In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India

  • Kumarasamy Thangaraj1Email author,

    Affiliated with

    • Gyaneshwer Chaubey1, 2Email author,

      Affiliated with

      • Vijay Kumar Singh1,

        Affiliated with

        • Ayyasamy Vanniarajan1,

          Affiliated with

          • Ismail Thanseem1,

            Affiliated with

            • Alla G Reddy1 and

              Affiliated with

              • Lalji Singh1Email author

                Affiliated with

                BMC Genomics20067:151

                DOI: 10.1186/1471-2164-7-151

                Received: 10 December 2005

                Accepted: 15 June 2006

                Published: 15 June 2006

                Abstract

                Background

                Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. Macrohaplogroup N in India has already been defined in previous studies and recently the macrohaplogroup M among the Indian populations has been characterized. In this study, we attempted to reconstruct and re-evaluate the phylogeny of Macrohaplogroup M, which harbors more than 60% of the Indian mtDNA lineage, and to shed light on the origin of its deep rooting haplogroups.

                Results

                Using 11 whole mtDNA and 2231 partial coding sequence of Indian M lineage selected from 8670 HVS1 sequences across India, we have reconstructed the tree including Andamanese-specific lineage M31 and calculated the time depth of all the nodes. We defined one novel haplogroup M41, and revised the classification of haplogroups M3, M18, and M31.

                Conclusion

                Our result indicates that the Indian mtDNA pool consists of several deep rooting lineages of macrohaplogroup 'M' suggesting in-situ origin of these haplogroups in South Asia, most likely in the India. These deep rooting lineages are not language specific and spread over all the language groups in India. Moreover, our reanalysis of the Andamanese-specific lineage M31 suggests population specific two clear-cut subclades (M31a1 and M31a2). Onge and Jarwa share M31a1 branch while M31a2 clade is present in only Great Andamanese individuals. Overall our study supported the one wave, rapid dispersal theory of modern humans along the Asian coast.

                Background

                Variability in human mitochondrial DNA (mtDNA) offers valuable information to trace the genetic history of humans, because of the high rate of mutation and absence of recombination. Analyses of the frequency of variation and distribution of mtDNA haplogroups have been used to evaluate current models concerning the process of colonization of world. South Asia, particularly India, lies on the path of the earliest human dispersal from Africa [1, 2] and hence this holds an important site of information on early human migrations.

                Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. A number of mtDNA studies based on HVS I in Indian populations have been carried out, and some information have been made available about the genetic structure of Indian gene pool [39]. Macrohaplogroup N in India has already been defined [10], and recently the macrohaplogroup M among the Indian populations has also been characterized [11].

                The origin of mtDNA macrohaplogroup M has been an issue of controversy. Macrohaplogroup M is found mainly in Asia, and its various clades makeup the great majority of Indian and Mongoloid lineages. It was hypothesized that its high frequency and diversity in Ethiopia may indicate an African origin for the entire M [14]. Nevertheless, M is geographically limited to Africa, while it is prevalent in Asia. If M originated in Africa, then it must have occurred at an ancient time, since it had to spread throughout Asia and the New World. However, it is paradoxical that M crossed such a vast distance and failed to accomplish other populations of Africa, except Ethiopians and few Egyptians. The lack of time depth and classification of subhalogroups in the case of most of the lineages in the recent paper [11] tends us to reconstruct the phylogeny of macrohaplogroup M, which harbors more than 60% of the Indian mtDNA lineage [1, 39].

                Results and discussion

                In this study we defined one novel haplogroup M41, and revised the classification of haplogroups M3, M18, and M31. The remaining haplogroups are also classified into subhaplogroups (M3a, M4a, M6b, M33a, M34a, M37a and M40a) by including our complete sequence information (Fig. 1 and also see Additional file 1). The geographical distributions of these samples with their haplogroup affiliation are given in Fig. 2 and the populations and their linguistic affiliations are described in Table 1.
                http://static-content.springer.com/image/art%3A10.1186%2F1471-2164-7-151/MediaObjects/12864_2005_Article_534_Fig1_HTML.jpg
                Figure 1

                The 'autochthonous' haplogroups of Indian macrohaplogroup M.

                http://static-content.springer.com/image/art%3A10.1186%2F1471-2164-7-151/MediaObjects/12864_2005_Article_534_Fig2_HTML.jpg
                Figure 2

                Geographical distribution of completely sequenced (mtDNA) samples used for the reconstruction of Indian M phylogeny. (*) Random sample from Karnataka state.

