Chromosome Painting, in its simplest form, is simply a method of visualizing shared segment matches between a primary and one or more matches.
Often this simplified form uses a tool called a Chromosome Browser and is simply called chromosome browsing. A Browser is a tool provided by vendors to visualize how you share matching segments with others. 23andMe was the first to provide such a tool. The visualized matching segments indicate where on each of your respective chromosomes the DNA was contributed by a MRCA between you and a match.
Chromosome Mapping is the technique of painting where the matching segments displayed are identified with an ancestor of the primary tester. Unlike for browsing, you are purposely merging multiple matches overlapping painted segments and making the oldest common ancestor override any newer common ancestor that may overlap. Generally, as you go back in time, the older ancestors have smaller segments. So in mapping, these are no longer matching segments identified with a single match but segments identified with an ancestor of the primary tester that is in common with the matches.
Beside this difference in the segment identification, a big difference between browsing and mapping is persistence. With a persistent database you can identify the matching segments due to a particular match with an MRCA. When merging multiple, un-related matching segments, you form a map of your chromosomes with segments from multiple contributing matches and thus ancestors. With this information, you can then look at new, unknown matches and see where they overlap with known ancestor-contributed DNA segments to then get a hint as to where in your family tree that match may share an ancestor from.
The real Mapping part comes from identifying segments with the MRCA. Often, one might start with a near 100% painting of the autosomes into four colors representing the four grandparents. It is assumed you can quickly determine paternal versus maternal. As you identify matches from more distant relatives, you are able to break earlier large matching segments into smaller, older ones tied to farther-back-in-time ancestors. So your map becomes a real patchwork of colors as you have some non-overlapping segments identified only with a parent, grandparent or further back-in-time ancestors. If a new, unknown match overlaps with an ancient ancestor and a newer one, you know they must be related with the newer ancestor. The goal is to "paint" 100% of your DNA with as few gaps as possible. And with as many identified "small segments" from furthest ancestors as possible. This then helps to more quickly localize unknown matches matching segments to distant ancestors.
This expanded technique of Mapping is a growth out of autosomal matching segment analysis initially performed with spreadsheets. Spreadsheets of matching segments from many matches would be sorted by chromosome then segment start point. Eventually, techniques to visualize these segments with graphics in the spreadsheet were developed. Then tools to ease the spreadsheet work. "Autosomal DNA Segment Analyzer", "xWorks" series of tools and "GenomeMatePro" are early examples of this. The introduction in 2018 of "DNA Painter" simplified and focused on this visualization and mapping process and has become wildly popular; enabling expanding this technique to the masses. So tools to support chromosome mapping have a persistence compared to the browsers. Where the segment matches are loaded, colored and retained so you can load even more.
Chromosome Mapping goes by many different terms in genetic genealogy. Chromosome mapping is also known as Chromosome painting, Some use Segment Mapping because this is really using matching segments. Others may simply generalize chromosome to DNA.
Unlike simple clustering of shared match lists, chromosome mapping requires you have the individual matching segments available for analysis. Very similar to how the Leeds method is a simplified, near term form of clustering; something called visual phasing was an early outgrowth of the spreadsheet segment analysis to create a visual method of grouping segments to particular grandparents.
Not all test companies provide the segments or a chromosome browser. 23andMe was the first we recall providing a chromosome browser tool for comparing the segment matches with multiple people. FTDNA) and others quickly followed. Ancestry is the major player where this form of match analysis cannot occur. Because they do not provide the segments used internally to determine the match lists. GEDMatch has long had a useful, more detailed chromosome browser that highlights half identical and full identical matching areas.
An important aspect to understand with segment match analysis is that the results we start with are unphased. See the page on half identical matching for an understanding of this. The results of particular SNPs tested come back as an unordered pair. One from each autosome but it is not known which value is from which. A phased value set is ordered. You know which value came from which parent. And thus the individual copies of each chromosome are determinable. With unphased data, it is difficult to determine the actual matching segment values and which parent (or copy of the autosome) it applies too.
There is an extreme form of this mapping termed inferred or deductive where, like in visual phasing, you merge sibling or similar very close match data. So you are using two different primary testers to compare with other matches. And then deducing unmatched segments to the opposite grandparent or ancestor. This can help fill in some gaps you may still have in your personal, primary map that you could not get otherwise.
Examples of Chromosome Browsing appear on the shared segment, segment matching and half identical pages. We have not included an example of Chromosome Mapping here yet.
