published literature for CYTB (He et al. 2010), CO1 (Zeng et al. 2013), ND2 and IRBP (Cheng et al. 2017), GHR and LCAT (Abramson et al. 2009), BRCA1 (Dubey et al. 2007) (see Suppl. material 1: table S1 for details). The thermal cycling profile was as follows: initial denaturation at 94 °C for 5 min; followed by 40 cycles of denaturation at 94 °C for 45 s, annealing at 49–56 °C for 45 s, and extension at 72 °C for 90 s; with a final extension at 72 °C for 10 min. The PCR products were sequenced at the Sangon Sequencing Center in Chengdu, China. This effort yielded new sequences from five specimens of Alticola yarlungia sp. nov. (33 sequences), 64 specimens of Alticola (201 sequences), and 24 specimens from Myodes, Craseomys, Neodon and Volemys (58 sequences). All these newly generated sequences have been deposited in GenBank, and their corresponding accession numbers are provided in Suppl. material 2: appendix 1. Phylogenetic analyses and species delimitation We established three datasets to reconstruct the phylogeny of sequenced individuals as follows: dataset 1 included mtDNA (CYTB+CO1+ND2); dataset 2 included nuDNA (GHR+LCAT+BRCA1+IRBP); dataset 3 included all mtDNA and nuDNA data. Sequence alignment was initially conducted with MAFFT v7.526 (Katoh and Standley 2013), and conserved regions were subsequently refined using GBLOCKS v0.91b (Castresana 2000) under the -b5 = h parameter. The final lengths of CYTB, CO1, ND2, GHR, LCAT, BRCA1, and IRBP used for phylogenetic analyses were 904 bp, 1,545 bp, 1,031 bp, 713 bp, 497 bp, 807 bp, and 1,217 bp, respectively. The Partition Homogeneity (ILD) test implemented in PAUP v4.0a169 using a heuristic search revealed significant incongruence among the three datasets (p < 0.05). Based on these results, a concatenated partitioned approach was adopted for phylogenetic trees reconstructions of the three datasets. The optimal model for each gene was identified with PartitionFinder v2.0.0 (Lanfear et al. 2012). The fitness of the model was evaluated using the Akaike information criterion (AIC, Luo et al. 2010). Phylogenetic reconstruction employed Bayesian inference (BI) in MrBayes v3.1.2 and maximum likelihood (ML) in RAxML-NG v1.1.0, with support values from 1,000 bootstrap replicates (Ronquist and Huelsenbeck 2003). The BI analysis was run for 1,000,000 generations with four Markov chain Monte Carlo (MCMC) algorithms (temp = 0.1), sampling every 100 generations, calculating diagnostics every 5,000 generations, and discarding the initial 25% as burn-in. The ML analysis was performed with the parameter --bs-trees 1,000 --brlen linked and using the best-fit models for the seven partitions (Suppl. material 1: table S1). The average interspecific genetic distannces for CYTB were calculated in MEGA v11 (Tamura et al. 2021) using both the Kimura 2-parameter (K2P; Kimura 1980) and the p-distance models. Variance was estimated using the bootstrap method with 1,000 replicates. Dataset 3 (mtDNA+nuDNA) was used in the species delimitation analysis. Bayesian species delimitation was performed using the A10 model in BPP v4.8.4 (Yang 2015). A guide tree reconstructed with RAxML-NG served as the phylogenetic framework, employing the JC69 nucleotide substitution model. Two independent MCMC runs were executed, each with 1,000,000 generations and a burn-in of 8,000 generations. A posterior probability threshold of > 0.97 was considered strong support for species boundaries. The Assemble Species by Automatic Partitioning (ASAP) analysis was performed on the online platform: https://bioinfo.mnhn. fr/abi/public/asap/asapold.html (Puillandre et al. 2021) with Kimura (K80) ts/tv 2.0. Multi-rate PTP (mPTP) v0.2.5 was used with the Raxml-ng result of Dataset 3 based on the Maximum-likelihood heuristic method by the --ml --multi parameter (Kapli et al. 2017). Divergence time estimation Divergence estimations were calculated using Bayesian evolutionary analysis in BEAST2 v2.7.7 (Bouckaert et al. 2019) on dataset 3. The analysis employed a partitioned framework where substitution models for individual genes were optimized through PartitionFinder2 v2.0.0 (Lanfear et al. 2012), with the selected models subsequently integrated into the