How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses

2018·7.7 MB·

by  Liu, Shao-Ying

ZOOLOGICAL RESEARCH
How many species of Apodemus and Rattus occur in
China? A survey based on mitochondrial cyt b and
morphological analyses
Shao-YingLiu1,*,KaiHe2,Shun-DeChen2,3,WeiJin1,RobertW.Murphy4,Ming-KunTang1,RuiLiao1,Feng-JunLi3
1SichuanAcademyofForestry,ChengduSichuan610081,China
2KunmingInstituteofZoology,ChineseAcademyofSciences,KunmingYunnan650223,China
3CollegeofLifeSciences,SichuanNormalUniversity,ChengduSichuan610066,China
4CentreforBiodiversityandConservationBiology,RoyalOntarioMuseum,TorontoM5S2C6,Canada
ABSTRACT BlackDeathplaguethroughoutEuropeandtheMediterranean
duringthe14thcenturyandkilled30%–60%oftheEuropean
Apodemus (mice)andRattus (rats)arethetoprodent
population (Barnett, 2001; Duplantier et al., 2003). More
reservoirs for zoonoses in China, yet little is known
recent examples of small mammal zoonoses include severe
about their diversity. We reexamined the alpha
acute respiratory syndrome (SARS) caused by a coronavirus
diversityofthesetwogenerabasedonanewcollection andEbolahemorrhagicfevercausedbyEbolavirus,withhosts
of specimens from China and their cyt b sequences including, butnotlimitedto, batsandcivets(Klein&Calisher,
in GenBank. We also tested whether species 2007; Menachery et al., 2015). Rodent-borne diseases
such as plague and hantavirus have made considerable
could be identified using external and craniodental
contributionstohumanillnessesandareresponsibleformore
measurementsexclusively. Measurementsfrom147
deathsthanallwarscombined(Klein&Calisher,2007). New
specimens of Apodemus and 233 specimens of
pathogens, especially hantaviruses, have been isolated from
Rattus wereusedformorphologicalcomparisons. We rodents in China and adjacent countries annually (Huang et
analysed74cytb sequencesofApodemus and100 al., 2017). Because different species have specific immune
cyt b sequences of Rattus to facilitate phylogenetic systemsanddifferentlevelsoftolerancetozoonoticinfections,
identification of rodent reservoirs of zoonotic pathogens is a
estimations. Resultsdemonstratedthatninespecies
highpriority(Meerburgetal.,2009).
of Apodemus and seven species of Rattus, plus a
Rats and mice often top the zoonoses reservoir list of the
new subspecies of Rattus nitidus, are distributed
Chinese Center for Disease Control and Prevention (China
in China. Principal component analysis using CDC) because of the large number of species, substantial
external and craniodental measurements revealed population sizes, and high potential for carrying zoonotic
that measurements alone could not separate the pathogens (Wu et al., 2017). Unfortunately, we still do
not know how many species of rats and mice occur in
recognizedspecies. TheoccurrenceofRattuspyctoris
inChinaremainsuncertain.
Keywords:Alphadiversity;Apodemus;DNA-barcoding;
Received: 20March2018;Accepted: 07May2018;Online: 19June
Rattus;Taxonomy;Phylogenies;Newsubspecies
2018
INTRODUCTION Foundation items: This research was funded by the National Natural
Science Foundation of China (31470110; 31301869; 31670388), Key
Small volant and nonvolant mammals are important
ResearchProgramoftheChineseAcademyofSciences(KJZD-EW-L07),
components of ecological communities and play vital roles in
Yunnan Applied Basic Research Projects (2014FB176), and China
ecologicalsystems.Theyareamongthemostcommonagents
for infections and, thus, have strongly affected human history. PostdoctoralScienceFoundation(2015M570801)
For example, black rats (Rattus rattus) are considered likely *Correspondingauthor,E-mail:[email protected]
agents for the spread of Oriental rat fleas, which drove the DOI:10.24272/j.issn.2095-8137.2018.053
SciencePress ZoologicalResearch39(5):309–320,2018 309
China, or which species carry what pathogens, even for the Rattus in China based on a collection of more than 400
most common genera such as Apodemus and Rattus. The specimens and the integration of cyt b sequences. We
reasonsforthisarecomplicated. BothApodemus andRattus evaluated the species of both genera in China and assessed
have complex evolutionary and taxonomic histories, with iftheycouldbeidentifiedeasilyusingtraditionalmorphometric
classificationscontinuouslybeingupdated. Switchingbetween approaches.
valid species and synonyms causes considerable confusion,
MATERIALSANDMETHODS
especially for non-specialist researchers. Furthermore, many
species occur only in remote mountains or near national Morphologicaldiagnosesandanalyses
borders with high species diversity, such as Yunnan, Xizang We examined 147 specimens of Apodemus and 233
(Tibet), and Xinjiang. Indeed, the rats and mice of southern specimens of Rattus collected from multiple localities across
Xizang and western Xinjiang remain to be studied carefully. China. External and skull measurements followed Liu et
Finally, many rodents are difficult to identify to species level al. (2012). External measurements of fresh specimens in
duetothenumberofmorphologicallysimilarspecies(Galanet the field were taken to the nearest 0.5 mm using a steel
al.,2012). tape.Theseincludedhead-bodylength(HBL),hind-footlength
ThelatestversionofMammalSpeciesoftheWorld(Musser (HFL),earlength(EL)andtaillength(TL)(museumspecimens
& Carleton, 2005) recognized 20 species of Apodemus and from original records). We measured eight skull variables
162 synonyms. Several scenarios for the classification of using a digital caliper graduated to the nearest 0.01 mm
Apodemushavebeenproposed(Filippucci,1992;Martinetal., from 147 intact skulls of Apodemus and 233 intact skulls
2000;Musseretal.,1995;Serizawaetal.,2000;Zimmermann, of Rattus, including greatest length of skull (SGL), nasal
1962), but none are strongly supported, and phylogenies bonelength(NBL),zygomaticbreadth(ZB),skullbasallength
remain poorly resolved despite molecular efforts (Liu et al., (SBL),uppertoothrowlength(UTRL),uppermolarrowlength
2004;Serizawaetal.,2000;Suzukietal.,2003). Furthermore, (UMRL), auditory bulla length (ABL), and mandible length
the number of species in China remains unknown, with (ML). Examined specimens (Supplementary Table S1) were
previousestimationsvaryingfromsix(Corbet,1978;Xia,1984), deposited in the Kunming Institute of Zoology (KIZ), Sichuan
seven (Liu et al., 2002; Liu et al., 2004), eight (Smith et al., AcademyofForestry(SAF),BeijingInstituteofZoology(BIZ),
2008), and nine species (Nowak, 1999; Wang, 2003). Many Guangdong Key Laboratory of Animal Conservation and
authors have suggested that A. sylvaticus occurs in Xinjiang, Resource Utilization, and Fujian Center for Disease Control
China(Corbet,1978;Xia,1984;Wang,2003),whereasothers Prevention.
havearguedthatthespeciesisA.uralensis(Smithetal.,2008). Specimens were roughly identified based on external and
The former species occurs in Western Europe (Bousbouras, craniodental morphology, following Kaneko (2010) and Smith
1999; Macholán et al., 2001; Mezhzherin & Zykov, 1991; et al. (2008). External and craniodental measurements largely
Michaux et al., 1996), and its incorrect identification in China overlappedbetweenspecies(seeResults)andwereinadequate
likelyrelatestooutdatedtaxonomy. for identification. However, several diagnostic characters on
Rattus,anotherproblematicgenus,hashad25subgeneraand the upper molars were constructive in classification, including
morethan550speciesandsubspeciesnamed(Simpson,1945). the number of lingual angles of the first and second upper
Currently, 66 species are recognized but uncertainty persists. molar, presence/absence of cusp t3 on the first upper molar,
Previous supermatrix analysis did not obtain a monophyletic and numbers of internal lobes on the third upper molars. We
Rattus,indicatingthatsystematicsisfarfromresolved(Steppan also cross-checked results based on morphological diagnoses
&Schenk,2017). Argumentsalsopersistforthemostcommon withmolecularsequences(whenavailable)torefineidentification.
species, including black rats whose species boundary remains Allspecimenswereidentifiedbythesameresearcher(SYL)for
unfixed (Aplin et al., 2011). The number of species of Rattus consistency. Wefinallyassignedourspecimenstoninespecies
in China is also uncertain and varies from four (Corbet, 1978), ofApodemus,sevenspeciesofRattus,andanewsubspeciesof
seven(Smithetal.,2008),andnine(Wang,2003). Rattusnitidus,respectively.
Similar to other rodents, species in these two genera We analyzed morphometric variation using principal
are difficult to identify or distinguish morphologically due to component analyses (PCAs) on log10-transformed variables
theirsimilarappearance,overlappingmeasurements,andkey usingtwodatasetsforeachspecies.Thefirstdatasetincluded
factors involving the single cusp on their teeth. Diagnosis both external and craniomandibular variables, whereas
often requires clean skulls, which are not always available or the second dataset included craniomandibular variables
correctly prepared. DNA barcoding is a promising approach only. Inclusion of the external data tested whether these
but requires a solid reference database (Moritz & Cicero, measurements could increase the accuracy of identification.
