Research Article |
Corresponding author: Alexander E. Balakirev ( alexbalakirev@mail.ru ) Academic editor: Melissa TR Hawkins
© 2021 Alexander E. Balakirev, Alexei V. Abramov, Viatcheslav V. Rozhnov.
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.
Citation:
Balakirev AE, Abramov AV, Rozhnov VV (2021) Distribution pattern and phylogeography of tree rats Chiromyscus (Rodentia, Muridae) in eastern Indochina. Zoosystematics and Evolution 97(1): 83-95. https://doi.org/10.3897/zse.97.57490
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The study combines available data on species distribution in eastern Indochina to investigate the phylogeographical genetic and morphological diversity of tree rats (Chiromyscus, Rodentia, Muridae) and to specify their natural ranges. We examined the diversity and distribution of tree rats over its range, based on recent molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, RAG1 and GHR) genes. The study presents the most complete and up-to-date data on the distribution and phylogeography of the genus in eastern Indochina. As revealed by mitochondrial genes, C. langbianis splits into at least four coherent geographically-distributed clades, whereas C. thomasi and C. chiropus form two distinctive mitochondrial clades each. Chiromyscus langbianis and C. chiropus show significant inconsistency in nuclear genes, whereas C. thomasi shows the same segregation pattern as can be traced by mitochondrial markers. The Northern and Southern phylogroups of C. thomasi appear to be distributed sympatrically with northern phylogroups of C. langbianis in most parts of eastern Indochina. The mitochondrial clades discovered are geographically subdivided and divergent enough to suspect independent subspecies within C. langbianis and C. thomasi. However, due to the insufficiency of obvious morphological traits, a formal description is not carried out here. The processes of recent fauna formation, species distribution patterns, dispersion routes and possible natural history in Indochina are discussed.
biodiversity, Indochina, Southeast Asia, taxonomy, tree rats, Vietnam
Genus Chiromyscus Thomas, 1925 is currently assigned to the Dacnomys division of the tribe Rattini (
To date, Thomas’ tree rat, C. thomasi, is known to be distributed from southwest China (
The evolution of the genus Chiromyscus was affected by the natural history of this region. Continuous forest cover in Indochina existed during a considerable proportion of the Pliocene and Pleistocene (
A great number of Chiromyscus specimens, obtained in Vietnam during a series of field expeditions of the Joint Russian-Vietnamese Tropical Research and Technological Centre between 2007 and 2018, were sampled for genetic analysis in full agreement with current Vietnamese regulations in the field of Nature Protection and Biodiversity Conservation. We followed the guidelines of the American Society of Mammalogists during the collection and handling of the animals used in this survey (Gannon et al. 2011). The museum specimens were kept in the Zoological Museum, Moscow State University, Moscow, Russia (
New samples were combined with sequences available in GenBank, including our sequences previously submitted (
List of geographical localities of Chiromyscus specimens used for genetic and morphological analyses.
No. (Fig. |
Species | DNA lineage | Locality | Elevation (m asl) | Latitude / Longitude |
---|---|---|---|---|---|
1 | C. langbianis | N lineage | China, Yunnan, Xishuangbanna | 22.0°N, 100.8°E | |
5 | C. langbianis | N lineage | Vietnam, Tuyen Quang, Khong May | 102 | 22.383°N, 105.339°E |
6 | C. langbianis | N lineage | Vietnam, Vinh Phuc, Tam Dao | 850 | 21.452°N, 105.636°E |
7 | C. langbianis | N lineage | Vietnam, Lang Son, Huu Lien | 230 | 21.661°N, 106.362°E |
8 | C. langbianis | N lineage | Vietnam, Nghe An, Pu Hoat | 840 | 19.756°N, 104.796°E |
13 | C. langbianis | N lineage | Laos, Khammouane | 17.5°N, 105.33°E | |
13 | C. langbianis | N lineage | Laos, Khammouane, Pha Deng | 17.57°N, 105.23°E | |
