COI基因条形码技术在广东沿岸钳蛤科动物分类鉴定中的应用

罗浩; 余语湘; 林奕慧; 陈耀辉; 纪小康; 张敬怀

doi:10.12284/hyxb2026018

COI基因条形码技术在广东沿岸钳蛤科动物分类鉴定中的应用

doi: 10.12284/hyxb2026018

罗浩^{1, 2, 3,},
余语湘^{1, 2, 3},
林奕慧^{1, 2, 3},
陈耀辉^{1, 2},
纪小康^{1, 2, 3},
张敬怀^{1, 2, ,}

1.
自然资源部南海生态中心，广东广州 510300
2.
自然资源部海洋环境探测技术与应用重点实验室，广东广州 510300
3.
华南农业大学海洋学院，广东广州 510642

基金项目: 广东省科技计划项目（2021B1212110001）；国家自然科学基金（42076129）。

详细信息

作者简介:
罗浩（1999—），男，湖南省双峰县人，主要从事牡蛎礁礁栖生物多样性调查研究。E-mail：1455878429@qq.com

通讯作者:
张敬怀，正高级工程师，主要从事底栖生物生态学、海洋环节动物系统分类学研究。E-mail：zhangjinghuai@scs.mnr.gov.cn

中图分类号: Q959.1
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出版历程
- 收稿日期: 2025-07-02
- 修回日期: 2025-09-30
- 刊出日期: 2026-01-25

Application of COI DNA barcoding for taxonomic identification of Isognomonidae in the Guangdong coast, China

Luo Hao^{1, 2, 3
,},
Yu Yuxiang^{1, 2, 3},
Lin Yihui^{1, 2, 3},
Chen Yaohui^{1, 2},
Ji Xiaokang^{1, 2, 3},
Zhang Jinghuai^{1, 2
, ,}

1.
South China Sea Ecology Center, Ministry of Natural Resources, Guangzhou 510300, China
2.
Key Laboratory of Marine Environmental Survey Technology and Application, Ministry of Natural Resources, Guangzhou 510300, China
3.
College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China

摘要

摘要: 钳蛤科Isognomonidae动物广泛分布于热带和亚热带海域的潮间带，具有重要的生态和经济价值。但由于物种形态受生境影响显著，基于传统形态学的钳蛤物种分类存在较大争议。本研究通过对广东沿岸潮间带采集的钳蛤样本进行线粒体COI基因序列测定，结合GenBank数据库中的同源序列，构建系统发育树，运用DNA分子条形码技术分析该地区钳蛤科的物种组成。结果显示，基于不同模型构建的COI基因系统发育树均支持钳蛤科单系发育，125条COI序列能形成68个单倍型，并被分为16个获得支持的物种水平分类单元，但这些分类单元间的进化关系还存在争议。各分类单元组内Kimura 2-parameter（K2P）遗传距离为0.000～0.009，组间遗传距离为0.029～0.595。钳蛤COI基因片段的A+T和C+G含量平均分别为55.0%和45.0%，不同物种间存在差异。广东沿岸采集的标本共鉴定出5种钳蛤，包括1个已记录种方形钳蛤Isognomon nucleus和4个隐存种。DNA分子条形码技术能有效支持并修订钳蛤系统分类，揭示新物种，对海洋物种多样性保护具有重要意义。
- 南海北部 /
- 钳蛤 /
- COI /
- 物种鉴定 /
- 隐存种
Abstract: Isognomonids are widely distributed in the intertidal zones of tropical and subtropical regions, where they play important ecological and economic roles. However, due to significant morphological variability influenced by environmental factors, morphology-based taxonomic classifications of Isognomonidae remain contentious. In this study, mitochondrial COI sequences were obtained from specimens of Isognomonidae collected along the Guangdong coast, supplemented with homologous sequences retrieved from GenBank to construct phylogenetic trees, and DNA molecular barcoding techniques been applied to analyze the species of Isognomonidae distributed in the Guangdong coast. Results demonstrated strong support for the monophyly of Isognomonidae. A total of 125 COI sequences yielded 68 haplotypes, which clustered into 16 well-supported species-level units, although their evolutionary relationships remain uncertain. Intraspecific Kimura 2-parameter (K2P) genetic distances ranged from 0 to 0.009, while interspecific distances ranged from 0.029 to 0.595. The average nucleotide composition of the COI fragments showed 55.0% A + T and 45.0% C + G, with variation observed among species. Five species were identified from Guangdong samples, including the previously recorded Isognomon nucleus and four cryptic species. This study confirms that DNA barcoding is an effective tool for supporting and revising the taxonomy of Isognomonidae and reveals cryptic diversity, which is crucial for marine biodiversity conservation.
- northern South China Sea /
- isognomonids /
- COI /
- species delimitation /
- cryptic species

