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Article

Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes

1
Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
2
University of Chinese Academy of Sciences, Beijing 100049, China
3
Department of Evolution, Ecology & Biodiversity, University of California, Davis, CA 95616, USA
4
Department of Wildlife, Fish and Conservation Biology, University of California, Davis, CA 95618, USA
5
National Nature Conservation of Snake Island and Laotieshan Mountain, Dalian 116041, China
6
Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
7
Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin 150040, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2025, 16(3), 276; https://doi.org/10.3390/genes16030276
Submission received: 2 January 2025 / Revised: 12 February 2025 / Accepted: 14 February 2025 / Published: 25 February 2025

Abstract

:
Background: The phylogenetic resolution within the Gloydius halys-intermedius Complex remains debatable due to the following reasons: loci selection in previous studies varied between authors; limited dataset (1−5 mitochondrial or nuclear gene fragments); lack of sampling density; and nodal supports at specific nodes remain weak, specifically within Gloydius cognatus, G. halys, and G. stejnegeri. Objectives: To revise the taxonomic and phylogenetic relationships within the G. halys-intermedius Complex, we reconstructed the molecular phylogeny and performed species delimitation based on the complete mitochondrial genomes. Methods: In this study, twelve nomenclatural groups of Gloydius species were involved in the computation of Bayesian phylogenomic inference, five of the twelve nomenclature groups were newly sequenced, while the rest were acquired from the National Center for Biotechnology Information (NCBI). The Bayesian phylogenomic inference was constructed based on 13 mitochondrial protein-coding genes. Species delimitation was performed by two distance-based methods (ABGD and ASAP) and two tree-based methods (GMYC and bPTP). Results: This research resolved the systematic relationship within the G. intermedius Complex with the support of mitogenome-based phylogenomics, while indicating cryptic diversity within the Gloydius halys-intermedius Complex: G. intermedius samples from South Korea show as paraphyletic to the cluster of the samples from northeastern China. Species delimitation results based on four models resemble each other, supporting Gloydius caucasicus, G. cognatus, G. halys, and G. stejnegeri, each representing full species. The species delimitation results of this research also resemble the nomenclatural species based on previous morphometrical results. This research indicates that species delimitation efforts based on the phylogenomic approach would likely resolve complex evolutionary relationships.

1. Introduction

The Asian pit vipers, genus Gloydius Hoge & Ramano-Hoge, 1978, a group of small-bodied anterior-fanged snakes, widely distributed from northeastern to central Asia. This genus contains more than 23 specific-leveled clades spread throughout diverse habitats from temperate forests at lower elevations to alpine meadows at higher elevations, such as the Qinghai–Tibetan Plateau [1,2,3,4]. Morphometrics and previous molecular phylogenetics conducted in this genus indicate three intragenic lineages: the G. blomhoffii Complex, G. intermedius-halys Complex, and G. strauchi Complex [5,6].
The current molecular phylogenetics inference has resolved the systematic relationship at specific levels under both the G. blomhoffii Complex and G. strauchi Complex with strong nodal support [2,3,4,7,8,9,10]. However, due to complex overlapping distributions, possible interspecific gene flows, and less genomic data involvement within the G. intermedius-halys Complex, the evolutionary relationships and the species delimitation under this species complex remain debatable [5,11,12,13]. In the molecular phylogeny of Sino-distributed Gloydius species constructed by Xu et al. [14], the two taxa labeled as “G. intermedius” did not display monophyletic topology [14], and were subsequently clarified as misidentifications of specimens of the two different subspecies under G. halys. Shi et al. [13] initially reconstructed the molecular phylogenetics of the G. intermedius-halys Complex with combined mtDNA ND4 and Cyt b [13], indicating G. halys and G. stejnegeri each represents a valid taxon at specific level. This taxonomic conception has been accepted by most studies [1,2,3,11,15,16]. However, in several recent publications, the diversity of the G. intermedius-halys Complex is still underestimated, these species are still conflated as G. halys without illustrations or reliable data support [12,17,18].
In previous studies, little genomic data were used to construct molecular phylogeny compared to the accumulating sampling and sequencing strength in recent years. Previous data usually contains 2–5 mtDNA gene sequences or a combination of both mtDNA and nucDNA [1,2,3,4,13,14,16,19]. As a result, some nodal supports remain at questionable levels.
Recent studies on molecular species delimitation in reptiles and insects [20,21,22] have provided new approaches for resolving taxonomic problems at specific level. However, these efforts have not been applicated to Asian pit vipers yet. To provide higher-resolution molecular phylogenomic inference within the G. intermedius-halys Complex, with the support of accumulated genomic data and strong sequencing strength, multiple mtDNA genomes of the Sino-distributed Gloydius species were acquired. Hence, to further investigate the inter-specific evolutionary relationship within the G. intermedius-halys Complex, an initial phylogenomic inference and molecular species delimitation of Gloydius species were performed in this study.

