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Geographical distribution and genetic diversity of Gymnogobius sp. “Chokai-endemic species”

Geographical distribution and genetic diversity of Gymnogobius sp. “Chokai-endemic species”
Geographical distribution and genetic diversity of Gymnogobius sp. “Chokai-endemic species”

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Geographical distribution and genetic diversity of Gymnogobius sp.‘‘Chokai-endemic species’’(Perciformes:Gobiidae)

Satoru N.Chiba ?Ryosuke Kakehashi ?Kouichi Shibukawa ?Takahiko Mukai ?Yasuyuki Suzuki ?Naoto Hanzawa

Received:1December 2013/Revised:20May 2014/Accepted:30May 2014/Published online:26June 2014óThe Ichthyological Society of Japan 2014

Abstract The geographical distribution and intraspeci?c genetic diversity of an endangered freshwater goby,Gym-nogobius sp.‘‘Chokai-endemic species’’,was surveyed based on mitochondrial cytochrome b gene sequences in Yamagata Prefecture and adjacent areas on the island of Honshu,Japan.An extensive ?eld survey showed that the species is distributed in 11locations from Gosen,Niigata Prefecture to Yuza,Yamagata Prefecture.The species was not collected together with Gymnogobius sp.‘‘widely

distributed species’’at each location,although the distri-bution of these two species overlaps.A maximum likeli-hood phylogenetic analysis showed that Gymnogobius sp.‘‘Chokai-endemic species’’is genetically divergent from other Gymnogobius castaneus species complex and the species consists of Niigata and Yamagata sub-clades.The result suggests that the Niigata and Yamagata regional groups can be distinguished from each other by their sequence divergence and the two groups should be treated as provisionally distinct ‘‘evolutionarily signi?cant units’’.The indices of intra-population genetic diversity were noticeably low,suggesting that each population has prob-ably experienced bottleneck events.The geographical dis-tance between the two populations in the Yamagata group,where the haplotypes are completely different from each other,was within 3km.This suggests that habitat loss,fragmentation and isolation occurred in the Yamagata area due to some arti?cial cause.Conservation measures may be needed not only to protect individual habitats but also to promote genetic exchange among habitats in the Yamagata area.

Keywords Gymnogobius castaneus complex áconservation áphylogeography áYamagata áNiigata

Introduction

In Japan,the ?oating goby,Gymnogobius castaneus (Perciformes:Gobiidae)(Japanese name:Juzukake-haze),normally inhabits freshwater lakes and surrounding streams (Stevenson 2002;Mukai et al.2010).The species is dis-tributed from the Kanto and Hokuriku districts to the Sakhalin and Kuril Islands in the south (Stevenson 2002;Mukai et al.2010).Previous genetic studies,based on

Electronic supplementary material The online version of this article (doi:10.1007/s10228-014-0415-x )contains supplementary material,which is available to authorized users.

S.N.Chiba (&)

Center for Molecular Biodiversity Research,

National Museum of Nature and Science,4-1-1Amakubo,Tsukuba,Ibaraki 305-0005,Japan e-mail:chiba_s@kahaku.go.jp

S.N.Chiba áR.Kakehashi áN.Hanzawa Faculty of Science,Yamagata University,

1-4-12Kojirakawa-machi,Yamagata 990-8560,Japan R.Kakehashi

Institute for Amphibian Biology,Graduate School of Science,Hiroshima University,1-3-1Kagamiyama,Higashi-Hiroshima,Hiroshima 739-8526,Japan

K.Shibukawa

Nagao Natural Environment Foundation,3-3-7Kotobashi,Sumida ku,Tokyo 130-0022,Japan

T.Mukai

Faculty of Regional Studies,Gifu University,1-1Yanagido,Gifu 501-1193,Japan

Y.Suzuki

Publishers’Association of Fishes in Gakko-gawa River,1-2-10Eki-higashi,Sakata,Yamagata 998-0022,Japan