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图 1 钳蛤科动物在广东沿岸的采集站位及个体数量分布

Fig. 1 Sampling stations and individual abundance distribution of isognomonids along the Guangdong coast

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图 2 广东沿岸5种钳蛤动物的形态特征：Isognomon sp.1（标本号：SCSMBC031070）左壳外视图（a）与右壳内视图（b）；Isognomon sp.2（标本号：SCSMBC031138）左壳外视图（c）与右壳内视图（d）；Isognomon sp.3（标本号：SCSMBC031147）左壳外视图（e）与右壳内视图（f）；Isognomon sp.4（标本号：SCSMBC031152）左壳外视图（g）与右壳内视图（h）；方形钳蛤 Isognomon nucleus（标本号：SCSMBC031067）左壳外视图（i）与右壳内视图（j）

Fig. 2 Morphological characteristics of five Isognomon species from the coast of Guangdong: Isognomon sp.1 (SCSMBC031070), external view of left valve(a) and internal view of right valve(b); Isognomon sp.2 (SCSMBC031138), external view of left valve (c) and internal view of right valve (d); Isognomon sp.3 (SCSMBC031147), external view of left valve (e) and internal view of right valve (f); Isognomon sp.4 (SCSMBC031152), external view of left valve (g) and internal view of right valve (h); Isognomon nucleus (SCSMBC031067), external view of left valve (i) and internal view of right valve (j)

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图 3 基于68个单倍型线粒体COI序列，采用GTR + F + I + G4 模型构建的Bayesian系统发育树。节点数字为后验证系数（Posterior probability，PP）

Fig. 3 Bayesian phylogenetic tree constructed based on 68 mitochondrial COI haplotypes using the GTR + F + I + G4 model. Numbers at the nodes indicate posterior probabilities (PP)

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图 A1 基于68个单倍型线粒体COI基因构建的邻接法（NJ，GTR + G + I模型）与最大似然法（ML，TIM3 + F + I + G4模型）系统发育树。节点数字为自展支持度（Bootstrap，BS）

Fig. A1 Phylogenetic trees constructed based on 68 mitochondrial COI haplotypes using neighbor-joining (NJ, based on the GTR + G + I model) and maximum likelihood (ML, based on the TIM3 + F + I + G4 model) methods. Numbers at the nodes indicate bootstrap (BS)