2. Materials and Methods

2.1. Samples and DNA Extraction

In this study, five taxa of Gloydius were sampled. The detailed specimen information is listed in Table 1. In addition, the mitochondrial genome of seven Gloydius species were downloaded from GenBank for phylogenomic analysis. The distribution map of Gloydius in this study was drawn with ArcGis (Figure 1). Ophis okinavensis, a close relative of Gloydius, was selected to be the outgroup. Liver tissues were dissected to extract the whole genome using a TGuide Smart Universal DNA Kit (TIANGEN, Beijing, China) with the TGuide S16 Nucleic Acid Extractor. And the whole genome sample was deposited in a refrigerator at −20 °C at the Institute of Zoology, Chinese Academy of Sciences (IOZ, CAS).

2.2. Genome Sequencing, Assembly, and Annotation

The genomes were sequenced by the Illumina HiSeq 6000 platform at BerryGenomics (Beijing, China) with a 400 bp insert size and a pair-end 150 bp sequencing strategy. The sequence reads were first filtered with MitoZ 3.6 [23] at default parameters. Then, the remaining clean paired reads were assembled using GetOrganelle-1.7.7.1 [24]. The annotation of genes was performed by MitoZ and manually double-checked with Geneious 8.0.5 [25]. The composition of the mitochondrial genome was calculated with MEGA7 [26].

2.3. Phylogenetic Tree Construction and Pairwise Distance Estimation

The phylogenetic tree was constructed based on 13 mitochondrial protein-coding genes (PCGs, Appendix A). All the PCG sequences were extracted by the script, extract_genes.py (https://github.com/tjcreedy/biotools, accessed on 8 July 2024). After aligning each gene sequence with MAFFT v7.526 [26], all alignments were concatenated with PhyloSuite v1.2.2 [27]. Model determination for MrBayes (Bayesian inference, BI) was generated with ModelFinder [28]. The phylogenetic tree was reconstructed using MrBayes version 3.2.7a [1]. Two Markov chains in the Bayes phylogenetic tree ran simultaneously, totaling 600,000 generations. Samples were collected every 5000 generations, and the first 25% was discarded as burn-in. The phylogenetic trees were visualized with iDOL (https://itol.embl.de/, accessed on 15 July 2024). Pairwise distances of each two species were computed using the bootstrap method of 1000 replications, calculating the p-distance with MEGA7 [26], other detailed parameters and the results can be seen in Appendix B.

2.4. Molecular Species Delimitation

This research focused on the molecular species delimitation for the genus Gloydius (Appendix C). To conduct a molecular species delimitation, two distance-based methods (ABGD [20] and ASAP [27]) and two tree-based methods (GMYC [28] and bPTP [22]) were performed. The ABGD (Automatic Barcode Gap Discovery) is a convenient method for alignment-based species delimitation, it enables rapid classification of species, performing under the JC69 Jukes-Cantor model with relative gap width (X = 0.015). ASAP (Assemble Species by Automatic Partitioning) can automatically delineate species, reducing intervention and enhancing the objectivity and accuracy of species delimitation, performed at default settings. GMYC (Generalized Mixed Yule Coalescent) takes into account evolutionary processes, such as speciation and gene flow, to provide more precise species delimitation, with an ultrametric tree generated from MrBayes using multiple sequences per species. bPTP (Bayesian Poisson Tree Processes) delineate species by identifying temporal shifts between interspecific and intraspecific branches, offering high accuracy and resolution, executing 100,000 Markov chain Monte Carlo generations with a thinning of 100 and with 20% discarded as burn-in.