BEAUti-generated XML configuration. To accommodate rate heterogeneity, a relaxed log normal molecular clock was applied, while tree topology and node ages were calibrated using a birth-death tree prior to account for potential shifts. The earliest known fossils assigned to each of the following genera were used to set a bound on the age of each group: Alticola, 1.5 million years ago (Mya, Serdyuk and Tesakov 2006); Myodes, 2.6 Mya (Repenning 1990). Fossil calibrations for Alticola (mean = 1.5 Mya, σ = 0.5) and Myodes (mean = 2.6 Mya, σ = 0.8) were applied as normal priors, followed by MCMC analysis (500 million generations, sampling every 5,000 steps). After checking convergence (ESS > 200 for all parameters) in Tracer v1.7.2 (Rambaut et al. 2018), the first 25% of generations were discarded as burn-in. The resulting posterior tree distribution was then processed in TreeAnnotator v2.7.4 (Bouckaert et al. 2019) to generate a Maximum Clade Credibility tree, with mean node heights calculated from the post-burn-in samples. Morphological analyses Morphological comparisons of Alticola yarlungia sp. nov. with congeners distributed in China included 88 adult specimens as follows: nine specimens for A. yarlungia sp. nov., zse.pensoft.net Tang, M.K. et al.: A new species of Alticola from Tibet2390 17 for A. albicauda, eight for A. argentatus, three for A. barakshin, 12 for A. macrotis, 15 for A. semicanus, 11 for A. stoliczkanus, and 13 for A. strelzowi. Among these taxa, only A. yarlungia sp. nov., and A. stoliczkanus occurred in Tibet (Fig. 1). Two individuals of A. barakshin, and three individuals of A. macrotis were deposited at the Xinjiang Center for Disease Control and Prevention (XJCDC), Xinjiang, China; and two specimens of A. macrotis were deposited at the Sichuan Center for Disease Control and Prevention (SCCDC), Chengdu, China. All remaining specimens are deposited at SAF, Chengdu, China (Suppl. material 2: appendix 2). External, cranial, and dental characteristics were measured for all the specimens. To increase sample sizes, measurable indicators of partial specimens whose skull was damaged were used for statistical analysis. The following external measurements were taken by the collectors in the field on freshly captured specimens and recorded to the nearest 0.1 mm: head body length (HBL), tail length (TL), hind foot length excluding claws (HFL), and ear length (EL). Cranial measurements were taken by Ming Kun Tang and Shao Ying Liu with a Vernier caliper to the nearest 0.01 mm following Yang et al. (2005), Xia et al. (2006) and Tang et al. (2018). Measurements included the skull greatest length (SGL), condylobasal length (CBL), zygomatic breadth (ZB), interorbital breadth (IOB), nasal length (NL), height of braincase (HB), length of maxillary toothrow (LMxT), length of upper molar row (LUMR), width of upper molar rows (M–M), length of lower molar row (LLMR), mandible greatest length (MGL), and mandible length excluding tooth (ML) (Suppl. material 2: appendix 2). Morphometric analyses were performed using SPSS v19.0. We compiled two datasets from 16 measurements: dataset 1 included Alticola yarlungia sp. nov. and the seven other species of Alticola distributed in China (A. albicauda, A. argentatus, A. barakshin, A. macrotis, A. semicanus, A. stoliczkanus, and A. strelzowi); dataset 2 comprised the three phylogenetically proximate or morphologically similar taxa (A. yarlungia sp. nov., A. stoliczkanus, and A. macrotis). Dataset 1 (n = 67 intact specimens) was subjected to factor analysis (FA) with principal component analysis as the extraction method. Prior to FA, data suitability was confirmed by Kaiser-Meyer-Olkin (KMO = 0.863) and Bartlett’s sphericity tests (P < 0.01). For dataset 2, we conducted: (1) one-way multivariate analysis of variance (MANOVA) using Pillai’s trace statistic to assess overall group differences; (2) one-way analysis of variance (ANOVA) for each measurement; and (3) post-hoc comparisons (Tukey’s test for equal variances, Tamhane’s T2 for unequal variances) between A. yarlungia sp. nov. and A. macrotis, and A. yarlungia sp. nov. and A. stoliczkanus. The glans penis was prepared following the methods of Hooper (1958). Description of baculum followed Liu et al. (2012, 2022). All organs and bacula were illustrated to scale using a camera lucida. Three species’ glans penes were prepared, including Alticola yarlungia sp. nov., A. stoliczkanus, and A. macrotis. Results Molecular results The trees resulting from the BI and ML analyses for each dataset had similar topologies and, therefore, only the BI trees were presented here (Figs 2A, 3). The topologies based Figure 1. Collection localities of specimens of Alticola from China examined in this study. Zoosyst. Evol. 101 (4) 2025, 2387–2403 zse.pensoft.net 2391 Figure 2. Phylogenetic relationships and species delimitation within Alticola and relative genera. A. Bayesian inference tree based on concatenated mitochondrial (three genes) and nuclear (four genes) sequences; B. Results of species delimitation analysis. Nodal support is indicated as Bayesian posterior probabilities (PP) / maximum likelihood bootstrap percentages (BP). The clade containing A. yarlungia sp. nov. is highlighted in orange, indicating its position within the genus and its sister-species relationship (consistent with Figs 3, 4). csd2046 WL18337 RAP09N074 NC_016055 GGS22353 GGS22010 GGS22011 VT439 CHBS015 CHBS016 KT725595 NC_029477 SKCPcb1 XJ174 AL4445 AT61090 AB179592 XJ18410 HS5743 RAP09138 Alem555 ZINRAS_90981 XJ24063 XJ17086 DQ845185 MC692 Aolc3124 AT2461 AB179584 Aa21745 MSB_269628 CHBS018 MK482363 AL554 XJ24041 XJ21089 XJ24062 MSB_158508 XJ289 Aolc3125 AT2470 AT2472 AS27253 XZ22081 XZ23512 XZ23458 XZ23459 XJ93141 AB233811 VT447 XJ21183 XJ21127 MSB_269629 AL149892 XJ24007 XJ24027 AS2564 AS94156 AS98512 AO61009 XJ20007 XJ20008 GB0828002 XZ23504 XJ23027 XJ23002 XJ23016 XJ21175 XJ21179 XJ21090 XJ21006 XJ21101 AS5969 DQ845190 AS179045 AS2474 AS2476 AO61010 AO61013 XZ16078 XZ16N119 XZ16N121 XJ23001 VT406 AS233671 XJ21007 AS179593 XZ16N120 XZ16N126 NMG22015 NMG22013 NMG22012 NMG22014 0.03 A. strelzowi A. olchonensis A. semicanus A. tuvinicus A. stoliczkanus A. yarlungia A. barakshin A. montosus A. albicauda sp. nov. A. macrotis M. rutilus M. centralis A. lemminus C. rufocanus V. millicenss N. irene Alticola s. str. Aschizomys + Myodes Outgroups A. argentatus Platycranius mtDNA+nuDNA 0.9/80 0.9/86 1/100 1/100 1/99 1/100 1/99 1/89 1/99 1/97 1/100 1/100 1/96 0.72/43 1/100 ASAP mPTP XJ23028 BPP AB Craseomys zse.pensoft.net Tang, M.K. et al.: A new species of Alticola from Tibet2392 on datasets 1 and 3 were similar, but these differed from that of dataset 2. Notwithstanding, the five specimens of Alticola yarlungia sp. nov. formed a well-supported clade in each tree, and as the sister clade of A. stoliczkanus with high Bayesian posterior probability (PP) and bootstrap percentages (BP) values. The BPP, ASAP and mPTP analyses on dataset 3 supported 12, 11 and 14 species within Alticola, respectively, with all methods consistently delimiting A. yarlungia sp. nov. as an independent lineage (Fig. 2B). The K2P distances for CYTB among Alticola taxa ranged from 4.0% to 12.3%, while the p-distances ranged from 3.9% to 11.1% (Table 1, Suppl. material 1: table S2). The lowest values were observed between A. yarlungia sp. nov. and A. stoliczkanus, while the highest were between A. macrotis and A. strelzowi. The K2P distances (and p-distances in parentheses) between A. yarlungia sp. nov. and the other 11 species ranged from 4.0% (3.9%) to A. stoliczkanus to 10.3% (9.5%) to A. macrotis, with an average of 8.1% (Table 1, Suppl. material 1: table S2). BEAST analyses revealed that the divergence between Alticola and Myodes approximately occurred at approximately 1.76 (95% highest posterior density (HPD) interval = 0.82–2.68) Figure 3. Bayesian phylogenetic trees of Alticola and related taxa inferred from A. Three concatenated mitochondrial genes and B. Four concatenated nuclear genes. Nodal support is indicated as Bayesian posterior probability / maximum likelihood bootstrap percentage (PP/BP). A. strelzowi A. olchonensis A. semicanus A. tuvinicus A. stoliczkanus A. yarlungia A. barakshin A. montosus A. albicauda sp. nov. A. macrotis M. rutilus M. centralis A. lemminus C. rufocanus V. millicenss N. irene Alticola s. str. Aschizomys + Myodes Outgroups A. argentatus