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表 A1 分子序列信息

Tab. A1 Molecular sequence information

物种（GenBank物种名）	标本编号（序列号 GenBank Acc. No）	样品采集地	参考文献
I. alatus	J.11.2(KU758979, Hap_15), J.12.1(KU759005, Hap_21), J.12.2(KU759006, Hap_15), 786D(KU758995, Hap_15), 787D(KU758997, Hap_15), 787H(KU758998, Hap_15), FMNH:311813.2(KU758996, Hap_19), J.54.1(KU758993, Hap_16), J.54.3(KU758994, Hap_17), J.41.20(KX369031, Hap_22), J.43.5(KX369032, Hap_23), J.51.3(KU758991, Hap_19), J.11.1(KU758978, Hap_15), J.11.4(KU758980, Hap_20), J.41.6(KU758981, Hap_18), J.41.8(KU758982, Hap_16), J.42.1(KU758983, Hap_17), J.42.3(KU758984, Hap_15), J.42.4(KU758985, Hap_15), J.11.2(KU758979)	USA: Florida	[16]
	20_673(KP455069, Hap_14), C.13 Case20(KP455064, Hap_13)	Panama: Bocas del Toro	[32]
	BivAToL-30(KC429096, Hap_12)	USA: Florida	[33]
I. bicolor	J.Bicolor5(KX373613, Hap_56), J.Bicolor9(KU758999, Hap_55)	Jamaica: Frankfield,	[16]
I. ephippium	MCLY1-1(MW339757, Hap_50), MCLY1-2(MW339756, Hap_48), RICH2-2(MW339758, Hap_48), TWD4-2(MW339760, Hap_51), BRNS3-2(MW339759, Hap_49)	Australia: NSW	[8]
I. ephippium	MIEE2015-6IE1(KY081310, Hap_47)	/	unpublished
I. isognomum	IP0186(MN690578, Hap_6)	Singapore: PSL SE	[34]
I. legumen	BivAToL-425(KX713469, Hap_5)	China: Hong Kong	[35]
	(AB076950, Hap_4)	Japan: Kanagawa	[29]
	225(MT802137)	/	[36]
I. lobata	JWNTAlb1(KU759003, Hap_63)	Australia: NT	[16]
I. nucleus	TIKARTP9-69(MK934687, Hap_10)	French Polynesia: Moorea Island	unpublished
	(KT290125, Hap_8)	French: Moorea Island	[37]
	ZZ14(KU341970, Hap_9)	China: Hainan	[15]
	Acu1(KU759001, Hap_11)	Japan: Itoman, Kyan	[16]
	S.031067(PX504808, Hap_9), S.031068(PX504810, Hap_9), S.031069(PX504791, Hap_9)	China: Guangdong	this study
	(AB076926, Hap_7)	Japan: Okinawa	[29]
I. perna	TIKROCP10-38(MK934692, Hap_3)	French Polynesia: Moorea Island	unpublished
	(AB076918, Hap_1)	Japan:Okinawa	[29]
	ZZ6(KU341963, Hap_2), ZZ7(KU341964, Hap_1)	China: Hainan	[15]
I. quadrangularis	JWNTNucA(KU759000, Hap_64), JWNTNucB(KX369030, Hap_64)	Japan: Itoman, Kyan	[16]
I. quadrangularis	JWNTAlb2(KU759004, Hap_65)	Australia: Northern Territory	[16]
I. recognitus	CSUF_DNA_DE1918(KT317610, Hap_52)	Mexico: Sonora	[38]
I. recognitus	CSUF DNA DE1757(KT317608, Hap_53), CSUF DNA DE2227(KT317607, Hap_52)	Mexico: Baja California Sur	[38]
I. recognitus	CSUF_DNA_DE1913(KT317609, Hap_53)	Mexico: Sonora, Guaymas	[38]
I. recognitus	Rec(KU759007, Hap_54)	Panama: Panama City	[16]
Isognomon sp. KML-2015	18_181(KP455072, Hap_31), C.10 Case23 18(KP455061, Hap_24), C.11 Case22 18(KP455062, Hap_26), C.12 Case22 18 14 23(KP455063, Hap_26), C.14 Case19 14 23 18(KP455065, Hap_27), C.15 Case19 14 18(KP455066, Hap_25), 19_425(KP455071, Hap_29), 19_427(KP455070, Hap_30)	Panama: Bocas del Toro	[32]
Isognomon sp. KML-2015	C.16 Case14 22(KP455067, Hap_28), 22_973(KP455068, Hap_39)	Canal-Caribbean	[32]
Isognomon sp. KML-2015(Isognomon. sp. nov. JW-2017)	J.53.1(KU758992, Hap_34), J.44.2(KU758986, Hap_32), J.44.3(KU758987, Hap_35), J.44.4(KU758988, Hap_38), J.51.1(KU758989, Hap_36), J.51.2(KU758990, Hap_33), J.53.3(KX373612, Hap_37)	USA: Florida	[16]
I. spathulata	JWNTSpath(KU759002, Hap_68)	Australia: NT	[16]
Isognomon sp.1	S.031070(PX504773, Hap_61), S.031091(PX504806, Hap_58), S.031098(PX504807, Hap_58), S.031099(PX504804, Hap_58), S.031100(PX504805, Hap_58), S.031102(PX504777, Hap_62), S.031104-01(PX504782, Hap_62), S.031106-01(PX504788, Hap_61), S.031106-02(PX504786, Hap_61), S.031106-03(PX504787, Hap_58), S.031110(PX504803, Hap_58), S.031111-01(PX504789, Hap_58), S.031113(PX504790, Hap_58), S.031115-03(PX504784, Hap_58), S.031116-01(PX504783, Hap_58), S.031117-01(PX504785, Hap_58), S.031121-01(PX504779, Hap_61), S.031121-02(PX504795, Hap_58), S.031121-04(PX504794, Hap_60), S.031128-03(PX504793, Hap_58), S.031129(PX504771, Hap_58), S.031130-01(PX504774, Hap_58), S.031130-02(PX504775, Hap_62), S.031131-01(PX504772, Hap_61), S.031131-02(PX504799, Hap_58), S.031131-04(PX504800, Hap_61), S.031132-02(PX504798, Hap_58), S.031134-05(PX504797, Hap_58), S.031134-08(PX504796, Hap_62)	China: Guangdong	this study
Isognomon sp.1 (I. legumen)	ZZ68(KU341965, Hap_58), ZZ69(KU341966, Hap_58), ZZ77(KU341967, Hap_58), ZZ79(KU341968, Hap_58), ZZ81(KU341969, Hap_59)	China: Guangdong	[15]
Isognomon sp.2	S.031138(PX504811, Hap_66), S.031139(PX504778, Hap_66), S.031140(PX504792, Hap_66), S.031144(PX504813, Hap_66), S.031145(PX504801, Hap_67), S.031126(PX504802, Hap_66), S.031146(PX504815, Hap_66)	China: Guangdong	this study
Isognomon sp.3	S.031147(PX504809, Hap_57), S.031148(PX504814, Hap_57)	China: Guangdong	this study
Isognomon sp.4	S.031149(PX504780, Hap_45), S.031125-01(PX504781, Hap_44), S.031151(PX504812, Hap_44), S.031152(PX504776, Hap_46)	China: Guangdong	this study
Isognomon sp.4 (I. ephippium)	ZZ8(KU341971, Hap_40), ZZ9(KU341972, Hap_41), ZZ10(KU341973, Hap_43), ZZ11(KU341974, Hap_45), ZZ12(KU341975, Hap_42)	China: Guangdong	[15]
Pinctada albina	(AB261165)	Japan: Kagoshima	unpublished
P. fucata	(GQ355871)	Japan	[39]
P. margaritifera	(GQ355869)	Tanzania	[39]
P. margaritifera	(AB259166)	Japan: Okinawa	unpublished
Pteria loveni	(AB07692)	Japan: Okinawa	[29]
注：S. 为SCSMBC缩写；J. 为JWFL缩写；C. 为 Contig缩写。