2004). Unfortunately,GenBankdataareproblematicbecause Statistical analysis was performed using SPSS v16.0 (SPSS
many rodent sequences are uploaded by non-specialists Inc., USA). When two or more recognized species were not
such as epidemiological researchers. This reduces the wellseparatedintheprincipalcomponent(PC)plots,analysis
reliability of environmental assessment reports and hampers of variance (ANOVA) was applied to analyze among group
ourunderstandingofhostanddiseaseassociations. differences.
Herein, we revisited the alpha diversity of Apodemus and
310 www.zoores.ac.cn
Molecularanalysis (PCR)wasconductedina25-µLreactionvolume,including2.5
We sequenced mitochondrial cyt b for 74 and 100 µLof10×EXTaqbuffer(Mg2+ Free),2µLof2.5mmol/LdNTP,
specimens of Apodemus and Rattus, respectively. Localities 1.5 µL of 25 mmol/L MgCl , 1 µL of 10 µmol/L primers, and
2
of molecular samples used from China are mapped in 1unitofEXTaqpolymerase(TaKaRaBiotech,Dalian,China).
Figure 1. All sequenced specimens were deposited in the TheproductwaspurifiedusinganEZNATM GelExtractionKit
SAF. Total genomic DNA was extracted using the standard (Omega,USA),andwassequencedusingthesameprimersfor
phenol-chloroform method (Sambrook & Russell, 2001). We amplificationonanABI3730XLsequencer. Sequenceswere
usedthFeuignivuerrseal Lpreimgeresnofdmsam maliancytbL14724/H15915 assembledandeditedusingSeqManandEditSeq(DNASTAR,
foramplification(Irwinetal.,1991).Polymerasechainreaction Lasergenev7.1)beforesubsequentanalyses.

Figure1FLigocuarlietie s1o Lfmoocleacluitlaierssa mopfl emsforolmecCuhilnaari nstahimssptuldeys from China in this study
To a void misidentification, we first conducted a “naïve than800bp.Wealsoincludedcytbdatarepresentinganother
identification” for the obtained sequences using the “identify 12speciesofApodemusand14speciesofRattusfromoutside
organis m” workflow in Geneious v11 (Biomatters, New of China. An additional five sequences of R. pyctoris from
Zealand ). The software blasted each sequence against the Nepal were included. For better estimation of phylogenetic
GenBanknucleotidecollection(nr/nt)database.Whenpairwise relationships, we downloaded the mitochondrial genomes

identity between the query (our sequence) and subject (in (mitogenomes)ofsevenspeciesofApodemusand14species
GenBan k) sequences was higher 98%, Geneious considered ofRattus (SupplementaryTableS2). Onemitogenomeunder
them as the same species. We cross-checked the results of thenameof“Apodemuschejuensis”maynothavebeenavalid
bothmorphologicalandmolecularidentifications,andwhenthe species. Cyt b of Tokudaia spp. (n=3) and a mitogenome of
identification was inconsistent, we revisited the skin and skull Bandicota indica were selected as outgroup representatives
specimensbeforeapplyinganidentity. for Apodemus and Rattus, respectively, following Steppan &
ToprovideabetterpictureofspeciesdiversityinChina,we Schenk(2017).Intotal,thedatasetsforApodemusandRattus
downloadedcytbsequencesofApodemus(n=477)andRattus included 572 (with seven mitogenomes) and 397 sequences
(n=273)inChinafromGenBank,discardingsequencesshorter (15mitogenomes),respectively. Wealignedthesequencesfor
ZoologicalResearch39(5):309–320,2018 311
eachgenususingMAFFTv7.3implementedinGeneiousv11. first and second principal components accounted for 57.6%
WeremovedalltRNAs,D-loop,andND6 sequencesfromthe (eigenvalue=6.9; Table 2, a) and 11.7% (eigenvalue=1.4) of
alignments,andonlyusedrRNAsand13protein-codinggenes totalvariation,respectively,withallotherprincipalcomponents
for phylogenetic analyses. Sequence genetic distances were having eigenvalues smaller than 1. PC1 was positively
calculatedforcytbusingMEGAv.5(Tamuraetal.,2011)under correlatedwithallcraniodentalvariables(loadings>0.63), and
theKimura2-parametermodel(Kimura,1980). PC2 was positively correlated with external measurements
(loadings>0.55). The PC1 and PC2 plot (Figure 2A) did not
Phylogeneticanalyses
clearly separate the species. Apodemus latronum plotted on
We employed RAxML v8.2.10, a maximum likelihood-based
the positive regions of PC1 and PC2, indicating a large body,
approach, for phylogenetic analyses. We partitioned the
long tail, long hindfeet, and long ears. In accordance with
alignmentsbygenes,exceptforcytb,whichwepartitionedinto
its small skull and small external measurements, A. uralensis
the1st+2ndand3rdcodonpositions. Analyseswereperformed
occurred along the negative regions of PC1 and PC2. The
on the CIPRES Science Gateway. We used GTR+G as the
sister- or closely related species A. agrarius and A. chevrieri
evolutionary model for each partition because RAxML does
aswellasA.pallipesandA.uralensiswerewellseparated,but
not accept models other than GTR or GTR+G. We ran each
bothpairsoverlappedwithA.peninsulae,A.draco,andA.ilex,
analysisusingtherapidbootstrappingalgorithmandletRAxML
which,inturn,largelyoverlapped. ForthesecondPCA,using
halt bootstrapping automatically. We also repeated analyses
eight craniodental measurements (n=141), the first principal
using alternative strategies, such as different partitioning
component accounted for 69.5% of variation (eigenvalue=5.6;
schemes (e.g., partitioned by gene and codon positions
Table 2, b). The other principal components accounted for
for all coding genes) and evolutionary models (e.g., using
lessthan9.4%(eigenvalue≤0.75)oftotalvariation, indicating
GTR model instead of GTR+G), none of which strongly
they were not stable (Shankardass, 2000). Seven variables
altered phylogenetic relationships (i.e., different relationships
werepositivelycorrelatedwithPC1(loading>0.56), exceptfor
supportedbybootstrapvalues(BS)≥75)).
UMRL (loading=0.076), which was positively correlated with
RESULTS PC2 (loading=0.93). The PC1 and PC2 plot (Figure 2B) was
similartothepreviousplot.Noneofthesespecieswereclearly
Morphologicalanalysis
separatedfromallothers.ApodemuschevrieriandA.latronum
MorphologicalanalysisofApodemus
plotted on the positive regions of PC1, indicating a relatively
Morphological measurement statistics of the eight Apodemus
largeskull,andA.uralensisoccurredalongthenegativeregion
species, excluding A. semotus, are given in Table 1. In
ofPC1inaccordancewithitssmallskull.
the first PCA, using all 12 measurements (n=139), the
A B
Figure2PrincipalcomponentanalysisofthefirstthreeprincipalFcigoumrep 2o nPernintcsipaaml coonmgpothneenet iganhatlysspise coife stheo ffirAspt othdreeem pursincbiapsael dcoomnponents
bothexternalandcraniomandibularvariables(A)andcraniomandibularvariablesonly(B)
among the eight species of Apodemus based on both external and
craniomandibular variables (A) and craniomandibular variables only (B)
312 www.zoores.ac.cn
Table1MeasurementstatisticsofApodemus
SGL NBL ZB SBL
n Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum
A.latronum 15 28.03 2.54 20.23 30.86 11.12 0.60 9.70 12.17 13.41 0.67 12.38 14.96 25.21 1.58 22.37 27.52
A.peninsulae 38 27.76 1.60 24.31 31.75 10.64 1.02 8.09 12.42 13.49 0.96 12.01 15.35 25.58 1.87 22.50 29.81
A.chevrieri 8 29.02 0.83 27.83 29.99 10.65 0.74 9.16 11.63 13.63 0.34 13.06 14.02 26.29 1.24 24.47 27.57
A.agrarius 41 26.57 0.97 24.55 28.51 9.55 0.53 8.50 10.67 12.56 0.52 11.23 13.34 24.65 1.20 20.82 26.73
A.ilex 10 26.63 1.25 25.31 28.88 10.10 0.79 9.13 11.44 12.61 0.37 12.09 13.31 23.42 1.19 22.17 25.45
A.draco 9 26.80 1.63 23.83 29.19 10.56 1.06 8.65 11.80 12.59 0.52 11.83 13.27 23.64 1.59 20.97 25.41
A.pallipes 12 26.84 0.58 25.76 27.98 10.37 0.37 9.45 10.95 12.73 0.26 12.26 13.13 23.63 0.56 22.37 24.30
A.uralensis 14 24.37 0.89 22.49 25.45 8.72 0.48 7.96 9.74 12.38 0.52 11.68 13.20 22.66 0.96 20.49 23.82
UTRL UOSL TBL ML
n Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum
A.latronum 15 14.41 0.76 12.94 15.60 5.00 0.23 4.47 5.39 5.52 0.35 4.90 6.38 10.48 3.58 6.16 14.41
A.peninsulae 38 13.71 0.94 11.52 15.82 4.27 0.29 3.41 5.10 5.34 0.40 4.53 6.17 13.25 1.11 11.02 15.79
A.chevrieri 8 14.55 0.64 13.57 15.52 4.59 0.23 4.24 4.91 5.90 0.25 5.52 6.19 14.61 0.67 13.70 15.74
A.agrarius 41 12.97 0.73 10.99 14.64 4.18 0.27 3.45 4.84 5.22 0.31 4.55 5.69 12.61 0.70 10.28 14.06
A.ilex 10 12.74 0.66 11.98 13.95 4.42 0.37 3.97 4.97 5.33 0.25 4.90 5.73 13.21 0.83 11.97 14.97
A.draco 9 13.10 0.72 11.98 14.03 4.24 0.06 4.15 4.35 5.23 0.35 4.50 5.62 13.03 1.09 11.36 14.32
A.pallipes 12 13.25 0.32 12.73 13.83 4.34 0.16 4.14 4.67 4.83 0.13 4.62 5.12 13.51 0.40 12.98 14.10
A.uralensis 14 11.23 0.47 10.51 12.00 3.60 0.25 2.89 3.82 4.68 0.29 4.30 5.23 11.57 0.50 10.50 12.28
HBL TL HFL EL
n Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum
A.latronum 15 100.90 9.84 88.00 115.00 104.27 8.41 90.00 122.00 24.17 0.98 22.50 26.00 20.20 0.80 19.00 22.00
A.peninsulae 38 100.32 11.96 73.00 137.00 94.26 10.96 72.00 121.00 22.95 1.59 18.00 25.00 16.08 1.58 14.00 21.00
A.chevrieri 8 102.50 8.78 90.00 113.00 94.12 9.40 82.00 105.00 23.63 1.69 21.00 26.00 16.12 1.89 13.00 18.00
A.agrarius 41 100.17 8.28 85.00 120.00 82.54 11.55 50.00 101.00 19.55 1.86 14.00 24.00 13.39 1.05 12.00 16.00
A.ilex 10 86.30 5.83 80.00 98.00 92.80 11.24 72.00 107.00 21.90 1.10 20.00 24.00 17.50 1.43 15.00 19.00
A.draco 9 92.11 9.85 75.00 103.00 105.11 12.08 84.00 119.00 48.89 77.30 21.00 255.00 17.33 0.71 16.00 18.00
A.pallipes 12 93.75 3.93 87.00 99.00 95.67 4.14 90.00 104.00 21.58 0.67 21.00 23.00 16.58 0.52 16.00 17.00
A.uralensis 14 83.86 7.31 67.00 94.00 74.36 4.99 65.00 83.00 19.82 1.14 18.00 22.00 12.11 2.65 9.00 17.00
AbbreviationsareexplainedintheMaterialsandMethodssection.Allmeasurementsareinmm.