3. Results

3.1. The Composition of the Mitochondrial Genome

In this study, all Gloydius species contained a typical 37 genes (22 tRNA and 2 rRNA genes, and 13 PCGs, Appendix A). The five newly sequenced mitogenomes resembled the order in previous sequenced samples [1,2,3,4,13,16]. The gene rearrangement phenomenon is not present in this genus. The nucleotide compositions of these mitogenomes are shown in Table 2. These Gloydius species exhibited the same AT nucleotide bias: 58%. Moreover, these mitogenomes had both a positive AT skew (0.10–0.11) and a CG skew (0.37 to–0.38).

3.2. Phylogenetic Relationships

The topology of the Bayesian inference (BI) tree displayed an identical cladogram with those in previous studies [1,2,3,4,7]. Gloydius species were clustered in a strongly supported monophyletic group with 100/100 posterior probabilities on all of the nodes (Figure 2). Figure 2 illustrates the Bayesian phylogenetic inference based on 13 mitochondrial protein-coding genes. The topology reveals a well-supported monophyletic lineage for the Gloydius halys-intermedius Complex, with strong Bayesian posterior probabilities at essential nodes. Notably, G. caucasicus and G. stejnegeri form distinct branches, supporting their divergence at specific level.
The phylogenetic position of Gloydius himalayanus from the southern slopes of the Himalayan ranges, is basal to, and considerably distant from, other species of Gloydius (p-distance: 11.7−13.2%). Nine samples that represent G. halys-intermedius are clustered in a monophyletic group sister to another monophyletic group comprising G. brevicaudus and G. ussuriensis (G. blomhoffii Complex). However, the samples of G. intermedius from South Korea did not form a monophyletic group with the samples from northeast China, as is mentioned by Lee et al. (2022) [19]. The four samples of four species, G. caucasicus, G. cognatus, G. halys, and G. stejnegeri, display paraphyly even though they were treated as subspecies of G. halys [5] or one single species in previous studies [10,12,18]. The taxonomic relationship between those clades will be discussed in the species delimitation section.

3.3. Species Delimitation

The results of specific delimitation by two distance-based methods (ABGD [20] and ASAP [27]) and two tree-based methods (GMYC [28] and bPTP [22]) are shown as vertical black bars (Figure 3). The summary of molecularly delimited species of all four approaches was identical: all four approaches revealed 11 molecular clades of Gloydius within the samples included in this study, and resemble the morphological species delimitation opinion [5,13].
The G. halys-intermedius Complex, G. cognatus, G. caraganus, G. caucasicus, G. halys, and G. stejnegeri each represent a valid specific taxon based on the species delimitation techniques. Note that the two populations of G. intermedius from northeast China and South Korea are determined as two distinct species (p-distance 2.1%), indicating cryptic diversity that requires further investigation.

4. Discussion

This study provides a higher-resolution molecular phylogenomic inference within the G. intermedius-halys Complex, based on the complete mtDNA genomes of the Sino-distributed species of genus Gloydius which face prolonged debate from different scientific publications. The specific-level taxonomic relationships within the Gloydius halys-intermedius Complex are clarified by both molecular phylogeny and specific delimitation models. The results correspond with previous morphological studies [5,13]. The complex situation of the taxonomy and phylogeny of the G. halys-intermedius Complex may be caused by the interspecific or intraspecies gene flows between different adjacent habitats. A further phylogenomic inference of Gloydius species with more samples included is required in order to investigate the origin, evolution, and migration of Asian pit vipers. The results indicate the specific-leveled genetic differentiation between the populations of G. intermedius from South Korea and northeast China. Further advanced species delimitation is encouraged to investigate this cryptic diversity.
Increasing the sample density and sequencing strength have provided a solid platform for species delimitation reviews, and phylogenomic inference construction. n globally widespread and complex species systems, the use of nuclear loci in phylogenomics is gaining increasing popularity. At the same time, sequencing known regions, combinations, and newly developed regions has become a trend in advanced species delimitation projects. The utility of mtDNA loci in molecular phylogenetics remains advantageous when it comes to accessibility, and many studies combine nucDNA and mtDNA when performing computations. Although nucDNA loci have been actively used in recent projects, mtDNA phylogenetic analysis remains essential for assessing systematics in complex biogeographical regions. While the trend encourages the combined use of mtDNA and nucDNA in constructing molecular phylogenomics, inferences based on mitochondrial genomes still provide a reference topology for subsequent topology comparisons.