                Table 1

                Samples that were sequenced for the complete mitochondrial DNA and their geographical location, linguistic affiliations and haplogroups assigned,

                Sl. No.

                Sample Code

                Haplogroup

                Population

                Location

                Linguistic Affiliation

                1

                P12

                M3

                Paniya

                Kerala

                Dravidian

                2

                Or89

                M5a

                Gadaba

                Orrisa

                Austro-Asiatic

                3

                P31

                M6b

                Paniya

                Kerala

                Dravidian

                4

                T9

                M33a

                Tadvi

                Gujarat

                Indo-European

                5

                M42

                M34a

                Random

                Karnataka

                Dravidian

                6

                Or82

                M18

                Oraon

                Bihar

                Austro-Asiatic

                7

                T12

                M4a

                Tadvi

                Gujarat

                Indo-European

                8

                R1

                M37a

                Rathwa

                Gujarat

                Indo-European

                9

                PS38

                M41b

                Pardhan

                Andhra-Pradesh

                Dravidian

                10

                PJ10

                M41c

                Pardhan

                Andhra-Pradesh

                Dravidian

                11

                O9

                M31a1

                Onge

                Andaman

                Andamanese

                We have revised the classification of haplogroup M3 that was previously characterized by a coding region mutation 4580 and two control region substitutions 482 and 16126. In our survey of >5000 samples across India, we found a considerable number of samples that have mutations at nps 482 and 16126 but don't have mutation at 4580 (our unpublished data). This suggests that 482 and 16126 are the basal mutations of this haplogroup, and 4580 might have originated later and this represent subhaplogroup M3a. Haplogroup, M18 was previously characterized by only the HVS I mutation (16318T), but now we have defined this haplogroup by two coding region mutations (12498 and 15942), and an additional control region mutation (194) (Fig. 1 and also see Additional file 1).

                Further, we have defined several subhaplogroups based on the sharing mutations between our own and Sun et al. [11] data [see Additional file 1]. Subhaplogroup M3a defined by a coding region mutation at 4580, M4a defined by two coding (6620 and 7859) and three control region (152, 16145 and 16261) mutations. Subhaplogroup M6b defined by two coding region mutations (3486 and 5585). M33a defined by two coding substitution (8562 and 15908); and M34a by six coding region (3447-8404-10361-11992-12311-14094) and three control region (146, 16095 and 16359) mutations. M37a defined by a single coding (7853) and two control region (151-152) mutations. M40a defined by a coding (13542) and three control region (200, 16179 and 16294) mutations. Interestingly, haplogroups M4, M18, M30, M37 and M38 shared a common coding region mutation (12007) from the root of haplogroup M (superhaplogroup M4'30) and later differentiated by coding and control region mutations (Fig. 1 and also see Additional file 1). We have defined one novel haplogroup, designated as M41, by six coding (870-6297-12398-12469-13656-15601) and three control (375, 16327 and 16330) region mutations with the T159 sequence of Sun et al. [11] (Fig. 1 and also see Additional file 1). M41 has also been tentatively classified in three subhaplogroups M41a, M41b and M41c. One complete sequence O9 from Andamanese specific haplogroup M31a has also been included here that defines subhaplogroup M31a1 by a single coding (13710) as well as a control region (200) substitution. Our reanalysis of this lineage suggests population-specific two clear-cut subclades of M31a in this island. M31a1 specific mutations 200 and 13710 are exclusively present in Onge and Jarwa populations while 9617 defining M31a2 clade is present in only Greater Andamanese individuals [see Additional file 1]. All the coding region diagnostic mutations of macrohaplogroup M subhaplogroups are listed in Table 2.
                Table 2

                Coding region diagnostic mutations of Indian (mtDNA) M subhaplogroups.