Ichthyol Res (2015)62:156–162DOI 10.1007/s10228-014-0415-x

allozyme and mitochondrial DNA markers,showed that G. castaneus,as previously recognized,can be classi?ed into several species(Aizawa et al.1994;Sota et al.2005; Shinozaki et al.2006).Recently,Mukai et al.(2010)sug-gested that G.castaneus forms a species complex,which consists of at least four species,Gymnogobius sp.‘‘widely distributed species(WD)’’,Gymnogobius sp.‘‘Chokai-endemic species(CE)’’,Gymnogobius sp.‘‘Toyama-ende-mic species(TE)’’and Gymnogobius sp.‘‘Kanto-endemic species(KE)’’.Gymnogobius sp.‘‘WD’’has a relatively wide distribution from the Kanto and Hokuriku districts northward to Hokkaido.The other species,Gymnogobius sp.‘‘CE’’,Gymnogobius sp.‘‘TE’’and Gymnogobius sp.‘‘KE’’,are endemic to relatively speci?c regions,i.e.,the area adjacent to Mt.Chokai in Yamagata and Akita Pre-fectures,a narrow region of Toyama Prefecture,and the middle course of four river systems in the Kanto district (the Naka-gawa,Tone-gawa,Ara-kawa and Tama-gawa rivers),respectively.In recent decades,these species have been threatened by destruction of their habitats and deci-mated by introduced predators;as a result,they are now listed as endangered species in the Red List of Nature Conservation Bureau of Japan Ministry of the Environment (2013).

Gymnogobius sp.‘‘CE’’is hitherto known only from several ponds and adjacent streams in Yamagata and Akita Prefectures;hence,the existence of this species is tenuous (Mukai et al.2010).The distribution area of this species and some adjacent areas is home to a very unique fresh-

water?sh fauna(e.g.,Takahashi et al.2001;Yokoyama and Goto2002;Yamazaki et al.2003;Aiki et al.2009), and phylogeographical studies of this species are essential to an understanding of biogeography in the areas.However, its taxonomic status,geographical distribution and genetic diversity within Gymnogobius sp.‘‘CE’’are still unclear. The main aim of the present study was to clarify the geo-graphical distribution and intraspeci?c genetic diversity of Gymnogobius sp.‘‘CE’’.Based on the results,its conser-vation and the common geographical and/or ecological factors affecting?sh in the Yamagata area are discussed. Materials and methods

Field survey and sample collection.Extensive?eld surveys to clarify the geographical distribution of Gymnogobius sp.‘‘CE’’were conducted in the Hokuriku and Tohoku dis-tricts of northern Japan during2009–2011(Fig.1).The surveys were carried out at52locations(23,16,and13 locations at Niigata,Yamagata,and Akita Prefectures, respectively),in ponds,reservoirs,and adjacent streams on the margins of montane areas.We had conducted more extensive?eld surveys in these prefectures,but many of the locations where we could not collect any?sh specimens were not recorded.Fish samples were collected by hand-nets and minnow traps.We collected a smaller number of specimens at each sampling site for conservation of the species.Species identi?cation followed Mukai et al. (2010).Gymnogobius sp.‘‘CE’’is unique within the G. castaneus species complex by lacking distinct yellow vertical bands on the side of the body in nuptial coloration of the female,and can be distinguished from the other congeners in the complex by having following combination of characters:32–34(usually33–34)vertebrae;sum of soft ray numbers of the second dorsal and anal?ns16–18 (usually18);total35–39caudal-?n rays(including pro-current rays);0–5predorsal scales.Although the habitat of Gymnogobius sp.‘‘CE’’is adjoined to that of Gymnogobius sp.‘‘WD’’,snout length,inter-orbital width,and jaw length of the former are relatively longer than those of the latter (Mukai et al.2010).A small portion of the pectoral?n or skeletal muscle was removed from the right side of each specimen and preserved in99.95%ethanol.Voucher specimens and tissue samples were deposited in the National Museum of Nature and Science,Tsukuba.Details of the specimens used in the study are summarized in Electronic Supplementary Material(ESM)Table

S1. Fig.1Distribution of Gymnogobius sp.‘‘CE’’.Open circles indicate sampling locations with population code.Open squares indicate an area where the geographical distribution of Gymnogobius sp.‘‘CE’’was surveyed.Shadings of gray on the map indicate different altitudes.Detailed locations are masked in the interest of conservation of the species