ZoologicalResearch39(5):309–320,2018 313
One-wayanalysisofvariance(ANOVA)revealedthattheseven R.nitidus andR.andamanensis; BL,HBL,andELbetweenR.
species differed significantly (P<0.05) in all external and cranial nitidus and R. norvegicus; SGL, NBL, ZB, SBL, UTRL, UMRL,
characterstested,exceptforNBL(P=0.497),TL(P=0.064),and ML,BL,HFL,andELbetweenR.nitidus andR.exulans; SGL,
HFL(P=0.094).Resultsshowedsignificantdifferencesasfollows: ZB, SBL, UMRL, HBL, HFL, and EL between R. losea and R.
UTRL,MRL,ABL,andMLbetweenA.peninsulaeandA.chevrieri; tanezumi; SGL, NBL, ZB, SBL, UTRL, UMRL, ML, BL, HBL,
ZB,SBL,UTRL,HBL,andELbetweenA.peninsulaeandA.ilex; HFL, and EL between R. losea and R. andamanensis; SGL,
SGL, ZB, SBL, HBL, TL, HFL, and EL between A. peninsulae NBL, ZB, SBL, UTRL, UMRL, ML, BL, and HFL between R.
andA.draco; ZB,SBL,andABLbetweenA.peninsulae andA. losea and R. norvegicus; ML, BL, and HFL between R. losea
pallipes;SGL,ZB,SBL,UTRL,ABL,ML,HBL,andELbetweenA. and R. exulans; in HBL, HFL, and EL between R. losea and
chevrieri andA.ilex;SGL,ZB,SBL,MRL,UTRL,ABL,ML,HBL, R. rattus; UTRL between R. tanezumi and R. andamanensis;
TL,andHFLbetweenA.chevrieri andA.draco; SGL,ZB,SBL, UTRL, ML, BL, HBL, HFL, and EL between R. tanezumi and
UTRL,MRL,ABL,andMLbetweenA.chevrieri andA.pallipes; R. norvegicus; SGL, NBL, ZB, SBL, UTRL, UMRL, ML, BL,
TLandHFLbetweenA.ilexandA.draco;andABL,TL,andHFL HBL,HFL,andELbetweenR.tanezumi andR.exulans; HBL,
betweenA.dracoandA.pallipes. Thus,morphologicalanalysis HFL, and EL between R. andamanensis and R. norvegicus;
indicatedthattheeightspeciesofApodemuscouldbeseparated SGL,NBL,ZB,SBL,UTRL,UMRL,ML,BL,HBL,HFL,andEL
by the 12 morphological characters, validating the taxonomic between R. andamanensis and R. exulans; UMRL between R.
statusofthesespeciesinChina. andamanensisandR.rattus;SGL,NBL,ZB,SBL,UTRL,UMRL,
ABL,ML,andHFLbetweenR.norvegicusandR.exulans;HBL
Table2Factorloadingsandpercentageofvarianceexplained
and EL between R. norvegicus and R. rattus; and SGL, SBL,
forprincipalcomponentanalysis
BL,HBL,HFL,andELbetweenR.exulansandR.rattus. Thus,
Apodemus Rattus the12morphologicalcharactersseparatedthesevenspeciesof
a b c d RattusandvalidatedtheiroccurrenceinChina.
Variables PC1 PC2 PC1 PC2 PC1 PC2 PC1 PC2 WhenallindividualsofthetwosubspeciesofR.nitiduswere
SGL 0.82 0.07 0.83 0.08 0.96 –0.05 0.97 –0.03 subjected to an independent sample t-test for each variable,
NBL 0.64 0.39 0.84 0.08 0.89 –0.06 0.90 –0.03 significantdifferencesappearedinUTRL,UMRL,ML,andTL
ZB 0.83 0.00 0.99 –0.24 0.92 –0.08 0.92 –0.08 betweenR.nitidusnitidusandR.nitidusfromXizang.
SBL 1.01 –0.17 0.95 –0.09 0.97 –0.08 0.97 0.01
UTRL 0.80 0.23 0.72 0.37 0.95 –0.16 0.97 –0.19 Molecularanalysis
UMRL 0.29 0.55 0.08 0.93 0.71 0.15 0.71 –0.35
We obtained cyt b sequences for 78 specimens of
ABL 0.77 0.00 0.56 0.34 0.68 0.14 0.70 0.65
Apodemus and 106 specimens of Rattus. De novo
ML 0.64 0.24 0.71 0.17 0.92 –0.14 0.93 0.02
HBL 0.69 –0.09 N/A N/A 0.79 –0.25 N/A N/A sequencesweredepositedinGenBankunderaccessionNos.
TL 0.13 0.74 N/A N/A 0.67 0.52 N/A N/A MG748165–MG748348(SupplementaryTableS3).
HZL –0.04 0.82 N/A N/A 0.74 –0.24 N/A N/A Cyt b K2P interspecies distances for Apodemus ranged
EL –0.09 0.94 N/A N/A 0.40 0.84 N/A N/A
from5.4%to20.7%(SupplementaryTableS4). Thesmallest
Eigenvalues 6.9 1.4 5.60 0.75 7.99 1.21 6.32 0.57
Totalvariance distance occurred between A. uralensis and A. pallipes, and
57.6 11.7 69.50 9.40 66.54 10.08 79.05 7.08
explained(%) largestbetweenA.sylvaticus andA.latronum. Thedistances
for Rattus ranged from 2.1% to 16.5% (Supplementary Table
ForabbreviationsseeMaterialsandMethods.N/A:Notavailable.
S5). The smallest distance occurred between R. baluensis
MorphologicalanalysisofRattus and R. tiomanicus, and the largest between R. leucopus and
Morphological measurement statistics of the seven species of R.argentiventer. TheK2PdistanceofR.nitidus fromXizang
Rattus and a putatively new subspecies of R. nitidus (from andR.nitidusnitiduswas0.019.
southern Xizang) are given in Table 3. In the first PCA, which
usedall12measurements(n=233),thefirstandsecondprincipal Matrilinealgenealogy(haplotypephylogeny)ofApodemus
componentsaccountedfor66.54%(eigenvalue=7.99)and10.08% Matrilineal genealogy using the mitogenome and cyt b
(eigenvalue=1.21)oftotalvariation,respectively(Table2,c),with data for Apodemus (n=569) did not fully resolve the
all other principal components having eigenvalues smaller than higher relationships (Figure 4), as in previous studies (see
1. Most species largely overlapped (Figure 3A). In the second Discussion). RepresentativeanimalsfromChinafellintonine
PCA,whichusedeightcraniodentalmeasurements(n=233),the cladesthatcorrespondedtoninespecies.Notably,A.uralensis
first and second principal components accounted for 79.05% fromXinjiang,China,fellintoaclade(BS=100)comprisedofA.
(eigenvalue=6.32)and7.08%(eigenvalue=0.57)oftotalvariation, pallipes from Xizang, China, and a sequence from GenBank
respectively (Table 2, d). The PC1 and PC2 plot (Figure 3B) (origin unknown), thus rendering A. pallipes paraphyletic
revealedlargelyoverlappingspecies. (BS=69).Asolemitogenomerepresenting“A.chejuensis”from
One-way ANOVA demonstrated significant differences Jeju Island was embedded in a clade containing A. agrarius.