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表 1 钳蛤科不同物种（组）COI基因片段的组内遗传距离及核苷酸组成

Tab. 1 Intraspecific genetic distances and nucleotide composition of COI gene fragments in different species (groups) of isognomonids

物种（组）	样品数 (n)	碱基数/bp			A + T/%	G + C/%	Kimura-2遗传距离
物种（组）	样品数 (n)	最小值	最大值	平均值	A + T/%	G + C/%	距离（D)	显著性水平 (P)
I. alatus	22	382	694	602	52.6	47.4	0.001	0.000
I. bicolor	2	312	677	495	56.0	44.0	/	/
I. ephippium	5	378	399	387	56.6	43.4	0.005	0.002
I. isognomum	1	320	320	320	55.1	45.0	/	/
I. legumen	3	399	759	520	54.7	45.2	0.000	0.000
I. lobata	1	694	694	694	56.3	43.7	/	/
I. nucleus GB	5	295	759	609	55.2	44.8	0.002	0.002
I. nucleus GD	3	759	759	759	55.2	44.8	0.000	0.000
I. perna	4	347	759	656	54.9	45.0	0.009	0.003
I. quadrangularis	3	694	694	694	53.3	46.6	0.000	0.000
I. recognitus	5	381	399	395	57.3	42.7	0.002	0.002
Isognomon sp. KML 2015	17	344	694	449	52.3	47.7	0.008	0.002
Isognomon sp.1 GB	5	759	759	759	56.3	43.8	0.000	0.000
Isognomon sp.1 GD	29	759	759	759	56.4	43.6	0.001	0.001
Isognomon sp.2	7	759	759	759	56.8	43.2	0.000	0.000
Isognomon sp.3	2	759	759	759	56.0	44.0	0.000	0.000
Isognomon sp.4 GB	5	759	759	759	57.1	42.9	0.005	0.002
Isognomon sp.4 GD	4	759	759	759	57.1	42.9	0.005	0.003
I. spathulata	1	694	694	694	53.7	46.3	/	/
总计	125	295	759	633	55.0	45.0	/	/

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表 A2 基于Kimura-2-parameter 模型计算的钳蛤科物种（组）间COI基因遗传距离

Tab. A2 Genetic distances between species (groups) of isognomonids based on COI gene sequences calculated using the Kimura 2-parameter model