14 | C. langbianis | N lineage | Vietnam, Quang Binh, Le Thuy, Sa Khia | 156 | 17.068°N, 106.601°E |
15 | C. langbianis | N lineage | Vietnam, Kon Tum, Kon Plong | 1030 | 14.722°N, 108.316°E |
16 | C. langbianis | N lineage | Vietnam, Kon Tum, Kon Chu Rang | 1020 | 14.505°N, 108.541°E |
17 | C. langbianis | N lineage | Vietnam, Gia Lai, Kon Ka Kinh | 900 | 14.203°N, 108.315°E |
19 | C. langbianis | S lineage | Vietnam, Lam Dong, Bi Doup-Nui Ba | 1400–1800 | 12.179°N, 108.679°E |
11 | C. langbianis | Hainan lineage | China, Hainan, Jianfengling | 18.74°N, 108.85°E | |
12 | C. langbianis | Hainan lineage | China, Hainan, Baoting | 18.641°N, 109.775°E | |
18 | C. langbianis | Cambodian lineage | Cambodia, Kaoh Kong,Thmar Bang, Tatai Leu | 11.961°N, 103.303°E | |
3 | C. thomasi | N lineage | Vietnam, Lao Cai, Bat Xat, Y Ty | 1830 | 22.624°N, 103.629°E |
4 | C. thomasi | N lineage | Vietnam, Son La, Muong Coi | 547 | 21.343°N, 104.749°E |
5 | C. thomasi | N lineage | Vietnam, Tuyen Quang, Khong May | 102 | 22.383°N, 105.339°E |
2 | C. thomasi | S lineage | Laos, Houay Sai, Houay Khot Station | 20.267°N, 100.4°E | |
9 | C. thomasi | S lineage | Vietnam, Nghe An, Xoong Con | 141 | 19.252°N, 104.318°E |
10 | C. thomasi | S lineage | Vietnam, Nghe An, Pu Mat | 200 | 18.957°N, 104.686°E |
13 | C. thomasi | S lineage | Laos, Khammouane, Pha Deng | 17.57°N, 105.23°E | |
15 | C. thomasi | S lineage | Vietnam, Kon Tum, Kon Plong | 1030 | 14.722°N, 108.316°E |
20 | C. chiropus | Vietnam, Lam Dong, Bao Loc | 650 | 11.837°N, 107.64°E | |
21 | C. chiropus | Vietnam, Dong Nai, Ma Da | 75 | 11.381°N, 107.062°E | |
22 | C. chiropus | Vietnam, Tay Ninh, Lo Go Xa Mat | 11.583°N, 105.933°E | ||
23 | C. chiropus | Vietnam, Ba Ria-Vung Tau, Binh Chau | 68 | 10.55°N, 107.483°E |
Small pieces of liver or muscle tissue were sampled in the field and stored in 96% ethanol. Total genomic DNA was extracted using a routine phenol/chloroform/proteinase K protocol (
Cyt b was amplified using H15915R, CytbRglu (
The PCR products were purified using a DNA Purification Kit (Fermentas, Thermo Fisher Scientific Inc., Pittsburgh, PA, USA). The resulting double-stranded DNA products were directly sequenced in both directions using the Applied Biosystems 3130 Genetic Analyzer with the BigDye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems, Waltham, Massachusetts, USA). All obtained sequences were deposited in GenBank (www.ncbi.nlm.nih.gov/Genbank; MK957014–MK957137). Niviventer spp., Rattus norvegicus and Mus musculus were used as outgroups.
Individual sequences were edited manually using BioEdit v. 7.1.11 (
Divergence time approximation was performed by Mega X (
In total, 63 intact skulls of adult Chiromyscus (15 C. chiropus, 35 C. langbianis and 13 C. thomasi) obtained from 19 genetically-investigated localities in Vietnam (see Table
Twenty measurements were taken from each skull by means of digital calipers to the nearest 0.01 mm: greatest length of skull (ONL), braincase breadth (BBC), braincase height (HBC), zygomatic breadth (ZB), interorbital breadth (IB), length of rostrum (LR), breadth of rostrum (BR), breadth of zygomatic plate (BZP), diastema length (LD), length of foramina incisive (LIF), breadth of foramina incisive (BIF), length of bony palate (LBP), breadth across the palatal bridge at the level of the first molar (BBP), distance from the anterior edge of the premaxillary to the posterior edge of the palatine (= postpalatal length, PPL), breadth of the mesopterygoid fossa (BMF), length of the bulla (LB), upper molar row length (CLM1-3), first upper molar breadth (BM1), first lower molar breadth (Bm1) and lower molar row length (CLm1-3). The cranial measurements followed
Principal components analysis (PCA) and canonical discriminant function analysis (DFA) were used to evaluate “distinctiveness” amongst the samples. A one-way analysis of variance (ANOVA) was performed to test the differences amongst groups on all cranial variables. The software programme Statistica 8.0 (StatSoft Inc., Tulsa, OK, USA) was used for all analytical procedures.