(P<0.05) between the seven species in all external and cranial Apodemus draco, A. ilex, and A. semotus fell together in a
characters tested. Results showed significant differences as well-supported clade (BS=100), but the relationships among
follows: SGL,NBL,ZB,SBL,UTRL,UMRL,ML,BL,HBL,HFL, the three species were not resolved (BS<50). Apodemus
andELbetweenR.nitidusandR.losea;NBL,UTRL,andHFL chevrieri,A.draco,A.ilex,A.latronum,andA.peninsulaealso
between R. nitidus and R. tanezumi; HBL and HFL between comprisedsubclades.
314 www.zoores.ac.cn
Table3MeasurementstatisticsofRattus
SGL NBL ZB SBL
n Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum
R.nitidus 46 41.93 3.22 28.40 47.05 16.13 1.68 10.54 19.00 19.87 1.16 17.64 22.30 38.30 2.36 32.82 43.00
R.nitidusnitidus 31 41.62 3.53 28.40 47.05 15.90 1.75 10.54 18.66 19.66 1.11 17.64 21.75 37.96 2.30 32.82 41.82
R.nitidusthibetanus 15 42.56 2.44 38.39 45.85 16.62 1.47 14.02 19.00 20.31 1.15 18.63 22.30 38.99 2.40 35.19 43.00
R.losea 31 37.12 3.32 31.24 46.53 13.51 1.77 10.06 18.35 17.99 1.38 15.02 21.12 34.37 2.61 29.72 40.55
R.tanezumi 34 40.11 2.06 33.98 43.27 14.50 1.26 11.69 16.57 19.57 1.03 16.73 21.67 36.50 1.96 30.75 39.80
R.andamanensis 44 41.49 3.06 34.87 46.80 15.13 1.75 11.25 17.84 20.33 1.63 16.88 24.05 37.69 2.93 31.76 42.72
R.norvegicus 69 41.63 3.52 31.75 52.13 15.33 1.69 10.79 20.22 20.42 1.88 15.33 25.63 38.16 3.30 29.95 48.56
R.exulans 4 32.86 2.15 31.09 35.88 11.33 1.64 9.91 13.14 15.77 0.73 15.15 16.79 30.49 1.22 29.15 32.04
R.rattus 5 39.86 2.10 37.96 43.15 14.11 1.24 12.93 16.02 18.83 0.71 17.93 19.58 37.75 2.18 35.75 41.03
UTRL UMRL ABL ML
n Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum
R.nitidus 46 21.29 1.38 18.62 24.36 7.39 0.54 6.15 8.92 7.36 0.56 6.03 8.32 21.70 2.02 16.41 26.17
R.nitidusnitidus 31 20.96 1.25 18.62 23.02 7.29 0.53 6.15 8.35 7.28 0.59 6.03 8.32 21.08 1.85 16.41 24.65
R.nitidusthibetanus 15 21.97 1.45 19.56 24.36 7.62 0.51 6.66 8.92 7.54 0.42 6.86 8.11 22.96 1.78 19.81 26.17
R.losea 31 18.95 1.62 15.86 21.97 6.53 0.42 5.79 7.63 7.17 0.40 6.54 7.84 19.85 1.66 15.76 22.69
R.tanezumi 34 20.13 1.22 16.76 22.47 7.38 0.38 6.39 8.18 7.45 0.51 6.22 8.62 20.76 1.09 17.81 22.59
R.andamanensis 44 21.36 1.73 17.89 24.02 7.55 0.62 6.11 8.70 7.39 0.52 6.25 8.89 21.70 1.84 17.70 24.65
R.norvegicus 69 21.66 1.93 17.01 27.14 7.35 0.47 6.32 8.55 7.40 0.56 6.51 8.68 22.02 2.33 17.02 29.63
R.exulans 4 16.87 0.87 15.73 17.84 6.12 0.45 5.56 6.51 6.51 0.26 6.15 6.73 16.24 0.94 15.21 17.49
R.rattus 5 19.61 0.83 18.83 20.88 6.73 0.38 6.41 7.39 7.41 0.48 6.99 8.24 19.48 0.98 18.43 20.70
HBL TL HFL EL
n Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum Mean SD Minimum Maximum
R.nitidus 46 164.59 18.34 123.00 205.00 168.09 18.38 131.00 210.00 34.14 2.12 30.00 40.00 23.25 2.21 18.00 28.00
R.nitidusnitidus 31 161.32 19.18 123.00 205.00 161.81 16.71 131.00 192.00 33.79 1.89 30.00 37.00 22.96 2.16 18.00 27.00
R.nitidusthibetanus 15 171.33 14.84 155.00 205.00 181.07 14.81 162.00 210.00 34.87 2.45 31.00 40.00 23.87 2.26 19.00 28.00
R.losea 31 152.07 20.82 103.00 192.00 145.58 15.64 110.00 192.00 28.58 2.04 24.00 32.00 19.12 2.95 12.00 27.00
R.tanezumi 34 162.91 10.46 128.00 180.00 173.09 16.06 144.00 205.00 31.25 1.72 28.00 35.00 21.72 2.24 18.00 26.00
R.andamanensis 44 173.02 19.54 126.00 212.00 186.89 24.45 115.00 231.00 31.65 1.87 27.00 36.00 23.15 2.29 19.00 32.00
R.norvegicus 69 182.62 24.50 120.00 274.00 152.67 20.80 82.00 222.00 34.42 3.59 26.00 41.00 17.72 2.23 11.00 21.00
R.exulans 4 115.50 14.27 101.00 135.00 138.00 8.17 126.00 144.00 23.70 1.39 22.00 26.00 16.75 0.50 16.00 17.00
R.rattus 5 170.80 16.99 150.00 194.00 190.60 11.80 180.00 210.00 33.00 2.24 30.00 36.00 22.60 1.82 20.00 25.00
AbbreviationsareexplainedintheMaterialsandMethodssection.Allmeasurementsareinmm.
ZoologicalResearch39(5):309–320,2018 315
Figure3PrincipalcomponentanalysisofthefirstthreeprincipalcomponentsamongthesevenspeciesofRattusbasedonboth
externalandcraniomandibularvariables(A)andcraniomandibularvariablesonly(B)
MatrilinealgenealogyofRattus Fully resolved phylogenies require many slowly evolving and
The interspecific relationships of Rattus using the mitogenome unlinkedgenes,whichisnotwithinthescopeofthecurrentstudy.
and cyt b sequences (n=396) were well-resolved (BS=95–100)
or moderately resolved (BS=55–77) (Figure 5). Sequences
representing animals from China fell into seven lineages that
corresponded with R. nitidus, R. norvegicus, R. exulans, R.
andamanensis,R.losea,R.rattus,andR.tanezumi. Theclade
ofR.nitidushadtwosubclades,onefromsouthernXizangand
theotherfromsoutheasternChina(Figure5). Thetreedepicted
GenBank sequences deposited under different names within a
shallowclade,mostcommonlywithR.andamanensis. However,
somespecimenswerealsoassociatedwithR.losea,R.nitidus,
R.tanezumiaswellasR.nitidusfromsouthernXizang.
DISCUSSION
Genealogyandtaxonomy
Species of Apodemus are among the most destructive of
all animal pests, yet little attention has been paid to their
evolutionaryrelationships. Ourtreeswereconsistentwiththose
from the robust study of Steppan & Schenk (2017), indicating
the repeatability of both. However, the created molecular
phylogenetictreeofRattuswasinconsistentwiththatofAplinetal.
(2011),whichmaybeduetothedifferentwaysinwhichthetrees
were constructed (ML phylogeny here, but BI and NJ methods
in Aplin et al. (2011)), different number of species, or different
sequencesofthecytb gene(onlytwoindividualsofR.pyctoris
(GenBankaccessionNo.JN675511andJN675512)fromAplinet
al.(2011)). TheunresolvedrelationshipswithinApodemuswere
Figure4MLmatrilinealgenealogyofApodemusderivedfrom
Figure 4 ML matrilineal genealogy of Apodemus derived from cyt b
notsurprisingandarelikelyduetoearlyradiationintheevolution
cytbN(uNmubmersb aebrosvea bbraoncvheesb rerafenr tcoh beoostsrtreapfe prrotboabbiliotieos.t strapprobabilities)
ofthisgenus,asindicatedbythesaturationofthemitochondrial
gene(Serizawaetal.,2000).Similarproblemslikelyalsooccurin De spiteuncertaintyinphylogeneticrelationships,questions
Rattusduetohybridizationandintrogression. Previously,Rattus regar ding taxonomy in both genera remain. The differences
wasrecoveredasaparaphyleticgenus(Steppan&Schenk,2017). between A. pallipes and A. uralensis have been discussed
316 www.zoores.ac.cn
previously in depth (Musser & Carleton, 2005). Our carefully reflecttheirlongevolutionaryhistoriesanddistinctdistribution
identifiedspecimensofA.pallipeswerefromsouthernXizang patterns. Nevertheless, future comprehensive morphological
(Pulan County). The average cyt b genetic distance between diagnosisisdesirable.