Author Contributions

Conceptualization, J.S. and M.B.; methodology, J.S. and L.J.; software, L.J.; validation, C.L., L.T. and S.F.; formal analysis, L.J., Z.X. and N.L.; investigation, C.L., L.T. and S.F.; data curation, J.S., S.H. and Z.X.; writing and original draft preparation, L.J., J.S. and Z.X.; writing—review and editing, Z.X. and N.L.; supervision, J.S.; project administration, M.B.; funding acquisition, J.S. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (NSFC No. 42202014, Jingsong Shi); the National Key R&D Program of China (No. 2022YFC2601200); and the project of the Northeast Asia Biodiversity Research Center (NABRI202203).

Institutional Review Board Statement

All experimental procedures were approved by the Animal Care and Ethics Committee at the Institute of Zoology, Chinese Academy of Sciences (IOZ-IACUC-2023-153, 1 January 2025).

Informed Consent Statement

Not applicable.

Data Availability Statement

All mitogenome sequences generated in this study were deposited in GenBank under accession numbers: PQ858434-PQ858438.

Acknowledgments

We are grateful to Qiu Xianchun, Wang Jinze, Zhou Shengbo, Yu Guoxu, Wu Zhongxun, Bao Yan, and Sun Baiyue for helping with the field work and molecular laboratory work. We thank Nikolai Orlov and Ananjeva Natalia for providing important samples for our study, and Seunghyun Lee for professional advice on data analysis. We are grateful to Jonathan Eisen for his assistance with language improvement.

Conflicts of Interest

The authors declare no conflicts of interest.

Appendix A

Table A1. The abbreviations and full names of 13 mitochondrial Protein-Coding Genes.
Table A1. The abbreviations and full names of 13 mitochondrial Protein-Coding Genes.
AbbreviationsFull Names
ND2NADH dehydrogenase subunit 2
COX1cytochrome c oxidase subunit I
COX2cytochrome c oxidase subunit II
ATP8ATP synthase F0 subunit 8
ATP6ATP synthase F0 subunit 6
COX3cytochrome c oxidase subunit III
ND3NADH dehydrogenase subunit 3
ND4LNADH dehydrogenase subunit 4L
ND4NADH dehydrogenase subunit 4
ND5NADH dehydrogenase subunit 5
ND6NADH dehydrogenase subunit 6
CYTBcytochrome b
ND1NADH dehydrogenase subunit 1

Appendix B

Appendix B.1

Table A2. The number of each species used for pairwise distances calculation.
Table A2. The number of each species used for pairwise distances calculation.
No.SpeciesVoucher Number
1G. caucasicusB474
2G. cognatusIA
3G. halysKM186844
4G. intermedius 2KM434236
5G. ussuriensisKP262412
6G. intermedius 1MW143075
7G. shedaoensisQ7
8G. stejnegeriS6
9G. brevicaudusB6
10G. himalayanusMK559438
11G. changdaoensisMT731652
12G. shedaoensisKT726956
13O. okinavensisAB175670-out