Phylogeography of Gymnogobius sp.‘‘Chokai-endemic species’’157

DNA extraction,PCR and sequencing.Total DNA puri?cation from tissue samples was performed according to the methods described by Chiba et al.(2009).Using total DNA and primer pair AJG15(Akihito et al.2000)and Simt12-Fb(Kuriiwa et al.2007),approximately2.3kbp fragments including the mitochondrial cytochrome b(cyt-b)gene were ampli?ed under the following PCR condi-tions.Thirty ampli?cation cycles were performed at94°C for45s,56°C for30s and72°C for2min.Two primers were used for sequencing the PCR products(L14736-TM: 50-AAY CAC CGT TGT AAT TCA ACT A-30as the forward primer of cyt-b and H15973-TM:50-TTG GGA GCT AGG GGT GGG AGT T-30as the reverse primer of cyt-b).Direct sequencing was performed using automated genetic analyzer models3130and3500(Applied Biosystems).

The obtained cyt-b sequences were multiply aligned using MUSCLE(Robert2004)and the aligned sequences were visually inspected.All haplotype sequences are available from DDBJ/EMBL/GenBank with accession numbers AB872269–AB872276.To construct a maximum likelihood tree of the Gymnogobius castaneus complex,the sequences were further multiply aligned following those of related species,Rhinogobius giurinus(accession number: AB018997)(Kumazawa et al.1999),Gymnogobius uchidai (AB073934),Gymnogobius isaza(AB073945),Gymnogo-bius macrognathos(AB073964)(Harada et al.2002); Gymnogobius urotaenia(AY450365),Gymnogobius breunigii(AY450368),Gymnogobius heptacanthus (AY450376),Gymnogobius opperiens(AY450379),Gym-nogobius petschiliensis(AY450380),Gymnogobius taran-etzi(AY450366,AY450367,AY450373,AY450374, AY450378,AY450381,AY450382,AY450385),and Gymnogobius castaneus(AY450383,AY450384,AY-450386–AY450388,AY461730,AY461731)(Sota et al. 2005).

Phylogenetic analysis.A maximum likelihood(ML) tree was inferred by likelihood ratchet(Vos2003)using all haplotype sequences of the gene detected in the study and 24sequences of related species from DDBJ/EMBL/Gen-Bank.A ML tree was heuristically searched using Tree-?nder(Jobb2008).The ML model adopted HKY? Gamma,HKY and TN?Gamma models for the1st,2nd and3rd codon positions,respectively,which were selected as the best-?t model of the nucleotide substitution by KAKUSAN ver.4.0(Tanabe2007)on the basis of Akaike Information Criterion(AIC;Akaike1973).A likelihood ratchet analysis was performed using Tree?nder with the parallel execution program Phylogears(Tanabe2008).This analysis was accomplished through the program TNT (Goloboff et al.2008),which generated3,000trees as a starting tree with a random re-weighting of15%of the characters.Subsequently,the ML trees were subjected to a heuristic search using Tree?nder.An ML tree was selected from3,000trees generated by the likelihood ratchet ana-lysis.The signi?cance of each branch of the tree was evaluated by bootstrapping with1,000replications using Tree?nder with Phylogears.In the analysis,the ML tree was used as the starting tree and the parameters were the same values as those used to construct the ML tree.To reconstruct the relationship among the haplotypes assigned to each tree clade,a statistical parsimony network was constructed using the program TCS1.21(Clement et al. 2000).

Genetic diversity and population structure analyses. Haplotype diversity(h)and nucleotide diversity(p)within populations were estimated using the program ARLEQUIN ver. 3.11(Excof?er et al.2005).Haplotype frequency distributions for each population were compared using an exact test of population differentiation(Raymond and Rousset1995).

Results

Geographical distribution.Gymnogobius sp.‘‘CE’’was found at11locations(Populations A–K)from Gosen in Niigata Prefecture northward to Yuza in Yamagata Pre-fecture(Fig.1;Table1).All locations are situated on the margins of montane areas(details of collection areas are not shown in the interest of habitat protection).Twenty specimens of Gymnogobius sp.‘‘WD’’were also col-lected for comparison with Gymnogobius sp.‘‘CE’’. Gymnogobius sp.‘‘CE’’and Gymnogobius sp.‘‘WD’’were not collected together at a single location,although both species are distributed in Niigata and Yamagata Prefectures.Gymnogobius sp.‘‘CE’’was collected from several ponds and adjacent streams on the margins of montane areas,whereas Gymnogobius sp.‘‘WD’’was found around the lower reaches of rivers and canals on the plains.