A.uralensisandA.pallipeswas5.4%,whichwasthesmallest Hodgson described R. pyctoris in 1845 from Nepal
interspecificgeneticdistanceinApodemus. Allourspecimens (Hodgson,1845).ThisnamewaslaterreplacedbyR.rattoides
of A. pallipes matched the original description and holotype orR.turkestanicus. Musser&Carleton(1993)resurrectedthe
(Musser & Carleton, 2005). Thus, A. pallipes undoubtedly oldestnameandithasbeenreportedtooccurinChina(Allen,
occurs in China. The sequences of A. pallipes in GenBank 1940;Corbet,1978;Ellerman&Morrison-Scott,1951;Musser
werefromAfghanistanandPakistan,nearthetypelocalityofA. & Carleton, 1993, 2005; Wang, 2003). Feng et al. (1986)
pallipesinPamirAlta. However,aswehadnoaccesstothese identifiedaseriesofspecimensofR.pyctorisfromXizangand
specimens,itwasnotpossibletodetermineiftheymatchedthe claimed that R. pyctoris closely resembled R. rattus but with
morphologicaldescriptionofA.pallipes. a pale underbelly, relatively long nasal bone, and cusp t3 on
M1. Our series of specimens from Xizang coincide with the
characteristics of R. pyctoris described by Feng et al. (1986).
However,phylogeneticanalysisassociatedthespecieswithR.
nitidus. The original description and comments of Musser &
Carleton(2005)onR.pyctorispointtoitsdiagnosticcharacters
as a very small cusp t3 on M1, a wide and short rostrum
(narrow and slender in R. nitidus), and chunky wide molars
(thinner and gracile in R. nitidus). Except for the morphology
of M1, the Xizang specimens differed from R. pyctoris.
Furthermore, many characters of the Xizang specimens
also differed from R. nitidus, including the cusp t3 being
present,gray-whiteunderbelly,andlargermeasurements. The
molecularphylogenyalsoplacedtheXizangspecimensandR.
nitidus in different clades. Accordingly, we assign the Xizang
specimenstoanew,undescribedsubspeciesofR.nitidus.
Peale (1848) described R. exulans from Society Island.
Nevertheless, its existence in Taiwan, China has been
recognized for a long time (Motokawa et al., 2001). The
GuangdongInsectsInstitutecollectedspecimensofR.exulans
from Yongxing Island in 1975. Rattus exulans is the smallest
Asian species in its genus. The specimens from Yongxing
Island conformed to the characteristics of R. exulans. Thus,
weconfirmthatR.exulansoccursinChinainYongxingIsland
andTaiwan.
TheearliestChinesespecimenofR.rattus(blacktype)was

Figure5MLmatrilinealgenealogyofRattusderivedfromcyt collectedbyA.B.HowellfromKuliang, Fukienin1929(Allen,
Figure 5 ML matrilineal genealogy of Rattus derived from cyt b
1940). In 1955 and 1956, the Fujian Epidemic Prevention
b(Numbersabovebranchesrefertobootstrapprobabilities)
Numbers above branches refer to bootstrap probabilities. StationcollectedspecimensfromFujian,whichwereconfirmed
Johnson&Jones(1955)describedA.chejuensis.Koh(1991) by Shou (1962) as being R. rattus. Our examination of
thesespecimensandonespecimenfromGuangdongProvince
also recognized the species based on its large body size and
resulted in the same conclusion. Thus, we confirm that R.
mtDNAgenotype. Corbet(1978)assigneditasasynonymofA.
rattusoccursinFujianandGuangdong.
agrariusningpoensis,whereasMusser&Carleton(2005)treated
it as a synonym of A. agrarius. Our phylogeny embedded A.
Morphometrics-andmolecular-basedspeciesidentifications
chejuensis in A. agrarius, and thus our results agree with the
assignmentofMusser&Carleton(2005). Regardless of skull and external measurements being similar
The taxonomic statues of A. draco remains uncertain. between species, many interspecies measurements differed
Apodemus ilex and A. semotus are close relatives to each significantly. Species of Apodemus were easier to identify
other(Figure4).Kaneko(2011)suggestedthatA.semotusdid thanRattus. Furthermore, thedifferentspeciesofApodemus
not differ significantly from A. draco. However, this endemic exhibited stronger geographic distribution. For example,
species of Taiwan was characterized by a dark gray pelage although measurements could not discriminate between A.
ratherthanthereddish-browncolorofallotherAsianspecies dracoandA.ilex(currentstudy)orA.semotus(Kaneko,2011),
of Apodemus. Further, our ANOVA results demonstrated allthreewerefoundtobeallopatric:A.ilexoccursinHengduan
significant differences in TL and HFL between A. ilex and A. Mountains,southoftheYangtzeRiverandwestoftheJinsha
draco. Thus, we recognize all three as full species to better River;A.semotusoccursinTaiwanonly;andA.dracooccurs
ZoologicalResearch39(5):309–320,2018 317
speciess peidceienst ificidaetionntif icadtuioen tod uec ontosi decroasnbpsleeidc eierisnaspt brelaecisd ipeeesnin cttiifrfiiaicdcsae ptnieovticanfsiir cpfiiaaced ttciiuooievennsa ritaadoidtnu ieodenn ct oiftnioacs anidtdcieo ornna sbilddeue erai nbtltreoa spicneotcrniafsiscipd eevcraaifbircilae t iovainnr tiraaatisnopdne ciaficn d variation and
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aspdedcitiieosna ,d cdidocitenoisonsnpnitsdie,fi edicccreioaearntsbaios lbeindl ei dein eerdtanrruarbtoeislfceris pcso pea inntiecntosticior ifGdaiinecesce sprdon aeidnBvbciusesdalieiefrpdenis c eeneki tc.rtrdyt iarifosa ieoivcboc pdsreolacsee drncct c siiistuooniiiidetionrn idyaGnsesns ed t no,ierird dntadacAcnieii fscdubtoBislircpupoeelnaeaeaernhn sbvsn stce,itailep dk oieitfrics freo.nein rdiac opcoc r ial nesari vietnssecsbceidso vptiivolirruede naneeaasnese r crsdisiGi i ratnaidpdiaeyddltetee ibri tsitedusnoooancil.orepee Bn sfitafFin en p ifaAbiciu,cnctce n ilpttoiafectacoeukiroconn tiav. srfia nsdoiedsa.ci tisn epcndr iFoiid ometdeaurnincertavtu idaiusoersfusabiirnprcddee sbl e eaeu i dltce nreyiaaiv d ft inbiioeoncn dl Rrctt etsorr ca aai cutvtssyotaripp cnusnroeoe tissarcicncnia tcdiisi fsfuoeisiicpcdrnre s eae vd cbreiivanvilafreaebi ancs rrlld eies as iivnttvpiyeotaei rrnnoaracti csairle acptssiasueop.npr cnesFdei cf uciiicneitaf u sincsr.de v eFa vvureiataruartirilaoe stn ipo enc aineadsn . dF uture
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opaacdcldliuiptrieoresnon,, c cccAeouc. noroarsmpfed iendRpdpnceria.tiee rniloaplh isponbyeuecf,lnel tascRso ,eoii rn.v,i nsA teprs A .ayii andsc.cp n eatpooCesdrdepmaren hdciabsmiiipiinnlnft lliieritsiocoapnee ut n e ihgudnilC,sasersi tva ,cerhn, na eato,isiAn osrvadnisvaApte.nds ie et dn.iiyitdp acsi eao oaeescni ocAfdcnnnernoiacecacd.,odmiml c sn ubyit cdtuuss osrpiliooeirnnraruevtroesanun eterlescie naylss,nchei rc .gncei,stne ccedn urer ,Aioesaane tassra y srncnsisreAtonnse iaaeps ivvofad. ven brdis eeecddey Rwoclsesac rc.ede Aec aa. taeidua ifreAcs .tlriinmapdr oincnuyru ossabmyi nfudt rbot np radclil eir yoeaRstin,enitoanpuii wvsopn snn c.cdcleasiee sepre,n t ioc/, p ileersesneoslc tCcunsiiyrgs ufpv iscroaai reshcci .rtebeiirndn nfyssaifstiaeudFrsisno pesd c tannrCpeo,iuaroi es vot ld icerdch t.sfhiecAcAdau sree ccie iai vcRpebrn.frI i.uir niane ebaeuoetlc a.ree un splbrrfss c eC s rd rael ipiRime.saioeiinih tlnnlnvy yilf.stitienii esrnn tnn.sRpaino oCeranesteFsyssrct.s g uh a vicupici tins lsiefysttaeunc oi e u prsecraafnoarocrus eii,n.eofclsec rc i ittcc cssnAiI hdif unupsnni ed.ecr sar e eris t Cevrcs ecd yievsieienhri.envmer pms iss nAerlssCii.iaoar tnt aetsynlFht ei rvuni iesityus oneysg.pwi t ca fr,u ne A oa c.irofssc acl ueu t unicInsre rnsbeutnpdsh swree .ies npcc AF r eseii s.eunuc ssest ibpsuuesv.asl rreseiFeatpr vtry ulioeaeen.t fclrngu AaisRse r lepii sn.sss e e pocwoefie c cRsscie.uu. sbrF .s uiFpntueu rctCeuie rhesin oaf. RIn.