Often this simplified form uses a tool called a Chromosome Browser and is simply called chromosome browsing. A Browser is a tool provided by vendors to visualize how you share matching segments with others. 23andMe was the first to provide such a tool. The visualized matching segments indicate where on each of your respective chromosomes the DNA was contributed by a MRCA between you and a match.
Chromosome Mapping is the technique of painting where the matching segments displayed are identified with an ancestor of the primary tester. Unlike for browsing, you are purposely merging multiple matches overlapping painted segments and making the oldest common ancestor override any newer common ancestor that may overlap. Generally, as you go back in time, the older ancestors have smaller segments. So in mapping, these are no longer matching segments identified with a single match but segments identified with an ancestor of the primary tester that is in common with the matches.
Beside this difference in the segment identification, a big difference between browsing and mapping is persistence. With a persistent database you can identify the matching segments due to a particular match with an MRCA. When merging multiple, un-related matching segments, you form a map of your chromosomes with segments from multiple contributing matches and thus ancestors. With this information, you can then look at new, unknown matches and see where they overlap with known ancestor-contributed DNA segments to then get a hint as to where in your family tree that match may share an ancestor from.
The real Mapping part comes from identifying segments with the MRCA. Often, one might start with a near 100% painting of the autosomes into four colors representing the four grandparents. It is assumed you can quickly determine paternal versus maternal. As you identify matches from more distant relatives, you are able to break earlier large matching segments into smaller, older ones tied to farther-back-in-time ancestors. So your map becomes a real patchwork of colors as you have some non-overlapping segments identified only with a parent, grandparent or further back-in-time ancestors. If a new, unknown match overlaps with an ancient ancestor and a newer one, you know they must be related with the newer ancestor. The goal is to "paint" 100% of your DNA with as few gaps as possible. And with as many identified "small segments" from furthest ancestors as possible. This then helps to more quickly localize unknown matches matching segments to distant ancestors.
This expanded technique of Mapping is a growth out of autosomal matching segment analysis initially performed with spreadsheets. Spreadsheets of matching segments from many matches would be sorted by chromosome then segment start point. Eventually, techniques to visualize these segments with graphics in the spreadsheet were developed. Then tools to ease the spreadsheet work. "Autosomal DNA Segment Analyzer", "xWorks" series of tools and "GenomeMatePro" are early examples of this. The introduction in 2018 of "DNA Painter" simplified and focused on this visualization and mapping process and has become wildly popular; enabling expanding this technique to the masses. So tools to support chromosome mapping have a persistence compared to the browsers. Where the segment matches are loaded, colored and retained so you can load even more.
Chromosome Mapping goes by many different terms in genetic genealogy. Chromosome mapping is also known as Chromosome painting, Some use Segment Mapping because this is really using matching segments. Others may simply generalize chromosome to DNA.
Unlike simple clustering of shared match lists, chromosome mapping requires you have the individual matching segments available for analysis. Very similar to how the Leeds method is a simplified, near term form of clustering; something called visual phasing was an early outgrowth of the spreadsheet segment analysis to create a visual method of grouping segments to particular grandparents.
Not all test companies provide the segments or a chromosome browser. 23andMe was the first we recall providing a chromosome browser tool for comparing the segment matches with multiple people. FTDNA) and others quickly followed. Ancestry is the major player where this form of match analysis cannot occur. Because they do not provide the segments used internally to determine the match lists. GEDMatch has long had a useful, more detailed chromosome browser that highlights half identical and full identical matching areas.
An important aspect to understand with segment match analysis is that the results we start with are unphased. See the page on half identical matching for an understanding of this. The results of particular SNPs tested come back as an unordered pair. One from each autosome but it is not known which value is from which. A phased value set is ordered. You know which value came from which parent. And thus the individual copies of each chromosome are determinable. With unphased data, it is difficult to determine the actual matching segment values and which parent (or copy of the autosome) it applies too.
There is an extreme form of this mapping termed inferred or deductive where, like in visual phasing, you merge sibling or similar very close match data. So you are using two different primary testers to compare with other matches. And then deducing unmatched segments to the opposite grandparent or ancestor. This can help fill in some gaps you may still have in your personal, primary map that you could not get otherwise.
Examples of Chromosome Browsing appear on the shared segment, segment matching and half identical pages. We have not included an example of Chromosome Mapping here yet.