NC_016055 GGS22353 csd2046 WL18337 RAP09N074 VT439 CHBS015 CHBS016 KT725595 NC_029477 SKCPcb1 XJ174 AL4445 AT61090 AB179592 XJ18410 HS5743 RAP09138 Alem555 ZINRAS_90981 XJ24063 XJ17086 DQ845185 MC692 Aolc3124 AT2461 AB179584 Aa21745 MSB_269628 CHBS018 MK482363 AL554 XJ24041 XJ21089 XJ24062 MSB_158508 XJ289 Aolc3125 AT2470 AT2472 AS27253 XZ22081 XZ23512 XZ23458 XZ23459 XJ93141 AB233811 VT447 XJ23028 XJ21183 XJ21127 MSB_269629 AL149892 XJ24007 XJ24027 AS2564 AS98512 AO61010 XJ20007 XJ20008 GB0828002 XZ23504 VT406 XJ23002 XJ23016 XJ21175 XJ21179 XJ21090 XJ21006 XJ21101 AS5969 DQ845190 AS179593 AS179045 AS94156 AS2474 AS2476 AO61009 AO61013 XZ16078 XZ16N119 XZ16N121 XJ23001 XJ23027 AS233671 XJ21007 NMG22013 XZ16N120 XZ16N126 NMG22015 NMG22012 NMG22014 0.05 Platycranius mtDNA 0.99/85 1/97 1/100 0.89/88 1/100 1/100 1/99 1/90 1/100 1/100 1/100 1/100 1/91 1/93 0.88/58 1/100 A. strelzowi A. olchonensis A. semicanus A. tuvinicus A. stoliczkanus A. yarlungia A. barakshin A. albicauda sp. nov. A. macrotis M. centralis A. lemminus C. rufocanus V. millicenss N. irene Alticola A. argentatus WL18337 CHBS016 GGS22353 XJ174 GGS22010 GGS22011 XJ21089 MSB_158508 XJ17086 RAP09138 XJ21127 CHBS015 RAP09N074 AB233811 XJ23001 XJ24062 XJ24007 XJ24027 XJ21090 XJ18410 XJ21183 XJ21175 XJ21179 XJ24041 XJ24063 XJ21101 NMG22015 XZ23459 XJ21007 NMG22013 AS2474 AS2476 XZ16N120 VT447 XJ23002 XJ23027 AS233671 XJ21006 NMG22012 NMG22014 AL4445 XJ20008 XZ22081 XZ16N119 XZ16N121 XZ16078 XZ16N126 GB0828002 XZ23512 XZ23458 XZ23504 XJ23016 XJ23028 Aolc3124 Aolc3125 AT2470 AT2472 AL149892 AL554 Alem555 0.005 nuDNA 1/100 1/100 1/91 1/98 1/83 1/85 0.52/64 0.44/26 0.75/26 0.82/73 1/52 1/92 1/98 1/100 AB Craseomys Myodes Craseomys Outgroups Table 1. Pairwise estimates of evolutionary divergence between Alticola taxa based on CYTB sequences, calculated under the K2P model. Taxon 1 2 3 4 5 6 7 8 9 10 11 1. yarlungia sp. nov. 2. stoliczkanus 0.040 3. macrotis 0.103 0.108 4. albicauda 0.081 0.093 0.117 5. argentatus 0.082 0.099 0.114 0.050 6. barakshin 0.057 0.062 0.110 0.087 0.083 7. semicanus 0.092 0.105 0.121 0.105 0.105 0.095 8. strelzowi 0.088 0.097 0.123 0.097 0.103 0.087 0.065 9. tuvinicus 0.092 0.103 0.117 0.108 0.106 0.102 0.053 0.065 10. montosus 0.082 0.102 0.095 0.074 0.063 0.079 0.099 0.106 0.102 11. olchonensis 0.084 0.097 0.113 0.097 0.096 0.090 0.045 0.059 0.041 0.093 12. lemminus 0.091 0.098 0.101 0.111 0.108 0.093 0.112 0.112 0.114 0.090 0.105 Zoosyst. Evol. 101 (4) 2025, 2387–2403 zse.pensoft.net 2393 Mya. The most recent common ancestor of A. yarlungia sp. nov. and A. stoliczkanus was reconstructed as the phylogenetically youngest divergence node (0.49 Mya, 95% HPD interval = 0.20–0.77), postdating the splits between the clades comprised of A. strelzowi and A. semicanus, and A. olchonensis and A. tuvinicus (Fig. 4). Morphological results The nine specimens of Alticola yarlungia sp. nov. (4 males, 5 females) were all adults, as indicated by complete ossification of the baculum even in the smallest individual (based on HBL). No sexual dimorphism was identified based on skull measurements of the male individual within the range of adult females. Comparisons of body and skull measurements between Alticola yarlungia sp. nov. and seven congeners, along with descriptions of morphological characteristics for all 12 species, were presented in Tables 2, 3, respectively. Side-byside photographic comparisons of pelages and molars were shown in Figs 5, 6. Morphological comparison of the penis and baculum were shown in Fig. 7. In terms of size, A. yarlungia sp. nov. was between A. macrotis and A. argentatus, being relatively bigger than A. stoliczkanus (Table 2). The following four morphological characters separated A. yarlungia sp. nov. from its congeners: (1) shortest LUMR and simplest structure of M3 with a significantly shortened posterior lobe (Fig. 6A1); (2) tail slender and indistinct bicolor, moderate in size, the length about a quarter (24.8%) of the HBL (Fig. 5, Table 3); (3) body dark brown dorsally compared to pale reddish-gray (A. albicauda), brownish Figure 4. Dated species tree of Alticola and related taxa based on three mitochondrial and four nuclear genes, with divergence times estimated using BEAST. Node annotations indicate: left - mean divergence times (blue; Mya) and 95% HPD interval (black; in square brackets); right - PP values (black). 