物种（组）	I. perna	I. legumen	I. isognomum	I. nucleus GB	I. nucleus GD	I. alatus	Isognomon sp. KML 2015	Isognomon sp.4 GB	Isognomon sp.4 GD	I. ephippium	I. recognitus	I. bicolor	Isognomon sp.3	Isognomon sp.1 GB	Isognomon sp.1 GD	I. lobata	I. quadrangularis	Isognomon sp.2 GD	I. spathulata
I. perna		0.048	0.055	0.056	0.054	0.047	0.065	0.060	0.059	0.068	0.059	0.055	0.052	0.064	0.064	0.064	0.056	0.058	0.059
I. legumen	0.378		0.039	0.051	0.050	0.053	0.048	0.063	0.063	0.066	0.056	0.056	0.047	0.058	0.058	0.058	0.059	0.054	0.069
I. isognomum	0.397	0.249		0.060	0.058	0.070	0.059	0.083	0.081	0.082	0.073	0.071	0.056	0.081	0.081	0.079	0.079	0.063	0.084
I. nucleus GB	0.489	0.429	0.403		0.001	0.047	0.049	0.061	0.062	0.063	0.059	0.055	0.048	0.064	0.064	0.062	0.052	0.051	0.063
I. nucleus GD	0.479	0.422	0.395	0.001		0.046	0.048	0.060	0.061	0.061	0.057	0.053	0.046	0.061	0.061	0.060	0.051	0.051	0.061
I. alatus	0.403	0.435	0.472	0.384	0.377		0.030	0.058	0.058	0.055	0.063	0.048	0.049	0.061	0.061	0.065	0.065	0.059	0.069
Isognomon sp. KML 2015	0.516	0.393	0.403	0.405	0.397	0.195		0.054	0.053	0.054	0.059	0.056	0.047	0.051	0.051	0.052	0.053	0.056	0.067
Isognomon sp.4 GB	0.515	0.504	0.551	0.523	0.515	0.466	0.432		0.002	0.023	0.064	0.060	0.049	0.053	0.053	0.053	0.070	0.063	0.064
Isognomon sp.4 GD	0.512	0.502	0.542	0.526	0.518	0.467	0.430	0.005		0.023	0.064	0.060	0.050	0.053	0.053	0.052	0.069	0.063	0.064
I. ephippium	0.583	0.550	0.579	0.517	0.506	0.441	0.452	0.140	0.143		0.058	0.056	0.050	0.056	0.056	0.055	0.070	0.062	0.054
I. recognitus	0.502	0.469	0.481	0.495	0.478	0.516	0.496	0.548	0.546	0.491		0.030	0.037	0.040	0.040	0.041	0.040	0.035	0.045
I. bicolor	0.467	0.494	0.499	0.449	0.436	0.404	0.474	0.517	0.511	0.476	0.203		0.034	0.037	0.037	0.039	0.041	0.035	0.041
Isognomon sp.3	0.440	0.384	0.388	0.389	0.378	0.408	0.397	0.431	0.433	0.425	0.287	0.261		0.034	0.034	0.034	0.036	0.036	0.036
Isognomon sp.1 GB	0.532	0.490	0.532	0.513	0.495	0.509	0.430	0.449	0.447	0.478	0.311	0.281	0.252		0.001	0.009	0.034	0.041	0.044
Isognomon sp.1 GD	0.532	0.490	0.531	0.513	0.496	0.510	0.430	0.449	0.447	0.479	0.311	0.281	0.251	0.001		0.009	0.034	0.040	0.044
I. lobata	0.533	0.484	0.523	0.508	0.494	0.548	0.450	0.450	0.448	0.477	0.316	0.302	0.252	0.029	0.029		0.033	0.040	0.041
I. quadrangularis	0.463	0.491	0.517	0.438	0.427	0.542	0.461	0.588	0.581	0.595	0.327	0.337	0.264	0.251	0.250	0.246		0.039	0.042
Isognomon sp.2 GD	0.505	0.459	0.448	0.420	0.413	0.488	0.472	0.525	0.521	0.500	0.280	0.269	0.260	0.295	0.293	0.288	0.298		0.042
I. spathulata	0.518	0.582	0.576	0.531	0.521	0.564	0.559	0.570	0.570	0.482	0.350	0.322	0.276	0.340	0.340	0.321	0.316	0.327
注：黑色字体数据表示遗传距离；蓝色字体数据表示显著性检验水平（P）；“GB”样品来源于GenBank数据库；“GD”样品采自广东沿岸。

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