                Haplogroups

                Diagnostic coding region substitutions

                M2

                447G-1780-8502-11083-15670

                M2a

                5252-7961-8396-9758-12810

                M3

                482

                M3a

                4580

                M4a

                6620-7859

                M4b

                511

                M5

                1888

                M5a

                709-3921-12477-14323

                M6

                461-3537-5082-5301-5558-9329-10640-13966-14128

                M6b

                5585-3486

                M18

                12498-15942

                M25

                15928

                M30

                15431

                M30a

                6366

                M30b

                5147-13980

                M30c

                12234

                M30d

                15259

                M31

                4907-11176-15440-15530

                M32

                3817-9064-12189-15754

                M33

                2361

                M33a

                8562-15908

                M34

                569-3010-6794-11101-15865

                M34a

                3447-8404-10361-11992-12311-14094

                M35

                12561

                M35a

                5432-10670-15924

                M36

                7271-15110

                M37

                10556

                M37a

                7853

                M38

                1808-6367-6899-9966-15314-15487

                M39

                1811-8679-15938

                M40

                8925-15721-15954

                M40a

                13542

                M41

                870-6297-12398-12469-13656-15601

                We have also calculated the age estimates for all M branches (Fig. 1) both by using the estimated mutation calibration rate of Mishmar et al. [16], which has been recently applied in most of the mtDNA studies [1, 2, 17], and ρ (the averaged distance to a specified founder haplotype) and a mutation rate of one transition per 20,180 years between nps 16090–16365 [18]. Standard errors for coalescence time calculation were calculated following Saillard et al [19]. We found some conflict between the age estimated by both of the methods. Since, the complete sequences do not reflect the actual population size and geographical distribution, former method [18] has been used for colescent time estimation. The detailed coalescent time list is given in Additional file 2.

                It is interesting to note that most of the new M lineages are deep rooting, and more likely arose in situ in the Indian subcontinent just after the arrival of the anatomically modern humans (Fig. 1). As shown in the figure 1, it is apparent that all the autochthonous lineages under analysis emerge directly from the root of the macrohaplogroup M. There is no intermediate lineage shared by any two haplogroups, except for haplogroup M4'30 (Fig. 1). The star-like and non-overlapping pattern (Fig. 1) indicates that all the lineages have originated independently from the root of the macrohaplogroup M, thus supporting a rapid dispersal of modern humans along the Asian coast after they left Africa, followed by a long period of isolation [2].

                Conclusion

                In summary, based on well-resolved mtDNA macrohaplogroup M phylogeny, it can be confirmed with the recent studies [1, 2] that a rapid dispersal of modern human took place in one wave along the Asian coast. The deep roots of M phylogeny clearly ascertain the relic of Indian lineages as compared to other M sub lineages suggesting 'in-situ' origin of these sub-haplogroups in South Asia, most likely in India. These deep rooting lineages are not language specific and spread over all the language groups in India. Moreover, our reanalysis of Andamanese-specific lineage M31 suggests population specific two clear-cut subclades. Onge and Jarwa share M31a1 branch while M31a2 clade is present only in Great Andamanese individuals [see Additional file 1].

                Methods

                A phylogenetic tree reconstructed from the data of Sun et al [11] including our complete sequence information of 11 complete sequences and 2231 partial Indian samples possessing M selected from 8670 HVS sequences across India to resolve some of the anomalies arising due to recurrent mutations in the control region. The geographical distributions of the samples that are used for the complete sequencing of mtDNA are given in table 2. We followed the experimental procedures, quality control measures and haplogroup nomenclature described in our previous study [1]. We have made the parsimonious tree by using our own data and data published elsewhere [1113, 15, 21, 22]. The maximum parsimonious tree obtained by this procedure is shown in the figure 1 and Additional file 1.

                Electronic database information

                Accession numbers [23] for data presented herein are as follows (for the complete mtDNA sequence accession numbers DQ408672-DQ408680 and DQ513521-DQ513522, and for the partial region sequence accession numbers DQ653413-DQ655643).

                Declarations

                Acknowledgements

                We thank Mait Metspalu for help in calculating the colescent time and M.G. Palanichamy for providing his raw tree file and comments. We thank all the students and staff of various Colleges and Universities, who actively participated in this study by collecting samples from different ethnic groups of India. We are also grateful to two reviewers of this manuscript.

                Authors’ Affiliations

                (1)
                Centre for Cellular and Molecular Biology
                (2)
                Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre

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                Copyright

                © Thangaraj et al. 2006

                This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.