The most representative tree was constructed for 66 Cyt b sequences. The trees were well supported (PP = 1) (Fig.
The phylogenetic tree (Cyt b, Bayesian inference) for Chiromyscus genetic lineages radiation. The posterior probability values are presented at the nodes, and the branch lengths (scale bar at the bottom) are indicated above the nodes. The sample labels and locality numeration are indicated as in Fig.
Genetic distances (d, TN93+G+I, gamma = 1.48) for geographic populations and species of Chiromyscus as calculated based on the Cyt b gene sequence (1140 bp). Standard error (S.E.) estimates are shown above the diagonal.
C. langbianis (Hainan) | C. langbianis (Northern) | C. langbianis (Southern) | C. chiropus | C. thomasi (Northern) | C. thomasi (Southern) | |||
between group distances | within groups distances | |||||||
d (TN93+G+I, Tamura-Nei) | S.E. | |||||||
C. langbianis (Hainan) | 0.005 | 0.008 | 0.012 | 0.015 | 0.016 | 0.0061 | 0.0013 | |
C. langbianis (Northern) | 0.036 | 0.007 | 0.011 | 0.015 | 0.015 | 0.0097 | 0.0015 | |
C. langbianis (Southern) | 0.063 | 0.052 | 0.013 | 0.016 | 0.016 | 0.0080 | 0.0017 | |
C. chiropus | 0.129 | 0.123 | 0.130 | 0.014 | 0.013 | 0.0074 | 0.0015 | |
C. thomasi (Northern) | 0.179 | 0.188 | 0.187 | 0.166 | 0.008 | 0.0039 | 0.0013 | |
C. thomasi (Southern) | 0.186 | 0.191 | 0.192 | 0.162 | 0.063 | 0.0071 | 0.0016 |
Genetic distances (d; T3P, T92+I) for geographic populations and species of Chiromyscus as calculated based on the COI gene sequence (680 bp). Standard error (S.E.) estimates are shown above the diagonal.
C. langbianis (Northern) | C. langbianis (Southern) | C. langbianis (Cambodia) | C. chiropus (Lam_Dong) | C. chiropus (others) | C. thomasi (Northern) | C. thomasi (Southern) | |||
---|---|---|---|---|---|---|---|---|---|
between group distances | within groups distances | ||||||||
d (T3P: GTR) | S.E. | ||||||||
C. langbianis (Northern) | 0.0106 | 0.0100 | 0.0176 | 0.0243 | 0.0289 | 0.0305 | 0.0045 | 0.0020 | |
C. langbianis (Southern) | 0.035 | 0.0128 | 0.0183 | 0.0243 | 0.0296 | 0.0278 | 0.0022 | 0.0021 | |
C. langbianis (Cambodia) | 0.033 | 0.044 | 0.0190 | 0.0242 | 0.0264 | 0.0292 | |||
C. chiropus (Lam_Dong) | 0.083 | 0.089 | 0.093 | 0.0121 | 0.0262 | 0.0277 | 0.0050 | 0.0024 | |
C. chiropus (others) | 0.124 | 0.130 | 0.127 | 0.040 | 0.0294 | 0.0307 | 0.0022 | 0.0021 | |
C. thomasi (Northern) | 0.156 | 0.161 | 0.138 | 0.155 | 0.172 | 0.0131 | 0.0110 | 0.0036 | |
C. thomasi (Southern) | 0.163 | 0.153 | 0.154 | 0.160 | 0.178 | 0.049 | 0.0037 | 0.0026 |
Another tree constructed using the mitochondrial COI gene of 43 samples revealed another additional specific phylogenetic lineage (Suppl. material
Phylogenetic reconstructions, based on nuclear genes, did not allow us to clarify the relationships and the taxonomic rank of the distinctive phylogroups identified. Thus, only species-level clusters were reliably traced by the RAG1 gene tree constructed for the 26 available samples (Suppl. material
In addition to low support levels for many nuclear gene clades, tree-bisection-reconnection branch-swapping (PBS) analysis indicates an existence of conflicting phylogenetic signals, especially for segments within C. langbianis. In general, the low posterior probability values for internal branches and the conflicting phylogenetic signals in many lineages can be explained by a significantly slower evolution rate of nuclear genes (generally weak phylogenetic signal) and incomplete lineage sorting that may be the result of symplesiomorphy. The tree which constructed the concatenated sequence (Fig.
