HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations

Donthu, Ravikiran; Marcelino, Jose A. P.; Giordano, Rosanna; Tao, Yudong; Weber, Everett; Avalos, Arian; Band, Mark; Akraiko, Tatsiana; Chen, Shu-Ching; Reyes, Maria P.; Hao, Haiping; Ortiz-Alvarado, Yarira; Cuff, Charles A.; Claudio, Eddie Pérez; Soto-Adames, Felipe; Smith-Pardo, Allan H.; Meikle, William G.; Evans, Jay D.; Giray, Tugrul; Abdelkader, Faten B.; Allsopp, Mike; Ball, Daniel; Morgado, Susana B.; Barjadze, Shalva; Correa-Benitez, Adriana; Chakir, Amina; Báez, David R.; Chavez, Nabor H. M.; Dalmon, Anne; Douglas, Adrian B.; Fraccica, Carmen; Fernández-Marín, Hermógenes; Galindo-Cardona, Alberto; Guzman-Novoa, Ernesto; Horsburgh, Robert; Kence, Meral; Kilonzo, Joseph; Kükrer, Mert; Le Conte, Yves; Mazzeo, Gaetana; Mota, Fernando; Muli, Elliud; Oskay, Devrim; Ruiz-Martínez, José A.; Oliveri, Eugenia; Pichkhaia, Igor; Romane, Abderrahmane; Sanchez, Cesar Guillen; Sikombwa, Evans; Satta, Alberto; Scannapieco, Alejandra A.; Stanford, Brandi; Soroker, Victoria; Velarde, Rodrigo A.; Vercelli, Monica; Huang, Zachary

doi:10.1186/s12859-024-05776-9

BMC Bioinformatics

Table 3 Results from the assignation of test samples using the genetic assignment software GeneClass2 (94)

From: HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations

AMERICA									AFRICA
HB REFERENCE SET I			HB REFERENCE SET II			HB REFERENCE SET III			HB REFERENCE SET I			HB REFERENCE SET II			HB REFERENCE SET III
Country	N	Sample ID	Country	N	Sample ID	Country	N	Sample ID	Country	N	Sample ID	Country	N	Sample ID	Country	N	Sample ID
Argentina	47		Argentina	47		Argentina	47		Kenya	59		Kenya	59		Kenya	59
	32	AHB		30	AHB		30	A		59	SSA		59	SSA		59	A
	11	EHB		2	EHB		14	C	Madagascar	14		Madagascar	14		Madagascar	14
	1	PRHB		0	PRHB		3	O		14	SSA		14	SSA		14	A
	3	SSA		3	SSA				Morocco	25		Morocco	25		Morocco	25
				8	EU DOM					3	AHB		3	AHB		25	A
				4	US DOM					22	SSA		22	SSA
Bolivia	60		Bolivia	60		Bolivia	60		Seychelles	16		Seychelles	16		Seychelles	16
	53	AHB		53	AHB		60	A		16	AHB		16	AHB		15	A
	7	SSA		7	SSA											1	O
Costa Rica	10		Costa Rica	10		Costa Rica	10		South Africa	52		South Africa	52		South Africa	52
	10	AHB		10	AHB		10	A		52	SSA		52	SSA		52	A
Mexico	46		Mexico	46		Mexico	46		Tunisia	15		Tunisia	15		Tunisia	15
	46	AHB		46	AHB		38	A		13	AHB		13	AHB		15	A
							8	O		2	SSA		2	SSA
Panama	36		Panama	36		Panama	36		Zambia	43		Zambia	43		Zambia	43
	26	AHB		26	AHB		36	A		37	SSA		37	SSA		37	A
	10	SSA		10	SSA					6	EHB		5	EHB		6	O
Puerto Rico, USA	169		Puerto Rico, USA	169		Puerto Rico, USA	169						1	carnica
	165	PRHB		164	PRHB		133	O
	4	AHB		4	AHB		32	C
				1	US DOM		4	M
USA	99		USA	99		USA	99
	4	AHB		2	AHB		82	C
	65	EHB		14	EHB		17	O
	30	PRHB		2	PRHB
				11	EU DOM
				70	US DOM

EUROPE									ASIA
HB REFERENCE SET I			HB REFERENCE SET II			HB REFERENCE SET III			HB REFERENCE SET I			HB REFERENCE SET II			HB REFERENCE SET III
Country	N	Sample ID	Country	N	Sample ID	Country	N	Sample ID	Country	N	Sample ID	Country	N	Sample ID	Country	N	Sample ID
Italy	42		Italy	42		Italy	42		Israel	20		Israel	20		Israel	20
	34	EHB		23	EHB		6	A		20	EHB		8	EHB		13	C
	1	PRHB		0	PRHB		36	C					2	EU DOM		7	O
	1	AHB		0	AHB								10	US DOM
	6	SSA		6	SSA				Rep. Georgia	26		Rep. Georgia	26		Rep. Georgia	26
				1	EU DOM					26	EHB		26	anatoliaca		26	O
				12	US DOM				Turkey	73		Turkey	73		Turkey	73
Malta	10		Malta	10		Malta	10			73	EHB		64	anatoliaca		68	O
	7	AHB		4	AHB		8	O					8	EHB		5	C
	1	EHB		6	US DOM		2	C					1	US DOM
	2	PRHB
Portugal	8		Portugal	8		Portugal	8
	8	AHB		8	iberiensis		8	M
Spain	4		Spain	4		Spain	4
	4	AHB		4	iberiensis		4	M

Samples were genotyped with the 251 SNPs in common with the reference samples from a total 272 SNPs in the Fluidigm assay. Assignations of the unknown samples are to the closest available in the two reference sets of samples given as input to GeneClass2. Reference Set I. Avalos et al. [84] (30 PRHB from Puerto Rico; 28 AHB from Mexico and 30 EHB from Hawaii); Wallberg et al. [53] (10 AHB from Brazil and 10 each of three species from Africa (SSA, Sub Saharan Africa), A. m. adansonii, A. m. scutellata, and A. m. capensis). Reference Set II. The above data plus the remaining samples from Wallberg et al. [53]; A. m. anatoliaca (10); A. m. mellifera EU Domestic (20); A. m. mellifera US Domestic (10); A. m. carnica (10); A. m. iberiensis (10), A. m. ligustica (10); A. m. syriaca (10), A. m. mellifera, Sweden, Norway, Europe (20). Reference Set III. Collapsed populations of main groups from Wallberg et al. [53]; Group M: A. m. mellifera, Sweden (10), Norway, Europe (10), A. m. iberiensis (10); Group C: A. m. ligustica (10), A. m. carnica (10); Group O: A. m. anatoliaca (10), A. m. syriaca (10); Group A: A. m. adansonii (10), A. m. scutellata (10), and A. m. capensis (10). Genotype data from the three sets of reference samples were run separately along with the genotypes of the unknown worldwide collection of HB test samples as input for GeneClass2. Group categories follow Wallberg et al. [53]
AHB African honey bee, EHB European honey bee, PRHB Puerto Rico honey bee, SSA Sub-Saharan African honey bee, US DOM United States domestic honey bee, EU DOM European domestic honey bee

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com