About mtDNAmap

The introduction of mtDNA information to population genetics in late seventies brought forth a revolutionary shift towards the historical and phylogenetic perspective on intraspecific population structure. Because of the maternal, non-recombining mode of the mtDNA inheritance (at least in most species), the molecule shows the same pattern of common ancestry. Moreover, mtDNA within many species have proved to be geographically localized. Such information brought about the introduction of the word “Phylogeography” which refers to the study of the principles and processes governing the geographic distributions of the genealogical lineages including those at the intraspecific level on the basis of the molecular data.

The use of mtDNA gene genealogies and geographic information of sampled populations depicts the genetic structure of the population. Understanding the path of the female lineage has helped population geneticists to trace the matrilineal inheritance of modern humans back to human origin in Africa and the subsequent spread around the globe.

mtDNAmap is the comprehensive open access database that provide frequency of the haplogroups in human population of different parts of world. The results are presented via world map that provides very quick handy interpretation of the geographic distribution of haplogroups according to the latest classification of the mtDNA haplogroups and Y-chromosome haplogroups (coming soon). However the mtDNA sequences are taken from the publically available resources like NCBI GenBank and carefully cited where required.

Leaflet JavaScript is free, open-source library for the development of the interactive map system. When the user enters a query, the database is searched for the given haplogroup and all occurrences are loaded that are further processed by leaflet functions for the interactive display.

The marker for frequency display are equipped with the popup (accessible on click) that has following information:

  • Frequency
  • Population Name
  • Country Name
  • Range of the analyzed Sequence
  • Reference to GenBank Accession numbers
The marker of customized icons of different colors provide the estimation of the variation. Zoom-in and zoom-out provide the user to adjust the map zoom to specific level.

The marker of customized icons of different colors provide the estimation of the variation. Zoom-in and zoom-out provide the user to adjust the map zoom to specific level.

The JavaScript library, Mapbox, An open source mapping platform was also used for custom designed maps. The Mapbox provided a great opportunity to generate heatmaps. There are two optional displays and a user switch between heatmap and a detailed map.

The important feature of mtDNAmap is the information of haplogroups of the variable sequence range.The sequence range used to define the haplogroups are as follows:

  • Complete mtDNA sequence
  • Complete Control Region Sequence
  • HV-I and/or HV-II and/or HV-III Sequence
mtprofiler helps researchers to analyze, compare mitochondrial DNA sequences with revised Cambridge Reference Sequence (rCRS), determination of sequence range and mtSNPs.

Haplogrep 2.0 was used for determination of haplogroups of sequences based on most recently updated Phylotree (van Oven M, Kayser M. 2009).
Frequency calculation, database management and display system are developed by our own team.