3 2 1 0 A. stoliczkanus A. yarlungia A. macrotis A. lemminus M. rutilus A.semicanus A.olchonensis V. millicens C. rufocanus A. argentatus A. strelzovi M. centralis A. albicauda N. irene A. barakshin A. montosus A. tuvinicus 0.6 2.09 0.98 1.18 3.11 0.7 0.67 1.76 1.45 1.04 0.6 1.29 2.24 0.49 0.64 1.35 [0.84,3.31] [0.43,1.5089] [0.45,1.63] [0.58,1.98] [0.20,0.77] [0.28,1.00] [0.60,2.07] [0.26,0.93] [0.53,1.84] [0.30,1.09] [0.29,1.08] [0.82,2.68] [0.67,2.22] [0.25,0.94] [1.02,3.44] [1.39,4.28] sp. nov. Piacenzian Gelasian Calabrian Middle late PlicocenePleistocene Mya 1 1 1 1 1 1 1 1 1 1 1 0.76 1 1 1 1 zse.pensoft.net Tang, M.K. et al.: A new species of Alticola from Tibet2394 gray (A.argentatus, A. barakshin), and gray (A. semicanus, A. strelzowi) in other species (Table 3); (4) glans and bacula morphology of A. yarlungia sp. nov. differed from A. stoliczkanus and A. macrotis as follows: outer crater papillae (Fig. 7b), shape of proximal bacula (Fig. 7m), distal bacula (Fig. 7a), and lateral bacula (Fig. 7k), urethral lappet (Fig. 7A3, B3, C3), and dorsal papillae (Fig. 7A4, B4, C4). As shown in Table 4, the first three factors with eigenvalues greater than 1.0 (9.604, 2.178, and 1.103) collectively explained 80.53% of the total variance. The first factor (Factor 1) accounted for 60.02% of the total original variance and most variables (but not TL, HFL, EL, and IOB) had high positive loadings, suggesting that it related to size variation. The second factor (Factor 2) explained 13.62% of the total variance and it was positively correlated with TL and EL with factor loadings 0.882 and 0.759, respectively. Factor 3 accounted for 6.90% of the total variance, the main morphological variable was IOB, with relatively higher factor loading (0.885). In scatterplot, specimens of A. yarlungia sp. nov. and A. macrotis overlapped heavily at the center of the scatterplot, but separating from the specimens of other six species distinctly. Some specimens of A. stoliczkanus plotted near to the morphospace occupied by A. yarlungia sp. nov. and A. macrotis, suggesting that they have relatively similar body proportions and skull characteristics (Fig. 8). This result was consistent with the molecular phylogenetic trees (Figs 2–4). The one-way MANOVA performed on morphometric dataset 2 obtained a significant difference among Alticola yarlungia sp. nov., A. stoliczkanus, and A. macrotis (Pillai’s trace = 1.925, F = 7.985, df = 32, error df = 10, P < 0.01). The ANOVA result also obtained significant differences between the three taxa for HBL, TL, HFL, EL, NL, and HB (Suppl. material 1: table S3). Further, Tukey’s (or Tamhane’s T2) post-hoc tests revealed statistically significant differences in HBL, TL, HFL, EL, and HB between A. yarlungia sp. nov. and A. stoliczkanus. Table 2. External and cranial measurements (mm) of eight taxa of Alticola from China (Mean ± SD (range; n = number of specimens); for abbreviations see Materials and methods). Measurement Holotype A. yarlungia sp. nov. A. stoliczkanus A. macrotis A. albicauda A.argentatus A. barakshin A. semicanus A. strelzowi HBL 104 102.00 ± 5.90 (92~110; n = 9) 91.91 ± 3.91 (85~98; n = 11) 96.74 ± 3.60 (88~101.4; n = 12) 104.94 ± 7.91 (92~120; n = 17) 102.25 ± 6.04 (94~111; n = 8) 111.67 ± 11.93 (102~125; n = 3) 110.8 ± 7.87 (100~128; n = 15) 104.38 ± 9.36 (90~124; n = 13) TL 24 25.22 ± 1.79 (23~28; n = 9) 20.09 ± 1.87 (17~23; n = 11) 29.76 ± 2.80 (27~36; n = 12) 45.32 ± 4.7 (39~55; n = 17) 39.63 ± 5.32 (33~47; n = 8) 23 ± 1 (22~24; n = 3) 34 ± 2.14 (30~37; n = 15) 41.31 ± 4.73 (35~50; n = 13) HFL 18 17.78 ± 0.67 (17~19; n = 9) 16.91 ± 0.83 (15~18; n = 11) 17.74 ± 0.57 (17~18.6; n = 12) 18.09 ± 1.18 (16~20; n = 17) 18.5 ± 1.2 (17~20; n = 8) 18.67 ± 1.53 (17~20; n = 3) 20.87 ± 0.92 (20~23; n = 15) 19.31 ± 0.75 (18~20; n = 13) EL 12 14.44 ± 1.24 (12~16; n = 9) 12.82 ± 0.4 (12~13; n = 11) 14.32 ± 0.81 (13~16; n = 12) 15.41 ± 0.87 (14~17; n = 17) 15.13 ± 0.64 (14~16; n = 8) 15.67 ± 1.15 (15~17; n = 3) 15.27 ± 0.96 (13~17; n = 15) 17.54 ± 1.13 (16~20; n = 13) SGL 24.77 25.03 ± 0.99 (23.43~26.2; n = 7) 25.18 ± 1.15 (23.46~27.01; n = 11) 25.29 ± 0.81 (23.9~26.21; n = 8) 26.33 ± 0.79 (25.03~27.96; n = 17) 26.48 ± 0.75 (25.75~27.86; n = 6) 28.13 ± 1.63 (27~30; n = 3) 28.4 ± 0.84 (27.5~29.84; n = 13) 27.09 ± 1.47 (24.87~29.11; n = 9) CBL 22.76 22.9 ± 1.00 (21.23~24.02; n = 7) 22.77 ± 1.17 (21.06~24.46; n = 11) 22.72 ± 1.07 (21.25~24.5; n = 8) 23.93 ± 0.93 (22.57~25.45; n = 17) 23.84 ± 0.83 (22.98~25.29; n = 6) 25.98 ± 1.74 (24.87~27.98; n = 3) 25.57 ± 1.02 (24.42~27.55; n = 13) 24.58 ± 1.3 (22.39~26.34; n = 9) ZB 13.35 13.53 ± 0.95 (11.71~14.88; n = 9) 13.14 ± 0.63 (12.25~14.04; n = 11) 13.38 ± 0.57 (12.5~14.1; n = 8) 13.8 ± 0.94 (12.62~15.38; n = 17) 14.03 ± 0.55 (13.51~14.99; n = 6) 15.2 ± 0.75 (14.5~16; n = 3) 14.91 ± 0.8 (13.87~16.44; n = 14) 14.57 ± 1.09 (13.4~16.22; n = 9) IOB 3.84 4.07 ± 0.15 (3.84~4.33; n = 9) 4.11 ± 0.23 (3.78~4.49; n = 11) 3.94 ± 0.17 (3.72~4.16; n = 9) 4.03 ± 0.2 (3.74~4.41; n = 17) 4.22 ± 0.2 (3.94~4.47; n = 6) 4.07 ± 0.06 (4~4.1; n = 3) 4.29 ± 0.15 (4.07~4.57; n = 14) 4.53 ± 0.23 (4.3~5; n = 9) NL 7.49 7.66 ± 0.47 (7.05~8.34; n = 9) 7.73 ± 0.6 (6.87~8.58; n = 10) 6.81 ± 0.44 (6.09~7.25; n = 6) 8 ± 0.36 (7.55~8.98; n = 16) 8.04 ± 0.49 (7.59~8.93; n = 6) 8.68 ± 0.55 (8.34~9.32; n = 3) 8.67 ± 0.43 (8.2~9.42; n = 13) 7.71 ± 0.77 (6.75~8.86; n = 8) HB 9.06 9.15 ± 0.37 (8.66~9.62; n = 7) 9.64 ± 0.32 (9.24~10.33; n = 11) 9.33 ± 0.45 (8.67~10.14; n = 9) 9.74 ± 0.4 (9.2~10.3; n = 17) 9.83 ± 0.29 (9.56~10.35; n = 6) 10.82 ± 0.4 (10.55~11.28; n = 3) 10.18 ± 0.3 (9.72~10.76; n = 14) 7.87 ± 0.33 (7.17~8.25; n = 9) M–M 4.81 5.13 ± 0.16 (4.81~5.37; n = 9) 5.11 ± 0.27 (4.81~5.61; n = 11) 5.06 ± 0.17 (4.84~5.27; n = 6) 5.11 ± 0.18 (4.88~5.46; n = 16) 5.16 ± 0.23 (4.85~5.48; n = 6) 5.66 ± 0.33 (5.46~6.04; n = 3) 5.55 ± 0.2 (5.26~5.9; n = 13) 5.1 ± 0.25 (4.64~5.49; n = 8) LMxT 14.44 14.78 ± 0.59 (13.83~15.54; n = 9) 14.64 ± 0.81 (13.57~15.99; n = 11) 14.08 ± 0.39 (13.57~14.54; n = 6) 15.37 ± 0.89 (14.47~17.74; n = 16) 15.35 ± 0.6 (14.68~16.15; n = 7) 16.2 ± 0.71 (15.74~17.02; n = 3) 15.98 ± 0.61 (15.3~17.09; n = 13) 14.8 ± 0.9 (13.77~16.28; n = 8) LUMR 5.12 5.58 ± 0.24 (5.12~5.85; n = 9) 5.53 ± 0.2 (5.31~5.82; n = 11) 5.60 ± 0.16 (5.43~5.86; n = 9) 5.81 ± 0.3 (5.46~6.48; n = 17) 5.72 ± 0.23 (5.49~6.13; n = 7) 5.79 ± 0.31 (5.56~6.14; n = 3) 6.07 ± 0.29 (5.71~6.52; n = 14) 5.6 ± 0.27 (5.2~6.17; n = 9) LLMR 5.29 5.57 ± 0.23 (5.29~6.05; n = 9) 5.53 ± 0.32 (5.14~6.1; n = 11) 5.29 ± 0.35 (4.48~5.62; n = 9) 5.81 ± 0.29 (5.42~6.4; n = 17) 5.67 ± 0.14 (5.43~5.91; n = 8) 5.82 ± 0.34 (5.61~6.22; n = 3) 6.1 ± 0.31 (5.74~6.68; n = 14) 5.34 ± 0.24 (4.89~5.76; n = 9) MGL 17.35 17.63 ± 0.84 (16~18.54; n = 9) 17.7 ± 1.07 (15.95~19.55; n = 11) 17.54 ± 0.60 (16.79~18.37; n = 9) 18.26 ± 0.84 (17.29~19.64; n = 17) 18.2 ± 0.47 (17.7~18.96; n = 8) 20.02 ± 1.23 (19.28~21.44; n = 3) 19.27 ± 0.74 (18.27~20.56; n = 14) 17.84 ± 0.91 (16.67~19.01; n = 9) ML 14.52 14.87 ± 1.02 (13.07~16.33; n = 9) 15.4 ± 0.85 (14.05~16.58; n = 11) 14.84 ± 0.23 (14.48~15.19; n = 6) 15.71 ± 0.63 (14.87~16.62; n = 16) 15.59 ± 0.59 (14.9~16.64; n = 8) 17.03 ± 1.2 (16.33~18.42; n = 3) 16.89 ± 0.58 (16.16~17.94; n = 13) 15.47 ± 0.73 (14.59~16.55; n = 8) Note: Sample sizes (n) vary for some measurements due to damage or incomplete preparation of specimens. Zoosyst. Evol. 101 (4) 2025, 2387–2403 zse.pensoft.net 2395 Also, A. yarlungia sp. nov. and A. macrotis differed significantly in HBL, TL, and NL (Suppl. material 1: table S3). The glans penis morphology of Alticola yarlungia sp. nov. exhibited distinct differences in outer crater papillae, proximal, distal and lateral bacula, urethral lappet, and dorsal papillae with A. stoliczkanus and A. macrotis (Fig. 7). It had 4–5 outer crater papillae each side, whereas A. stoliczkanus had only one, and A. macrotis lacked them entirely (Fig. 7b). The base of the proximal baculum was semicircular shape in A. yarlungia sp. nov., while it was slightly enlarged in A. stoliczkanus and A. macrotis (Fig. 7m). In A. yarlungia sp. nov., the distal and lateral bacula were slender, and the lateral bacula possessed a sharp tip, distinguishing them from those of A. stoliczkanus and A. macrotis (Fig. 