Mitochondrial DNA phylogenies.Partial cyt-b gene sequences(1,093bp)of194individuals were classi?ed into eight haplotypes.We used1,093homologous sites for the following analyses(except ML analysis).Five and three of the haplotypes were obtained from Gymnogobius sp.‘‘CE’’and from Gymnogobius sp.‘‘WD’’,respectively. The sequences were further multiply aligned with those of related species.We used640homologous sites for the following ML analysis.The eight haplotypes were distin-guishable with the640sites.ML analysis showed that Gymnogobius sp.‘‘CE’’was divergent from other G.cas-taneus species complexes(Fig.2).ML analysis showed that those haplotypes were divided into two divergent clades(clades A and B).Clade A consisted of?ve haplo-types(Hap-01,02,03,04and05).Hap-03was the same as

158S.N.Chiba et al.

that of the Yuza,Yamagata,as previously reported by Sota et al.(2005).Clade A was further divided into two sub-clades(Yamagata and Niigata sub-clades).In the haplotype network of clade A,the two sub-clades were connected by 24single-base substitutions(Fig.2).Haplotypes within the Yamagata sub-clade were generated from Hap-01by a single-base substitution.Those of the Niigata sub-clade were connected to another by two single-base substitutions. Clade B consists of three haplotypes(Hap-06,07and08). These haplotypes were generated from Hap-06by a single-base substitution.This clade was closely related to the lineage from the Yoneshiro River in Akita Prefecture,as reported previously(Sota et al.2005),and further formed a major clade with other?oating gobies found along the Sea of Japan coast of Honshu(Sota et al.2005)(Fig.2).

Genetic diversity.Three haplotypes,Hap-01,02and 03,were shared by more than one population(Table1); namely,Hap-01,02and03were found in populations D and J,populations A,B,F and H,and populations C,E,G, H and I,respectively.An exact test of the haplotype fre-quency distributions for each population resulted in sig-ni?cant differences(P\0.001),except for the comparison of populations C–D,C–H,G–H,and D–J(P[0.138) (Fig.3).Notably,although geographically distant two populations D and J(ca.34km in direct distance)shared and?xed same haplotype Hap-01,geographically close two populations C and D(ca.3km in direct distance)are ?xed different haplotype from each other(Table1;Fig.3). The other two haplotypes,Hap-04and05were only found in population K.The cyt-b gene sequences were mono-morphic in the eight populations,B,C,D,E,F,G,I and J (Table1).The level of haplotype diversity(h)in the Gymnogobius sp.‘‘CE’’populations was low,with observed values ranging from0.000to0.262for1,093bases in the cyt-b gene(Table1).In contrast,three hap-lotypes,Hap-06,07and08,were found in population L of Gymnogobius sp.‘‘WD’’and its haplotype diversity (h=0.468)was relatively high(Table1).Nucleotide diversities(p)were comparatively low in all populations (0.000–0.048%)(Table1).

Discussion

Distribution of Gymnogobius sp.‘‘CE’’.Our?eld surveys showed that Gymnogobius sp.‘‘CE’’is distributed from Gosen in the northern part of Niigata Prefecture northward to Yuza in the northern part of Yamagata Prefecture, although it was previously thought to be restricted to the region surrounding Mt.Chokai on the borders of Yamagata and Akita Prefectures(Sota et al.2005;Mukai et al.2010).

The distribution of Gymnogobius sp.‘‘CE’’is still uncertain within Akita Prefecture.Mukai et al.(2010) mentioned the distribution of this species in Akita Prefec-ture based on personal communication by T.Shinozaki. However,there is no information on voucher specimens and their sampling locations.Although we surveyed more than13ponds and streams in the southern part of Akita Prefecture,whose environments are quite similar to those of Yamagata and Niigata Prefectures,Gymnogobius sp.‘‘WD’’was the only species found.Further?eld studies are needed to verify the distribution of Gymnogobius sp.‘‘CE’’in Akita Prefecture.On the other hand,the present study uniquely revealed the existence of another regional group of Gymnogobius sp.‘‘CE’’in Gosen,northern Niigata. Jordan and Richardson(1907)described a new goby spe-cies,Chloea nakamurae,based on specimens collected from Nagaoka in Niigata Prefecture(approximately50km