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onspocecrvuceirmrgeisecnpnuce sencw, iioRmtaoifdsc. e uR cnrnapuso. t r rrtiweprvsuepye asndcag,sce tr iaoeecspnru dcirdossr ei f,abpR i nRRsean. o dr..itC ea tca nripadd chanoyssu uiterntc karsvuzfatrios eosnuei l sg,r miln soia wiascdc w i n eneiuoositsdn ohssckco: ct , cicR CnfcrRu uni .lRhbr ree.oswtr inea.canieprc niiadnetnatnceph it esCdue ccyta uiszuericdshscmrasuts s elio,enfornm sep onyiraaafosknei.l cisSl nn. utR oceo d A dFeluwinwil c.em n d uobencRasspa tfeocsueCsc:u y.ns nec prR rwcrthdko ic asepbiet.u i ncuowsn n rescdlr cpearrlaeCueadi rieuypers zebssa hyprcaia sunes sr.niiotsnr se nnmp opcadedApson na errerf deiei Ceiroocct. scdnv eo schpotleFh ileae edicecoai f minunips gwcn osrnwrRet iouiieea fut cnpCsc aoosr.sdn ruR :t e ihf ieu i ispttt snsso.ehhi abwR yn ,r sk nndeepssCecaRa.aio pn yst hsro.iatce eiy n i srrn tw.canp ia o ssainrteAirter thkcte.iohc ius sihenFpnnet s ao uecisi,nCnn wrlftwsaee e uthaoCRin cadrtirs hneednh. tyu h a s .eairR nbce sedsAials. asse p tre asnaaiynesa ken.noc surweenAictkled lzo h i nsns nut ae ius emnnonckwbwtefdeiuos i c otsRl phlsted cshe.u seaca eccbsupnri lsyeaerod.p sra s iyneA ndi.to c eeeCAfnid dephe R soniwnis .sne oak i wtsfu.et u hlFRdlsb eu .uas itnbpnu sedretpc h edireeece sispe eoosasf oriRtcfe h.dR i n.i nto tthhee
onSicitcicdhuuursrae nSins iA ccdehcSe ausoundacfbie ntrRisiom dbApc.uey ccespd auoc y idrafiscr ees Fetdsom nofe rocdryissele elc oos sirnotwfir cSb fFnys rCeu ioR:iot(d pbihMrcd. eti sacuniTpsopussaty1n rer c1fyriioc se1st o l(in 9ldeMornnc7ieswsoTei)s t t dis 1ci dno:1neru fi1esbnS sCS9Rccei ithic7uerids.dhi i)sb n pp udaussatysesaaipS c os nriifestsiycnoco . Ac rR hl drniliAicbouseeoaa ew assttndi tdncn snunede r : isaeAwi tmeCbni scdcns eihy etsuaicfid tiodsunsdoir dslubi aaeflpiuo assss mFSostwr ip siioydcf iysoecsot. rceh nhnc:elodAus lioiousb feerc twtarenFssr reinytnce sboano re:werA(nci febMcd eacseeRs a Ttassduor.d1ss yub fe1a a sbf(R1msorMps9y .lefy.l p7Too p cA.)ol1w yil eonf1 cs ns1wFot:eo 9ovsowr7:r if es) R ssiutn.r by Cs (phMeinTca1ie 1is1s 9 on7fo )R t .n ecessary. A new subspecies of R.
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or molecular data requires caution. Unlike fob1Hrr7Fo.tL0kh:e6 e4n m0)b.s m rmAop;dkm eAeuc;1nBl tiE7s)eLP..H:L :0s Aa X:F86 rd2Z.L au0m31:tl 8 yt64mms p20m:;m e6 XmAmAs0;ZB :,m;Sd 1L♀L5G;d6: M 1; E2L is87XtxH6Lp:.i. 0TZ0:o04eFP :8,1265c Ln a7 ♀63i .m:mrm4a. 2 3a4;m9m le5m8t0X yn3mm ; sZ;m m1ps, L ;pA1m7,e♂ mmM S6Be.sw;0;2 G;;x L:cS 6Xi 5TNEt:1bLi5hB Z:3mm87rLB : Lo7 ,1s..:s4 Lm00 :1k.♂epk2 53:86e42P ine;3;.8n1 n 384Aacbmm X ss9m).09mirrB0. mZ.:omma, 0amA0 mmL19kt♀e0n;; y1:d17e; mm;n dA; L p28um.n 5SNs0 XMm;B8.le), 1tsG0m1B.S sZ0sL sx;k78w0A: LL,1:.B:1Tu Zp. 4X:1d0i:♀m:87lL5t B e 5lh42u61Zs7..: ;m:00;c 56l :9s1. 4tXm s1386is.2p.;6Xm34k0 Z98 :Xb,meHL2mm .9iC 0. 1Xn0r♂ZceM69mF ;o 1mmYs0miZ m108n;mALk2xm 016, ;;Xmmesa:Tm6Bm e1 62A♀;L:n4nZ2 Lnm ;0.25mNMB(7 )0d; ,1:sS0 .6 99 ;. 1BLX ♂;x,8 3mA10B, s Z1: TMLZ.8;w, ,kdjL07 Bm :8 u:1 Xu ♀uB♀♀ i:87m7.:t1 v6;l0 Zlh4 :,l; .;t,19sme2 m E3 8s 13X9.:25s:n8 1L0 .m; m2.Z08k3 XX1 9:i0Nm7 li10.;,7mn82eZC 5 .Bm6 L♂7ms4 31m0sY;m2ML, 7 ;m64, ;Lm0 a5m: 0mX28x NM1.n3613m T6;,Z;0,d B9x3 : 0Z1M; 0♂ .TaL ,7,1B0sS 1 ::;Bd.♀ 2k0 : 3,G71 X 8u:u8 1;8 .♀m9 8LlZ30l9X lt.sm.:,8,1m0.s9 Z :941 ♀ 20m1m1.85X2 8 4;6 m;. 8mC.m 45X25N0m90Y;5Z0m, B ; N3041.m ♀; L1,18 B M;:mX2♂0, L X160ZB;;: 9 Z 211S:X1. ,1,60B9 Z1♂2♀0.L1205 ;1,:m 60 8X2422 ,mm8Z3 8, 0.1..♂m0♂ 51, 0;01.♀; X47m;8 7Z2Xm,,17 Z1;. 141Z177B207:63, 1239,, .♂9;8 X mZm11; 1M7B7,:
CiNonfhoitnmwAaipothorapsdntheadomnlhoduagisnvi,cgea,limltikwomesalyotsdpeisfioxpcpseasectiribioieelnesnctoetooidfdesaRntdrtaoiaftnyptugtssostmoealeerel989♂1XXsco7787ptZZ;ci ....oe110090iaan11PPnc1116ln20vaa004 iedm02arrr445♂XXh aae78ss550mZZ;ttaX,,si ;;; yybv11 ; ♀bZu98M app11a♀Aei781.lXXnee2098tT tsB;1..adi ss02ZZ78 09ne01LA t::78i11..X191127sgdn :09X,, 66d770455P0Z3 . 811♀22..45Zd ,,1a.0400♀ ss0555011Pi♂.r4516t pp8;♀991;;a2ia 500 ; eeo1 ,,mMt 0.rm ;;4MXycc 7n aX8M5mTiipZ3mJamm♀♀TtwX,Z;X0 yeu,1Tl; 0;; ;;1; eeZ2ipsZ1v♀ A0t3sX6L♀nnX0eh:e2112B5X98; p2M22ss,98n sZ0Z6.510 ,78L 5e,,s77Z♂78 i:821xX19 1,l♂2.. :9c..keJ ..ww09s,T 5617744;5♂Z091 8A0,ui ,sup11:P92 ..mii77M 111 1.ttv2:0;0♀27ed047ls0hh,5 00a1P04l2e 1M6♀T9e3cps45.,d8; 933rX2453an 60 .in0ssea502; i,m♀Tm3323508bZri mt 4kkX32sct;;l,,,ia50;2e;; ;y1iier5m oi5: MmZ ,nnm982m♀t43,s oM1pn;M,n yssX1787;1 988:5 ;TmX2k;;2es e ♂pTa 1♀ A...5Z188,T0X,0eL7094saaZnX lXe2;0 ;, ,P..♂B1; 72M.1127:nn sn 1199w sZ3ZN2s4Z 298♂XXs96aL,0,047,0dd986115p):12 01xi7X X 978115pB2ZZ r:t,;45.2.3 78244w e,T h,6 0114♀a.5...Z5ess1 L8 11Z♂50s932..092555:cA ♂232i7t 09a7kk9cP11 1:.;tp1;;.,♀511s19y00i1A7;s 0 h530 02 11muun1,d;i20 14eaMk4043p7,;;p m.M8;1 9,7♂XX135Md04lld M3029 iucr ll,X94e58s3een5 ss,,T374145 daZZ878♀Ti;e.m Tk1Xln5081cm♀TXXsZ::s 0,,598t500t7iX ,,11 n08bi ,s;;.i1♀;s. :tym Z0n01;mZZam♀,1XX8 ;;2; 9 11 e ♀i3r87aZs1 9 M :p3so 61♀;n5o,11.80M120;nCCXm(1m;;5.n: e 195,.X2♀ 15e 2 99 nXd k9668,T4 202Xs;X7L,1danYY1.AT 1MZ987s1; ,sm5Z e1 5 22a;2.