7a, k). Table 3. Morphological characteristics comparison between Alticola yarlungia sp. nov. and 12 congeners. Species Body Tail Skull and Molar A. yarlungia sp. nov. Dorsum dark brown, sides and venter gray with pure white tips, sharply demarcated. Tail relatively short and slender, sparsely haired (mean TL/HBL ratio 24.8%); indistinctly bicolored, light brown dorsally and gray white ventrally, with a terminal tuft approximately 7 mm long. Skull smallest in size. LUMR is the shortest. M3 is the simplest, characterized by a significantly shortened posterior lobe. It exhibits two lingual reentrant folds creating two well-developed angles, with the posterior lobe itself forming a third lingual angle. On the labial side, there are three angles; the first labial reentrant is very shallow, while the second is broad and deep. A. stoliczkanus* Tibetan specimens: dorsum bright ferruginous brown, venter white, the two colors sharply divided. Xinjiang specimens: dorsum dull pale brown. Tail shortest (mean TL/HBL ratio 21.9%); covered with stiff fulvescent-white hair, extending approximately 13 mm beyond the tail tip. Skull smallest in size. M3 reduced, with three labial and two lingual salient angles, and a slight trace of a fourth labial angle and a third lingual angle behind; the second labial reentrant is very wide, and the second lingual reentrant always shallow or absent; the posterior lobe is less than half of M3. A. macrotis* Dorsum generally dark brownish-gray; sides and venter gray, hairs tipped with pure white, coloration sharply demarcated. Tail relatively short (mean TL/HBL ratio 30.8%); distinctly bicolored, dark brown dorsally and whitish ventrally, with a distinct short hairy tip. Skull smallest in size. Depth of the first external reentrant angles of M3 is close to that of the second, occasionally almost as deep; M3 with three labial salient angles (occasionally a rudimentary fourth) and three lingual salient angles; posterior lobe of M3 usually points straight back; the surface of M³ typically exhibits only one closed space, with the second being nearly separate in some specimens occasionally with almost separated second. M1 has six closed fields, of which the first is occasionally incompletely separated from second. A. albicauda* Pale reddish-gray dorsally, venter hairs pure white with gray bases. Tail longest (mean TL/HBL ratio 43.2%); uniformly pure white, ending in a terminal tuft approximately 12 mm long. Skull moderate in size. LUMR longer; there are three outer and three inner salient angles in M3; the third labial reentrant fold is so reduced that the third triangle is rather broadly confluent with the posterior loop. A.argentatus* Dorsum a variable mixture of fawnbrown and gray tones, venter grayish to dirty-white, evenly demarcated from the sides. Tail moderate in length (mean TL/HBL ratio 38.7%); usually uniformly pale, but occasionally inconspicuously bicolored (dorsum light brown or straw-gray, venter pale). Skull relatively flat and moderate in size, with rather short orbit. M3 usually compressed anteriorly (with a narrow second labial infold) and possesses an elongated posterior loop; the third lingual angle is consistently well-developed and pointed. A. barakshin* Brownish-gray with dull rusty tone dorsally, venter dirty white. Tail shorter (mean TL/HBL ratio 20.8%); indistinct bicolored, light sandy-brownish dorsally and buffy white ventrally. Skull largest in size. M3 structurally simple, with only two lingual and three labial salient angles; the posterior lobe constitutes approximately half the tooth’s length. A. semicanus* Dorsum brownish mouse gray, venter buffy white, with dark based hairs. Tail relatively short (mean TL/HBL ratio 30.8%); uniformly buffy white with a terminal tuft, in some individuals the dorsum is light brown. Skull largest in size, angular and relatively flat. LUMR longest. M3 with three well-developed salient angles per side; its posterior loop shut off from the third triangle, rather long, with variable vestigial traces of fourth/fifth labial and fourth lingual angles. Enamel of M3 has four loops. A. strelzowi* Dorsum ashy gray, irregularly brightened by the yellowish or slightly rufous