Table1List of locations,number of specimens(n),haplotype diversity(h)and nucleotide diversities(p)

Species Population code(location)n Haplotype(n)h±SD p(%)±SD

Gymnogobius sp.‘‘CE’’

A(Yuza,Yamagata Prefecture)27Hap-02(23),Hap-03(4)0.262±0.0970.048±0.046

B(Yuza,Yamagata Pref.)2Hap-02(2)0.0000.000

C(Sakata,Yamagata Pref.)18Hap-03(18)0.0000.000

D(Sakata,Yamagata Pref.)23Hap-01(23)0.0000.000

E(Sakata,Yamagata pref.)2Hap-03(2)0.0000.000

F(Sakata,Yamagata Pref.)5Hap-02(5)0.0000.000

G(Sakata,Yamagata Pref.)18Hap-03(18)0.0000.000

H(Sakata,Yamagata Pref.)27Hap-02(4),Hap-03(23)0.262±0.0970.048±0.046

I(Sakata,Yamagata Pref.)5Hap-03(5)0.0000.000

J(Tsuruoka,Yamagata Pref.)27Hap-01(27)0.0000.000

K(Gosen,Niigata Pref.)20Hap-04(18),Hap-05(2)0.190±0.1080.035±0.038 Gymnogobius sp.‘‘WD’’

L(Tsuruoka,Yamagata Pref.)20Hap-06(14),Hap-07(1),Hap-08(5)0.468±0.1050.045±0.045 Phylogeography of Gymnogobius sp.‘‘Chokai-endemic species’’159

southwest of Gosen).Subsequently,Stevenson (2002)regarded the scienti?c name as a junior synonym of Gymnogobius castaneus .The morphological characteristics of C.nakamurae are almost identical to those of Gym-nogobius sp.‘‘CE’’.Unfortunately,despite extensive ?eld studies,we have not succeeded in collecting any specimens of the G.castaneus complex from Nagaoka.There is a distinct possibility that habitats of the G.castaneus com-plex disappeared in Nagaoka because of human activities.Taxonomic status of Gymnogobius sp.‘‘CE’’will be dis-cussed in detail by our forthcoming paper.

Genetic diversity in Gymnogobius sp.‘‘CE’’.Popula-tion genetic analysis of Gymnogobius sp.‘‘CE’’showed that most populations were monomorphic or polymorphic with only two haplotypes with one or two single nucleotide substitutions.The parameters of intra-population diversi-ties (h and p )were noticeably low (Table 1).As Grant and Bowen (1998)proposed,populations with low haplotype and low nucleotide diversities had possibly experienced

bottleneck and/or founder events during the last thousands to ten thousands years.The low intra-population diversity in Gymnogobius sp.‘‘CE’’is also probably caused by such bottleneck and/or founder events.

The phylogenetic tree indicated that Gymnogobius sp.‘‘CE’’was divergent from other G.castaneus species complexes (Fig.2).Similarly,other genetic studies have also shown that some freshwater ?sh or populations,such as nine-spine stickleback (Takahashi et al.2001),?uvial sculpin (Yokoyama and Goto 2002),Far Eastern brook lamprey (Yamazaki et al.2003),medaka (Takayama-Wa-tanabe et al.2006)and eight-barbel loach (Aiki et al.2009),collected from Yamagata Prefecture,were divergent from their relatives collected from neighboring areas.These unique phylogeographic patterns may have been formed by common geological and/or ecological factors across the ?sh fauna in the area.A large freshwater system,encompassing the Okitama and Shinjo Paleo-lakes,devel-oped in the present inland area of Yamagata Prefecture during the Pliocene (Yamanoi 2009).It can be hypothe-sized that the paleo-lakes may have promoted speciation of Gymnogobius sp.‘‘CE’’.Sota et al.(2005)estimated that the differentiation of Gymnogobius sp.‘‘CE’’has occurred since the Pliocene (ca.5million years ago).This agrees with the age in which the above ancient lake existed.On the other hand,this area was often exposed to active tec-togenesis and climatic changes during the Plio–Pleistocene era (Koike et al.2005).During the processes,the structure of freshwater systems has been changed through river capture and sea level changes.As a result of the changes of water systems,migration and isolation of Gymnogobius sp.‘‘CE’’might have occurred in the Niigata and Yamagata https://www.wendangku.net/doc/c411952749.html,parative biogeographical studies