♂5,7780 1 4ZMZ♂2 ns4 9 7p078.00jZ5N♂:9dn411X.55l10TuX.,,s247w,. ,987;1d25 1e54 2;1..11, X ,x )5 6d188kB35;v1♀,0097Z1 3Z s78.M6 .10s4 c,wi7 0002T♀P604Z2u♀ et,,3i1 21,1s01L,11p..A12p.i3h ;t50:,a 009 s09;mi7♀T15l n2 a11kX1i9 ♂04;3:1♀t;l1 5ee73 P0d3o7♂ p11. sh n11M ♀0179ui0r.♂♂12.45362s1;Zel9cc1;9; uX3;:6.2e,,aa n1e X0434,Xl3;d ♂XX7k 3050, 59.19i0lTn,;;1 i. Msl,5 c6tr m9sZs,a4X53,♀♀ mt5M iZ 388;;Z4.77ZZ2Xysk na6;s0,iX4 :,06l501J,, m♀,TC, ,M1 9.e.81,,,7iXp : 11st22♀22T Ze♀ m 98n000, uZ ;;6X♂61ya01;s1nX8 11. ;XY Pe50e7722wn01;1T8sZ1 6♀v4;♀ M21;81 2panC3mp,sm.20; ,s 8Z♂,n1..88XZ03a ,s.e 0 90Xi7a 56X8 74401nd5.e 9;t9m02ea21TY2:,a♂s..11X5r :;91n h4m12;0d822 Z(.677558d ,s Z1Z1578ca n99,790690,0 nN565i 5m40JZ3u;, X751,0000, l ♂:4..11X,,it d.61 .s121e a♂ 2 0♂1w .2 u2 ;5, ms3dlM21y.48B53344Z25t;6 ♀k ,5js41Z,40sn571066♀vks1♀1 0♂u,5; pi7,, ♂ ♀3388sAL101i2p tT e:7 25,d91e,X2 1u0.n033;vshX24 02 k;e,,,,1♂ ;s; :3; 5e;;Bn10w090♂ ,n 7l1 s ,e p30♀ 98u,329♂sZpl5Z X2M1 391cs3;3.;s Lsi6,♀nei1XX;18l 377.2 l:eX3 1t9,13iX,Z7al1: ;e235k2: :m,♀Th ics. M♀ ,.,.5 Z;cZ 2l a6,..Z 53ni1 ,s792, ,4Z5e1 XX8i: 0 0n.19i ;4mX,1e n21,1 ♀,d:m♀1T.182♂7s 4s.1 00 3CZs 5X5419s80nd561Z2 k,4.72009;e86; ;5;♀, e21. p75♀X218sC2Y8s 92m 20u 12a5.8331n82s6,J2n6XXe00k43,.,87 ;,5Z07 l0.6Y1n0.53, s.9 p5m lm ♂2u 9su2c34752 99.s8,8,w11ZZ23 d;,,91ae048, 7i.Xl53 8v00 J ,51m,1,.m,♀( l0253 ♂ 54dci17,11 s .9u8♀,,e3t4w.4Z 22s4053.1 ihX.25u:00;;♀e11, mv,♀3825k 9n01♂;i71 4, . 10l30Lj♂tZn eX2 t22u,,110;u.7hs;0,i9♂es 3; 31;M22sn l191M♂lC3;; v k08, e3 1nl3♀ ,,5, 7;Xsi6.7seXi3 x wl 3Y;802,snTs1eX4.2:X♀♀2k w,5ZnT12X4 Z ,59 si0,,:1.s987i 5ZtZX,:i. 1(72n;i7,1 Z45hl12 :1 t18 .9e8711 1ah.C8s10419. 872104♀,. s1M,21.6 n . X9237s7 18.8Y36j0759,as7124u2;dk133 04T,Z..82 10005kn5 3987♂5v5u6 42,3,91 51,i314.X ds,e31000m8ln 25,3;1 15l8308 k♀ sna1Z,43♀4,s110,82. m, s♀u,0, id2.♀♀5 38 1, 73;l8;02 kl e1a u11;0,,;l♂43;;.u772 s ♂s,n1 9l3;XN ,1tXX:l,.8; ,Xd s9l1 43♀; X sZ.B. ZZX 64Z♀7651X♀:Z,1swL2 11, C50 0.121;Z 1Xk; 1:726 ai10 347 1Y1tu12♂1.C821hd;X38.471Ml0 6649.5l9 uY;,,7567sZ12 27s.T86lX:0000,5t105k ,0 as,1, 30141,Z Xu08♂ 31n ♀13 081l1w,♂1C3md♂l♀; 7,0,;s6 ,7, iY;X 6 mt1;;2 4♂h♀ 0,Z,5, a. ;X 1, 128♀ s n♀01Z♀72,kd, 210;1 .8u; 4727 11.l♂l751.87,sX4 00;9 .,♀ Z75 346010,382, 1 34,,721 38♂.874,,. ;675 ,00 a34n♀38d;,,
onmorphologyalone,suchas,R.andamanensis,wAhdicdhitihobnraoaskle asnp).e Acdimuletsn: sX:b Zr11o56k e2sn6p)0e. ,Ac ♀idm;u eXltnsZs:1 Xb6(9Zr2o 51kj36ue,2vn ♂e6)n0.; ♂ Ai,Xl e♀;dZ su;1,a l X1tn6s2Zd: 81 aXA06dXZ,d2u Z1♀d5lt163si;12t ,Xi1 6ow♂7Z0ni3;t1, ah ,1X♀ l 2 Zs;♀s6 1kXp.21u Ze,2l Jl1♂cs8u6 i0;mv 2,Xe 5e♀nZ3ni;1l, se 1X♂:s1 Z:;71 1X751X,Z 2 Zs161p121e2,2 c8♂0i0m7;, ,eX♀ nZ♀;s 1X ;1 (Z19M71 17Tju2,1 v61e21n,7 il♂4e,s; ,X♀ Z6; 1a1Xd1Zu71l7t1s,1 7w6it,h ♀s;k ulls
unique white belly, R. norvegicus, which has veb8rr8yo.9kse1n4h)5o.0 rA;t d♂Meu;Tla ts0ra8:2sn 8XA0,d.,Zd9 ♂11dX64;iZ t25Mi1o601TGn0;1 0,aM7e 3♀l3 To5♂,;s0, g; Xp8 2♂♀reZ80aa,.Ac. 1, n92 pi6d♂dJm19h2d u4;. e25iviX5Mctn53ei0ZoT4,sn; 1 d9n♂0:iM1l e13ai;11s Ts,A5lX75 :90t,d 3 s♂Z r52♂s,dpXi1; .0pb ,2i1eZ t♀,eAu2a12 ci1♂co.9dn38i1t imn;im.d3d02 2oJaM 1,ie0e5u tXnl.♀Xn7i Tn4v oZ:s,sZe;s90 n 1p: nX113 ♀a1b(Te1i,51Z9l l2r1e;c9 ,h5o1 0 7ssi5♂1j kemM7u:3ps.2 e,2,v,pT ee 6n X2en1Aecn12)♀♀9nZ3e.dc1is,8 .im3;1 A.1wil2d: ♂m 8e11 7d5ie.sX1J2;.te94u4 n,ius50XZ on1,l9s tvu 761sZs4n1:es♀,1 b : 51a, p na( 21X1s0;l99e♀i d 051l;pZ5e cs uX8; 7Mje1. sipulsm2,7Zt:6 McspvTe 1,1e2 e♀iec03X1Tewn6nci213;1Zmss0 iii071ml1t 1e,hX,e61 .(1 is♀ e 9s♂nZ,72,s n ; 4s1;0k sj♀6 X1ru,:uM7 e 2v;Zl,(1 al♀T c9e3s15d0 no♀2 ;6 uj3i,ru2s;l lXe d5tpv5s♀sZ,Meee3 ,♂1n;c wd,T 16ii♂,mli11X et 2h1;7aseZ 91 X6,dn1s .7,Z2u1s6k 45l1 1u t,♀(s147 al9l 2;s95d♀ w 81,uj ;ui0, lt tv♀h,s9X e ♀5;Z nsw.;12kiX liX1etu1hZ1slZ3l 17s,31s 1 6116k1,2.u 9 a6l6♀lsd2,; u, l♂♂ts;; XwaZint1hd1 1s7k7u,ll s
andR.nitidusandR.norvegicus,whichdonothavAedtdhietiocnbuarslo pksepneA)c.d Aimddieutfirnlootssnm:: ab Xl1r ZoY5sk1a pe6sdeAnp2oc)e6d.inc 0mdAgi,mi dbet♀,iurneoo;Mln stnkXss:eao :Z b nl1Xt(1 ru)95osZ6. okpA21jseu,e56dpnvc32uNe)ei,6l.cm tn i♂0sAiemi:l,edl;e a X♀neuXsmnZsl,;Zt s:s1X6 1u :6b11 Z (,X29ra521o6Z ad 86kj0s1u0nu2ep,6l,v5 dtn e♀s2e♀3)c 6.n;,J; wi 0 AmiX♂iXleli,AdtoZ e;Zhs♀ ud1nnX1, l ;d6sts1g Zs6X 2ki21:t (u 5Zi6c19aXol312o2l dZsn,6,j8uu u 1a♂2♂0lvn6tl5,s ;;e2 t 3s ♀XiXn6ew,piZ ;Z0ls♂ eei1Xt,1,hc s;11♀Z , iX21s m1s;876 oZ1kXe07 12uuZan,,16lt ld1s♀h2s2u6: 8e,; l20t1♂Xrs5,n5Z ;3♀ w1X,s ;1iZ♂ ptX2h1e;6 Z 1cXs211imkZ,17 u♂127el16l,n;s 22sX 8, Z 0(♂91, ;1 ♀ 1jXu;7Z vX7e1,Z1n 11il17e27s,6, 26, ♂ad; uXltZs1 1w1i7th7 ,s kulls
t3 on M1, with the former also having distinctb♂lyr;o klaaenrndg) .e AXrdZXeu1Z♂l1at1s1;r1 b:7s 2arX3.o0n,Zk7 d1e,♀ 6nX.2♀) .Z6 ;JAX 01ud1,Xiv z1u♀Zea7Xlt♂n;1s3 nZ1iXb;:l,g 1e2 ZrX1so0,a♀1Z2:k8nC 6.10e,d 2X 6h7n J5Z2♀,)iuX n3.61 ;v♂AZ,♀a 10 e♂1d;2,.X;n 1u0♀;Zi1a lXl7Xet;17n♂s ,ZsX1ZX 3d:;: 12Z1 , Z ♀X1 3111aXXZ;2♀221 6nZZ108,2.M2d 6118 005 112♀,TJ,7 31 X26Xu1♀;,,♀7 00Z1v Z;♂37,1eX♀; 11 X,,♀71n;1Z ♂ ; XZ1 4iX0;1l♀♀; e71,Z♂X 12ZX .1s3;118 aZ1; Z♀:2 ,171, n 1JM1 62;a52♀1duX ♀623nT,82 v. Z2X,.b2d 10e0 X51♀♂Zr ,1 ,n8 oJ13Z 11;;X♀i,uk2, l ♀1 17e XZev0;♂11X4♀;s eZn11 7X7,:;Z1n; )1 7,6XZ X. 111i3 ♀X,l1AZ1XeZ 17♀,1Z1; 1ds73Z1♀ ;2911: u1♀7,1X ; 6116l2 ,M1.t X2Z27♀,s 82 T,051:Z0J.3 ♂1 ♂7,1X1u,2 1 1,J1;v;Z♀, ♀17 u2eX1♀;76av;0♀n 6Z X4,ne;7i 2 ;l1X,dnZe , 6♀1 M iZs1Xl1♀0e♀;1:1T 7 Z,s;21 ;1 7♀1X: 16 1,1XZM;9 211X ZX61,77T Z11,♂Z45 1112,1;1,11 ♂0 61X27♀7;♀27 Z06,;54 ;7, 1a 3,♀1,n X X,♀1d ;♀Z♂♀Z 7; 1 ;71M;; 1 1,X1X T1MZ7Z19T611611,111, 1271♀184♂770;,6; 4 ,, ♀,♀a ♀;n;♀ ;dX X; ZZX111Z12116171267,, 6♂♀,; ;X♀ Z; 11177,
