Molecular characterization of mitochondrial Amerindian haplogroups and the amelogenin gene in human ancient DNA from three archaeological sites in Lambayeque - Peru

Wester, Jorge Victor Wilfredo Cachay; Vilchez, Vanny Judith Soplapuco; Torre, Carlos Eduardo Wester La; Rodriguez-Delfin, Luis Alberto

doi:10.1590/1678-4685-GMB-2019-0265

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Human and Medical Genetics • Genet. Mol. Biol. 43 (4) • 2020 • https://doi.org/10.1590/1678-4685-GMB-2019-0265 copy

Molecular characterization of mitochondrial Amerindian haplogroups and the amelogenin gene in human ancient DNA from three archaeological sites in Lambayeque - Peru

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Important pre-Inca civilizations, known by their great political and religious structures, inhabited the northern coast of Peru. Archeological and anthropological studies have shown that people from these villages have hierarchical strata, but the genetic structure has been poorly studied. Here, we aimed to perform a molecular characterization of the Amerindian maternal lineages and the amelogenin gene in skeletons collected from three archeological sites in Lambayeque. Ancient DNA (aDNA) samples were analyzed with conventional PCR to assess the nine-base pair (9 bp) deletion corresponding to mitochondrial haplogroup B and the identification of haplogroups A, C, and D were obtained with PCR-RFLP experiments. The sex was characterized via amplification of the AMEL(X/Y) locus. Haplogroup frequencies were compared with available data from other ancient and modern civilizations from the Peruvian coast and highlands using statistical methods. Our results showed that haplogroup C had the highest frequency, while haplogroup B showed variable diversity in the analyzed populations. The meta-analysis revealed a positive correlation among some coastal villages. We concluded that ancient populations analyzed in our study showed the presence of four Amerindian mitochondrial haplogroups, which is consistent with previous studies.

Keywords:
Ancient DNA; AMEL (X/Y) locus; Amerindian haplogroup; Peru

Period	Year (C.E.)	Population	n	Relative frequencies				h _sk
Period	Year (C.E.)	Population	n	A	B	C	D	h _sk
Late Lamb.	1100-1375^a	Eten	12	0.083	0.25	0.5	0.167	0.7121±0.1053
Chimu	1375-1475^a	San Jose	5	0.2	0.4	0.4	0	0.8000±0.1640
Pre-colonial	1536-1640^a	Morrope	15	0	0.333	0.667	0	0.4762±0.0920

Location	Population	Period	n	Haplotype frequencies (%)					Author
Location	Population	Period	n	A	B	C	D	others	Author
Coast	Eten	MH	12	8.3	25	50	16.7	0	This study
	Morrope	LH	15	0	33.3	66.7	0	0	This study
	San Jose	MH	5	20	40	40	0	0	This study
	Ancient north coast	MH	36	19.4	22.2	5.6	30.6	22.2	*Shimada et al., 2004*Shimada I, Shinoda K, Farnum J, Corruccini R and Watanabe H (2004) An integrated analysis of pre-hispanic mortuary practices. Curr Anthropol 45:369-402.
	Paracas (Peninsula)	MH	10	0	0	30	70	0	*Fehren-Schmitz et al., 2010*Fehren-Schmitz L, Reindel M, Cagigao ET, Hummel S and Herrmann B (2010) Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis. Am J Phys Anthropol 141:208-221.
	Paracas (Palpa)	MH	28	7	0	14	79	0	*Fehren-Schmitz et al., 2010*Fehren-Schmitz L, Reindel M, Cagigao ET, Hummel S and Herrmann B (2010) Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis. Am J Phys Anthropol 141:208-221.
	Nasca-Rural (Palpa)	EH	37	2	11	22	65	0	*Fehren-Schmitz et al., 2010*Fehren-Schmitz L, Reindel M, Cagigao ET, Hummel S and Herrmann B (2010) Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis. Am J Phys Anthropol 141:208-221.
	Nasca-Urban (Palpa)	MH	28	0	18	43	39	0	*Fehren-Schmitz et al., 2010*Fehren-Schmitz L, Reindel M, Cagigao ET, Hummel S and Herrmann B (2010) Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis. Am J Phys Anthropol 141:208-221.
	Middle Horizon (Palpa)	MH	11	0	27	36	37	0	*Fehren-Schmitz et al., 2010*Fehren-Schmitz L, Reindel M, Cagigao ET, Hummel S and Herrmann B (2010) Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis. Am J Phys Anthropol 141:208-221.
Highlands	Ancient highlanders	LH	35	8.5	65.7	22.9	2.9	0	*Shinoda et al., 2006*Shinoda K, Adachi N, Guillen S and Shimada I (2006) Mitochondrial DNA analysis of ancient Peruvian highlanders. Am J Phys Anthropol 131:98-107.
	Pacapaccari	MH	16	0	69	31	0	0	*Fehren-Schmitz et al., 2010*Fehren-Schmitz L, Reindel M, Cagigao ET, Hummel S and Herrmann B (2010) Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis. Am J Phys Anthropol 141:208-221.
	Chen Chen	MH	23	39	39	17	4	0	Lewis Jr., Buikstra, & Stone, 2007Lewis Jr. CM, Buikstra JE and Stone AC (2007) Ancient DNA and genetic continuity in the south central Andes. Lat Am Antiq 18:145-160.
	San Martin	M	22	8	55	5	27	5	*Fuselli et al., 2003*Fuselli S, Tarazona-Santos E, Dupanloup I, Soto A, Luiselli D and Pettener D (2003) Mitochondrial DNA diversity in South America and the genetic history of andean highlanders. Mol Biol Evol 20:1682-1691.
	Ancash	MH	33	9	52	18	21	0	*Lewis Jr. et al., 2007*Lewis Jr. CM, Buikstra JE and Stone AC (2007) Ancient DNA and genetic continuity in the south central Andes. Lat Am Antiq 18:145-160.
	Arequipa	M	22	9	68	14	9	0	*Fuselli et al., 2003*Fuselli S, Tarazona-Santos E, Dupanloup I, Soto A, Luiselli D and Pettener D (2003) Mitochondrial DNA diversity in South America and the genetic history of andean highlanders. Mol Biol Evol 20:1682-1691.
	Tayacaja	M	60	21	33	30	13	3	*Fuselli et al., 2003*Fuselli S, Tarazona-Santos E, Dupanloup I, Soto A, Luiselli D and Pettener D (2003) Mitochondrial DNA diversity in South America and the genetic history of andean highlanders. Mol Biol Evol 20:1682-1691.