of

Fig.2Phylogenetic tree for the Gymnogobius castaneus

complex constructed based on mitochondrial cytochrome b gene sequences with

haplotype networks for clades A and B.A star with a thick line and a solid black circle indicate 24base substitutions and the missing haplotype in the

haplotype network,

respectively

Fig.3Result of the exact test for the difference in haplotype frequencies between populations of the Yamagata group.Asterisks indicate P \0.001.The geographical direct distance between pop-ulations is indicated by gray shadings

160

S.N.Chiba et al.

freshwater?shes in these areas could prove informative. Such studies are urgently required,as most species con-sidered are now endangered,as discussed below.

Conservation of Gymnogobius sp.‘‘CE’’.Gymnogo-bius sp.‘‘CE’’is assigned as a critically endangered species in the Red List of the Nature Conservation Bureau of Japan Ministry of the Environment(2013).The evolutionarily signi?cant unit(ESU)is a population unit that merits separate management and is highly valuable in conserva-tion(Ryder1986).Crandall et al.(2000)proposed the need for a broader categorization of population distinctiveness based on concepts of ecological and genetic exchange-ability.It is possible that genetic exchangeability is detectable from fundamental molecular analyses such as in the present study.There is no historical or recent genetic exchangeability between the Niigata and Yamagata groups of Gymnogobius sp.‘‘CE’’.The two groups should be treated as provisionally distinct ESUs to protect from outbreeding depression and retain the value of historical background of local populations.

In the Yamagata group,haplotypes in geographically close two populations C and D(ca.3km in direct distance) are?xed to different ones with signi?cantly different fre-quencies(Table1;Fig.3).In contrast,those in geographi-cally distant two populations D and J(ca.34km in direct distance)are shared and?xed to the same haplotype,Hap-01(Table1;Fig.3).The formation process of such genetic population structures in the Yamagata group may be explained by decrease of population size and habitat loss. As mentioned above,the populations might have experi-enced bottleneck and/or founder events.The genetic drift after bottleneck and/or founder events consequently leads to random?xation of a single or small number of haplotypes. If gene?ow is maintained between the populations within the Yamagata group,differentiation of haplotype frequen-cies would not occur.However,the signi?cant difference in haplotype frequencies was actually detected between the Yamagata populations;this suggests no gene?ow occurs among the populations after the?xation.Such absence of gene?ow might have been caused by habitat loss and fragmentation,which lead to the fragmentation and isola-tion of populations.An ancient population of Gymnogobius sp.‘‘CE’’is presumed to be distributed continuously in montane wetlands in this area.However,the population has been fragmented until the present.In the Yamagata area, rice paddy-?eld development has taken place,and notably more modern and large-scale development has taken for a number of decades(e.g.,Yamagata Prefecture and Mo-gamigawa River Land Improvement Of?ce1996).These development activities would have caused habitat destruc-tion,reduction and fragmentation of the goby.Although further consideration of the effect on the environment is required,conservation measures may be necessary not only to protect each habitat but also to promote genetic exchange among habitats in the Yamagata area.

In Niigata Prefecture,the existence of Gymnogobius sp.‘‘CE’’from only a single location in Gosen could be con-?rmed.In and around Gosen,there are numerous ponds and streams suitable for Gymnogobius sp.‘‘CE’’;however,these habitats have been unavailable because of the introduction of predator?sh species,viz.bluegill(Lepomis macrochirus) and/or largemouth bass(Micropterus salmoides)(see Nii-gata Prefecture2001).Field studies on the current status and distribution of the Niigata group of Gymnogobius sp.‘‘CE’’are of a priority for conservation of the species. Acknowledgments We thank H.Sugiyama(Akita Prefectural University),T.Kusanagi(SHIZEN KAGAKU),S.Honma,Y.Mi-shima,H.Kudo(Kamo Fisheries High School)and T.Kawaguchi (Bioindicator Co.Ltd.)for helpful advice and assistance during the ?eld survey.This study was partially supported by JSPS KAKENHI Grant Number23570105.

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卫生部关于印发《脐带血造血干细胞库设置管理规范(试行)》的通知

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