The Chinese population of R. rattus is black allXoZv11e2r0i7ts, Xb♀Zo; 1d1Xy0Z,2181,2 ♀0.8 , ♀X; ZX1Z11012283, 2♀, . ♀ ; XXZZ1111012785,, ♀♀. X; ZX11Z2101179, 6♀, ; ♂X; Za1n1d2 08, ♀; XZ11232, ♀; XZ11175, ♀; XZ11196, ♂; and
whereasR.exulans onlyoccursinislandsofthe♂XZ;S 1ao1n0ud2t h8X, C♀Z1h.X 1i Zn1♂71a13; 2, a0♀n7d,. ♀JXEu;Zt vy1eX1mXnZ1iZ♂l71oe113;sl 12,o: 2a 0g0♀n8X7yd,.Z , : 1♀JXX1♀uZ;2Z v;T10 1eX1h17XnXZ21,ei Z0l71Ze1♀1731s1n2,,1;: 2 3a2♀0♀M2X0m8,;.7ZT ,e, 11 ♀JX11♀u♀Z;21 iv;1s0;7 eX X174XnZXZ2,,Xdi Z 10l1ZeZe11♀♀181s1101r,1;;: 1i2 27 2v2♀385MXX0e♂02,,;8ZZ d T7 ;,♀ , 111,♀ X 11.a1♀ ♀f;Z121♀n r ;710;o7d ;X 16 74 mXZX2,,,XX Z 13ZZZ♀11♀♀21t1111,;1h;;1 119 2e1276♀MX3705,;2Z T38 ,t ,1♂y,1, X 1♀1p;♀Z1♀1♀ ;e71 ;7a.; 1 6 4Xn1X,J,lXd Z o7uZ Z♀15♀cv111,ea;1; 11 1nl92♀iX7itl63ye;5Z ,2,s ,1 ,X: 1♂ ♀Z1♀X;17 ; ;Z16 a11X,nX 19ZdZ2♀61 01,1; 1 711♂,9 7;6♀ 5, ,a; n♂♀Md; ; T a1Xn1Z1d17 141, 96♀,; ♂X;Z 1a1n1d7 6, ♀;
Sea, including Taiwan, and has a very small hXeZa1d12a0n7d, ♀bXo; ZdXX1y1ZZ011211822,00 ♀87,,s. o♀♀ u;;tX hZXXXe1ZZZr1111n01112222X8003i,z872 ♀Xa,,, Z.n ♀♀♀1g 1;;; X0(XXXT2Z8ZZZi1b,1111 e111♀01t222.) 7038, 582,C ,,,♀ h.♀♀♀ in ;;; aXXXX.ZZZZ111111110112X2973Z86521,,,, 1 ♀2♂♀♀. 0;;; 7 ,aXX nZZ♀d11; 11 11X97Z651,, 12♂♀0;; 8 ,aX nZ♀d1; 1 1X9Z61, 12♂3; 2,a n♀d; XZ11175, ♀; XZ11196, ♂; and
length.However,R.loseaandR.tanezumioccuXrZsy11m0p28a,t r♀ic. a lXlyZ11028,D ♀ia. g nXoZ1s1i0s2:8,C ♀u. s p t3 present on MXZ111in02fi8r, s♀t. t ransverse loop,
in southern China. They are easily confused due to similar
but very small; head and body relatively large; tail length
appearances and overlapping measurements. Most species
usually larger than head plus body length; belly gray-white;
showed significant overlap in the PCA plots (Figure 3A, B).
transition between darker dorsal and lighter ventral pelage
Perhapsduetochallengesinidentification,GenBankcontains
abrupt;dorsumoffeetwhite,notglossy.
many misidentifications. For example, sequences under the
nameofR.norvegicusoccurinalmostallclades(Figure5). Description: Summer pelage from neck to hip uniform
Ournewsamplingandsurveyofsequencessupportedthe brown-black.Ventralhairswithgray-blackbaseandgray-white
occurrenceofninespeciesofApodemusandsevenspeciesof tip,transitionbetweendarkerdorsalandlighterventralpelage
Rattus inChina. However, itisnecessarytobecautiouswith relatively abrupt. Dorsal and ventral tail uniform brown-black;
morphometricandmolecularanalysesforspeciesidentification hairsondorsalandventeroffeetwhite,notglossy.
due to considerable intraspecific variation and considerable
Skull sturdy (Figure 6), in dorsal profile straight and brain
errorsinGenBank.
caseflattened;highestpointofskullinmiddleofparietalbone.
AlphadiversityofApodemusandRattus Nasalbroadanteriorlynarrowingposteriorly. Posteriormargin
WedeterminedthatA.agrarius,A.chevrieri,A.draco,A.ilex, ofnasalsirregularandprotrudinginfrontofmaxilla. Posterior
A. latronum, A. pallipes, A. peninsulae, A. semotus, and A. and anterior of frontal broad, middle narrower. Interparietal
uralensisoccurinChina.Inaddition,considerableintraspecific broad, anterior part triangle-shaped and posterior margin
diversity occurs in several species. Future comprehensive arc-shaped(Figure6).Interorbitalandtemporalridgespresent.
and integrative analyses can determine if further splitting is Zygomatic arches medium in size, front part slightly broader.
necessaryand/ordesirable. Auditory bullae moderately sized. Incisory foramen broad.
WedeterminedthatR.andamanensis,R.exulans,R.losea, Mandiblesmedium-sized(Figure6).
R. nitidus, R. norvegicus, R. rattus, and R. tanezumi occur Upper incisors medium in size vertically downward and
in China. Future research into the occurrence of R. pyctoris orange. Molarsrooted; 1stuppermolarwiththreetransverse
in China is not necessary. A new subspecies of R. nitidus is dentalloops,firstdentalloopwith3cusps,t3presentbutsmall;
describedasfollows: 2nduppermolarwiththreetransversedentalloops,firstdental
looponlyonlingualcusp;3rduppermolarwiththreetransverse
Subspeciesdescription dental loops, first dental loop only on lingual cusp, third loop
onlysinglesemicircleandsecondlooprectangular;mandibular
Rattusnitidusthibetanussubsp.nov
condyleandcoronoidprocesslarge,butlowermolarsameas
Holotype: Adult female, collected by Liao Rui on 15 January
inotherspeciesofRattus.
2011.Thespecimenwaspreparedasaskinwithcleanedskull
anddepositedintheSichuanAcademyofForestry(MT11197). Habitat: Specimens were collected from an abandoned
farmland, along the footpath of a rice field where highland
Typelocality: MotuoCounty,Xizang,China,N29.24344°and barleywasgrown,forestedge,shrubland,surroundingahouse,
E95.169920°,783ma.s.l.. andsalvagestation.
318 www.zoores.ac.cn