A. The phylogenetic time tree (Cyt b/COI/RAG1/GHR/IRBP genes, concatenated analyses Bayesian inference) for Chiromyscus genetic lineages radiation. The posterior probability values and average divergence time (Mya, in brackets) are presented at the nodes. Branches lengths are indicated above the branches. B. The position of Chiromyscus among most closely relative groups of rodents of SE Asia, marked by arrow (see
The descriptive statistics of the craniodental measurements for phylogenetic lineages of C. langbianis (two of four phylogroups discovered were available) and C. thomasi that were identified by the abovementioned analyses are summarised in Suppl. material
In a principal components analysis (PCA) drawing on 20 craniodental measurements, the first two axes captured 60.9% (mainly reflecting general size) and 6.4% of the total variation, respectively. ONL, ZB, IB, LD, PPL and CLM1-3 were the six measurements that had the highest correlations with PC 1 (Suppl. material
The concordance of morphological and genetic traits and a good separation of samples in 3D factor space indicate the morphological specificity of the studied populations. On the other hand, the concordant pattern of morphological, genetic and clear geographic subdivision of the mitochondrial phylogroups allow us to question the taxonomic status of these populations; in particular, they allow us to attribute the observed genetic lineages to distinct taxa.
The Northern genetic lineage of C. langbianis must be undoubtedly assigned to subspecies C. l. indosinicus Osgood, 1932. This taxon was described as Rattus indosinicus by
The genetic distances between the two phylogroups of C. thomasi correspond minimally to the subspecific level (Baker 2006). However, despite their considerable ages, these groups have no visually remarkable morphological differences (see Suppl. material
Tree rats are usually confined to forest environments and their dispersal is restricted by the forest edge. They usually do not spread beyond these limits and never cross wide deforested areas as they do not feel confident on open ground surface (
Estimated time to most recent common ancestor (Mya) for Chiromyscus based on Reltime method and the General Time Reversible model. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.9185); The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 54.21% sites). The time tree was computed using 1 calibration constraints.
Calibration | Clade A | Clade B | Clade C | Clade D | Clade E | Clade F | Clade G | |
---|---|---|---|---|---|---|---|---|
Mus/Rattus divergence point | Chiromyscus/Niviventer common ancestor | C. thomasi divergence point | C. chiropus divergence point | Northern/Southern lineages of C. thomasi divergence point | Cambodian lineage of C. langbianis divergence point | Southern lineage of C. langbianis divergence point | Hainan lineage of C. langbianis divergence point | |
Mean | 11.65 | 4.85 | 4.09 | 2.70 | 1.19 | 1.248 | 0.950 | 0.621 |
95% CI lower | 11.0 | 2.89 | 1.78 | 0.73 | 0.545 | 0.041 | 0.032 | 0.020 |
95% CI upper | 12.3 | 7.02 | 5.90 | 3.58 | 3.49 | 2.88 | 2.01 | 1.39 |
The split of C. thomasi into the Northern and Southern phylogroups happened before the split of the corresponding C. langbianis phylogroups and apparently is associated with antecedent global natural factor fluctuations. However, the recent distribution pattern of these species indicates that their natural history differs significantly amongst the populations that originate from different dispersion centres/refugia. As far as can be traced by the data available, C. thomasi does not reach the Dalat Plateau and more southern regions inhabited by C. chiropus and the Southern lineage of C. langbianis. At the same time, C. thomasi (both Northern and Southern phylogroups) appears to be distributed sympatrically with the Northern phylogroup of C. langbianis in most of eastern Indochina. This indicates that their possible migration routes alongside the Annamite Range occurred in two opposite directions, with C. thomasi moving northwards and C. langbianis moving southwards. The fact that C. thomasi did not participate in mammal fauna formation on Hainan Island supports the recent natural area expansion of C. langbianis and are probably explained by ecological factors. Namely, these phenomena may reflect the ecological preferences of this species. C. thomasi is known to be more strictly associated with mountain forest formations than C. langbianis, showing greater habitat versatility, which apparently allowed the latter to spread much further eastwards along the plains of eastern Indochina. On the other hand, the significant genetic homogeneity of C. chiropus, which inhabits forest formations everywhere in the extreme south of Indochina and its basal position in relation to the genetic lineages of C. langbianis, may indicate that these recent populations diverged significantly earlier. This finding also indicates that forest refugia remained at the southern part of Indochina throughout the Holocene and even earlier. They could be associated not only with the Dalat Plateau, but also with the Cardamom Mountains, Bolaven Plateau and probably also with some of the offshore islands on the shelf of the Gulf of Siam.