Appendix B.2

Table A3. The pairwise distances of each two species of Golydius.
Table A3. The pairwise distances of each two species of Golydius.
12345678910111213
1 0.0050.0050.0040.0090.0050.0050.0040.0080.0080.0050.0050.009
20.045 0.0050.0050.0090.0050.0050.0050.0080.0080.0050.0050.01
30.0370.037 0.0040.0090.0040.0040.0040.0090.0090.0050.0050.009
40.0360.040.026 0.0090.0030.0030.0040.0090.0080.0050.0030.009
50.1080.1130.1120.112 0.0090.0090.0090.0080.0080.0090.0090.009
60.0390.0420.0260.0210.114 0.0040.0040.0090.0080.0050.0040.009
70.0350.0440.030.0150.1140.026 0.0050.0090.0080.0050.0030.009
80.0330.0410.0310.0330.1140.0340.038 0.0080.0090.0050.0050.009
90.1160.1230.1250.1270.1060.1190.1290.119 0.0090.0090.0090.009
100.1140.1180.1250.1210.1140.1220.1170.1190.132 0.0080.0080.008
110.0420.0540.0510.0470.1090.0490.0460.0480.1180.115 0.0060.009
120.0420.0490.0360.0190.1120.0290.0110.0440.1270.1230.052 0.009
130.1370.1370.1390.140.1280.1370.1370.1390.1470.120.1290.14
Note: Estimates of Evolutionary Divergence between Sequences. The number of base differences per site from between sequences are shown. Standard error estimate(s) are shown above the diagonal. Codon positions included were 1st + 2nd + 3rd. All positions containing gaps and missing data were eliminated. There were a total of 1602 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [26]. The values less than 0.03 were marked with pink background.

Appendix C

Table A4. The samples used in this study for molecular species delimitation of Golydius.
Table A4. The samples used in this study for molecular species delimitation of Golydius.
SpeciesVoucher Number
O. okinavensis *AB175670-Ovophis okinavensis
G. shedaoensisMK064736_G._shedaoensis_CHS329
MK064611_G._shedaoensis_CHS090
MK064610_G._shedaoensis_CHS089
KY040587_G._s_shedaoensis_JS1408D2
KT726956_G._shedaoensis_shedaoensis
G. intermediusMK064735_G_intermedius_CHS327
MK064733_G_intermedius_CHS324
MK064614_G_intermedius_CHS095
KY040589_G_s_qianshanensis_JS1306Q4
KY040588_G_s_qianshanensis_JS150722
KM434236_G_intermedius
G. stejnegeriMK064732_G_stejnegeri_CHS323
MK064731_G_stejnegeri_CHS322
KY040601_G_stejnegeri_JS1508S4
KY040600_G_stejnegeri_JS1409S3
G_stejnegeri_S6
G. ussuriensisMK064730_G_ussuriensis_CHS318
MK064729_G_ussuriensis_CHS316
MK064612_G_ussuriensis_CHS092
KP262412_G_ussuriensis
G. brevicaudusMH220717_G_brevicaudus_ZJ121106
MH220697_G_brevicaudus_ZJ100802
MH153664_G_brevicaudus_DWF4
MH153663_G_brevicaudus_DWF3
MH153662_G_brevicaudus_DWF2
MF099695_G_brevicaudus_DWF04
MF099694_G_brevicaudus_DWF03
MF099693_G_brevicaudus_DWF02
KY040616_G_brevicaudus_DL70
KR046009_G_brevicaudus_SR153
KR046007_G_brevicaudus_SR151
KR046006_G_brevicaudus_SR150
KR046005_G_brevicaudus_SR149
G. halysKY040592_G_halys_JSSD1607H9
KY040591_G_halys_JSSD1508X3
KY040590_G_halys_SYNU1301908
KM186844_G_halys
G. intermediusJQ798882_G_intermedius_NIBRRP0000100199
JQ798881_G_intermedius_NIBRRP0000100251
MW143075_G_intermedius
G. changdaoensiMT731652_G_changdaoensis
G. caucasicusG_caucasicus_B474
Note: The star * represents outgroup.