		1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
1	Eten		-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
2	Morrope	0,947^*		-	-	-	-	-	-	-	-	-	-	-	-	-	-
3	San Jose	0,760	0,838		-	-	-	-	-	-	-	-	-	-	-	-	-
4	Ancient highlanders	-0,707^**	-0,819^**	-0,688^**		-	-	-	-	-	-	-	-	-	-	-	-
5	Ancient north coast	0,283	0,000	-0,324^**	0,277		-	-	-	-	-	-	-	-	-	-	-
6	Paracas (Peninsula)	0,030	-0,267^**	-0,485^**	0,519	0,957^*		-	-	-	-	-	-	-	-	-	-
7	Paracas (Palpa)	0,234	-0,052^**	-0,301^**	0,409	0,978^*	0,970^*		-	-	-	-	-	-	-	-	-
8	Nasca-Rural (Palpa)	0,792	0,598	0,267	-0,222^**	0,796	0,611	0,766		-	-	-	-	-	-	-	-
9	Nasca-Urban (Palpa)	0,774	0,600	0,366	-0,116^**	0,712	0,554	0,738	0,960^*		-	-	-	-	-	-	-
10	Middle Horizon (Palpa)	0,437	0,532	0,793	-0,163^**	-0,334^**	-0,385^**	-0,198^**	0,125	0,362		-	-	-	-	-	-
11	Pacapaccari (Highlanders)	0,545	0,650	0,820	-0,266^**	-0,285^**	-0,383^**	-0,172^**	0,229	0,444	0,983^*		-	-	-	-	-
12	Chen Chen	0,165	0,204	0,698	-0,207^**	-0,518^**	-0,462^**	-0,423^**	-0,255^**	-0,110^**	0,654	0,545		-	-	-	-
13	San Martin	0,079	0,057	0,326	0,437	0,008	0,086	0,205	0,135	0,402	0,802	0,737	0,431		-	-	-
14	Ancash	0,414	0,397	0,622	0,101	0,004	-0,010	0,167	0,326	0,570	0,924^*	0,893	0,538	0,933		-	-
15	Arequipa	0,298	0,368	0,668	0,038	-0,282^**	-0,282	-0,117^**	0,079	0,340	0,979^*	0,938^*	0,638	0,901^*	0,957^*		-
16	Tayacaja	0,757	0,748	0,953	-0,508^**	-0,125^**	-0,246	-0,069^**	0,385	0,505	0,804	0,802	0,749	0,472	0,740	0,720

Source of variation	Sum of squares	df	Variance components	Percentage of variations	F_ST	p
Coastal populations
Among groups	4.712	2	0.02789 Va	7.64
Among population within groups	6.238	6	0.03772 Vb	10.33
Within populations	51.835	173	0.29962 Vc	82.04	0.17962	< 0.01
Highlands populations
Among groups	16.104	2	0.06015 Va	15.27
Among population within groups	11.153	13	0.02336 Vb	5.93
Within populations	117.360	378	0.31047 Vc	78.81	0.21195	< 0.01

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E-mail: editor@gmb.org.br

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[1] Send correspondence to
Jorge Victor Wilfredo Cachay Wester. Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Laboratório de Genética Humana e Médica, Avenida Bandeirantes, 3900, 14049-900, Ribeirão Preto, São Paulo, SP, Brazil. E-mail: jwester@usp.br.