subterminal bands on the hairs; venter white, irregularly darkened by the slate-colored bases of the hairs. Tail moderate in length (mean TL/HBL ratio 39.6%); uniformly white or cream, occasionally slightly darker above (cream-buff) than below (cream-white). Skull larger in size, remarkably broad and flat, HB approximately half of ZB. M3 much simplified with three salient angles on each side, the first outer triangle small and broadly confluent with the anterior loop. A. montosa (True 1894; Hinton 1926) Dorsum dull grayish brown; venter silvery gray, darkened by slate bases of fur and without buffy suffusion. Tail longer (mean TL/HBL ratio ≈33% or more); bicolored, dusky above and whitish below; terminal tuft very short. Skull rather longer, narrower and flatter than in A. roylei; auditory bullae considerably larger. M3 with four labial and three lingual angles; M1 with four labial and four lingual angles, its first labial angle as long as the subsequent ones. In M3, the middle labial and lingual angles alternate, creating a nonlozenge-shaped space between them. A. lemminus (Bodrov et al. 2016; Holden et al. 2017) Dorsum ash gray washed with brown, venter whitish gray, and flank demarcation distinct. Tail shortest, TL/HBL ratio about 16–24%; distinctly bicolored, blackish brown above and gray below, with a distinct tuft. Skull small, semicircular, and delicate. Molars resemble those of Myodes rather than Alticola. On M3, the first labial reentrant fold is distinctly deeper, enamel is thick, cement accumulation is modest, and angles are rounded. M3 has four salient angles on each side. A. olchonensis (Bodrov et al. 2016; Holden et al. 2017) Dorsum gray and washed brown, venter whitish with buffy shades. Tail relatively short (27–32% of HBL); bicolored and densely haired, with a distinct terminal tuft. Skull closely resembles the more widespread A. tuvinicus. M3 with three or four lingual angles and three labial angles; the second labial reentrant fold usually wide. A. roylei (Hinton 1926) Dorsum rich dark brown, venter gray, darkened by slate-based hairs, with no sharp demarcation from the dorsum. Tail moderate in length (TL/HBL ratio 33–36%); sharply bicolored, dark brown above and grayish-white below. Skull strongly built, with ZB sometimes exceeding 60% of CBL; auditory bullae small and rounded. Cheek teeth robust. M3 with at least three salient angles on each side; the third lingual angle is always well developed, often showing vestiges of a fourth angle on the lingual, labial, or both sides. M1 with four labial and five lingual salient angles. A. tuvinicus (Rossolimo et al. 1994; Bodrov et al. 2016; Holden et al. 2017) Dorsum generally dull ash-gray, often with brown tones, venter typically grayish-pale. The flank demarcation is usually straight. Tail longer (TL/HBL ratio 32–46%); sharply or gradually bicolored, with the dorsal color typically matching the tone of the back. Skull large; braincase rather flattened (though less so than in A. semicanus). 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Gene markers, primer sequences and best-fit models used for phylogenetic analysis in this study. table S2. Pairwise estimates of evolutionary divergence (p-distance) among Alticola taxa based on CYTB. table S3. Results of ANOVA and post-hoc comparisons (Tukey’s or Tamhane’s T2 test) among Alticola yarlungia sp. nov., A. stoliczkanus, and A. macrotis (*P < 0.05, **P < 0.01). Copyright notice: This dataset is made available under the Open Database License (http://opendatacommons. org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited. Link: https://doi.org/10.3897/zse.101.170704.suppl1 Supplementary material 2 Supplementary information 2 Authors: Ming Kun Tang, Hong Qiu, Bu Qing Peng, Rui Liao, Robert W. Murphy, Xu Ming Wang, Xuan Pan, Xin Wang, Shao Ying Liu Data type: xls Explanation note: appendix 1. Sampling information including localities and GenBank accession numbers for specimens used in this study. appendix 2. Information on specimens used for morphological analysis (see methods for abbreviations). Copyright notice: This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited. Link: https://doi.org/10.3897/zse.101.170704.suppl2