The distribution pattern of Chiromyscus species in the region also raises the problem of the initial intrusion and distribution of C. chiropus in eastern Indochina. The terra typica for this species is the Karen Mountains in eastern Myanmar, where the species inhabit mountainous forests. As we pointed out earlier (
We show that the genetic distances between phylogroups of C. langbianis and C. thomasi correspond to the subspecific level at least. However, these phylogenetic groups do not demonstrate obvious univocal diagnostic differences in cranial features suitable for species diagnoses without special statistical analysis. Our study shows that the recent phylogenetic structure of C. langbianis is the most recent within the genus and appears within several independent refugia that remained isolated throughout the Pleistocene. In turn, the phylogroups of C. thomasi are likely older than those of C. langbianis. Environmental factors and species preferences followed recent natural ecological shifts which drove allopatry. However, C. chiropus demonstrates the greatest age; the ways of formation of the area of this species still remain obscure and are likely to be associated with changes in forest cover in Indochina and Malacca Peninsula during the Pleistocene. The possibility of competitive interaction of these species in the process of formation of their recent natural areas also cannot be excluded.
This study was realised with the support of the Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam. We thank Dr. Sergei V. Kruskop (Zoological Museum of Moscow State University, Moscow, Russia) and Olga V. Makarova (Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russia) for giving access to the collections under their care. We are grateful to Dr. Viktor V. Suntsov and Dr. German V. Kuznetsov, whose field collections of skulls and skins we used to investigate morphology. We thank Dr. Nguyen Dang Hoi, Dr. Bui Xuan Phuong, Tran Quang Tien, Le Xuan Son and Tran Huu Coi (all from the Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam), who put considerable effort into the expedition’s preparations. We also thank the administrations of Huu Lien, Ke Go, Kon Chu Rang, Kon Plong, Vinh Cuu Ma Da, Pu Mat, Pu Hoat, Bi Doup-Nui Ba, Lo Go Xa Mat and Binh Chau National Parks and Nature Reserves for their help with managing our research. We are also very grateful to Dr. Miguel Camacho Sanchez (Estación Biológica de Doñana, Sevilla, Spain) and Dr. Melissa T. R. Hawkins (Smithsonian Institution, National Museum of Natural History, Washington, USA) for their helpful and constructive comments on an earlier version of the manuscript. The study was partly supported by the programme of the Ministry of Science and Higher Education of the Russian Federation (project AAAA-A19-119082990107-3).
All authors participated in samples collection, AEB did the genetic analyses and wrote the main part of paper, AEB and AVA together performed the morphological analyses and prepared illustrations; VVR provided funding and coordinated all our surveys in Vietnam.
The study was performed in full agreement with current Vietnamese regulations in the field of Nature Protection and Biodiversity Conservation. We followed the guidelines of the American Society of Mammalogists during the collection and handling of the animals.
Tables S1–S6, Figures S1–S5
Data type: phylogenetic, morphological
Explanation note: Tables, samples and other refference materials.