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Figure 1. Distribution of molecular samples in this study. Each star represents a species of Gloydius.
Figure 1. Distribution of molecular samples in this study. Each star represents a species of Gloydius.
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Figure 2. A MrBayes tree of Gloydius based on 13 mitochondrial PCGs. O. okinavensis was used as the outgroup. The numbers under branches indicate posterior probabilities, respectively. The red ones are newly added in this study.
Figure 2. A MrBayes tree of Gloydius based on 13 mitochondrial PCGs. O. okinavensis was used as the outgroup. The numbers under branches indicate posterior probabilities, respectively. The red ones are newly added in this study.
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Figure 3. The molecular species delimitation of Gloydius based on COI gene with four methods (ABGD, ASAP, GMYC and bPTP). The samples delimitated as a single species are represented by a black bar. Every intermittent vertical black bar on the right side of the taxon name represents a single species determined by species delimitation (from left to right: ABCD, ASAP, GMYC, and bPTP). The numbers under branches indicate 100% posterior probabilities. Each color of the tips represents a species.
Figure 3. The molecular species delimitation of Gloydius based on COI gene with four methods (ABGD, ASAP, GMYC and bPTP). The samples delimitated as a single species are represented by a black bar. Every intermittent vertical black bar on the right side of the taxon name represents a single species determined by species delimitation (from left to right: ABCD, ASAP, GMYC, and bPTP). The numbers under branches indicate 100% posterior probabilities. Each color of the tips represents a species.
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Table 1. Samples used in this study.
Table 1. Samples used in this study.
Vouchers SpeciesLocations
AB175670Ovophis okinavensis *Japan, Okinawa Islands
B474G. caucasicusAzerbaijan, Lankaran Region
B6Gloydius brevicaudusLiaoning, China
IAG. cognatusBayan Obo, Inner Mongolia, China
Q7Gloydius shedaoensisWafangdian, Liaoning, China
S6Gloydius stejnegeriLingshi, Shanxi, China
KM186844Gloydius halysInner Mongolia, China
KM434236Gloydius intermedius 2Heilongjiang, China
KP262412Gloydius ussuriensisHeilongjiang, China
KT726956Gloydius shedaoensisLvshun, Liaoning, China
MK559438Gloydius himalayanusHimachal Pradesh, India
MT731652Gloydius changdaoensisChangdao, Shandong, China
MW143075Gloydius intermedius 1Samcheok-si, Gangwon-do, South Korea
Note: * Outgroup.
Table 2. Nucleotide compositions of the whole mitogenomes of five newly sequenced Gloydius species. Both the AT skew and GC skew values from five species were positive, and the GC skew amplitude was greater than that of AT skew.
Table 2. Nucleotide compositions of the whole mitogenomes of five newly sequenced Gloydius species. Both the AT skew and GC skew values from five species were positive, and the GC skew amplitude was greater than that of AT skew.
SamplesSpeciesLength /bpT%C%A%G%AT SkewCG Skew
B474G. caucasicus17,22426.028.832.213.10.110.37
B6Gloydius brevicaudus16,65526.128.532.213.20.100.37
IAG. cognatus17,22825.928.832.412.90.110.38
Q7Gloydius shedaoensis17,21625.828.932.412.90.110.38
S6Gloydius stejnegeri17,22526.028.732.412.90.110.38
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MDPI and ACS Style

Jin, L.; Xia, Z.; Liu, N.; Hou, S.; Lv, C.; Tang, L.; Feng, S.; Shi, J.; Bai, M. Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes. Genes 2025, 16, 276. https://doi.org/10.3390/genes16030276

AMA Style

Jin L, Xia Z, Liu N, Hou S, Lv C, Tang L, Feng S, Shi J, Bai M. Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes. Genes. 2025; 16(3):276. https://doi.org/10.3390/genes16030276

Chicago/Turabian Style

Jin, Lijie, Zuyao Xia, Ning Liu, Shengyue Hou, Chuandong Lv, Lianyou Tang, Shuguang Feng, Jingsong Shi, and Ming Bai. 2025. "Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes" Genes 16, no. 3: 276. https://doi.org/10.3390/genes16030276

APA Style

Jin, L., Xia, Z., Liu, N., Hou, S., Lv, C., Tang, L., Feng, S., Shi, J., & Bai, M. (2025). Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes. Genes, 16(3), 276. https://doi.org/10.3390/genes16030276

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