Which tests to order?

A genealogist writes me:

**According to the documentary genealogical researches that I have completed so far, I possess Amerindian ancestors. Thus, Aboriginal women were the spouses of French immigrants and I am their descendant. How to highlight this contribution of Amerindian DNA? What tests do you suggest to me to order? **

There are several possibilities of testing according to whether, on the documentary level,  one of these ancestors (a) is part of your matriline or (b) your patriline, or (c) Not among these lines.

(A) If your Native American ancestor is in direct lineage with mothers, i.e. in your matriline (a lineage also referred to as uterine or umbilical line),  a test on your mitochondrial DNA (mtDNA) is appropriate and will be able to verify that your Matriarch was indeed an Native American.
Mt-DNA is transmitted from mother to son and daughter. Girls, once mothers pass it on to their children. Men do not transmit their mtDNA. We shall see later that they rather transmit their Y chromosome.
The ordered test should be able to determine the haplogroup of your mtDNA. It is in fact, thanks to the mutations that your mtDNA contains that it is possible to determine its haplogroup. Scientific research has been able to establish which haplogroups are Amerindians, European or Asian, & c.

Here are the tests that allow a man or woman to determine the haplogroup of belonging of his mitochondria:
MtDNA Plus FTDNA (http://bit.ly/NoW89i) ($ 70)
MtFullSequence (http://bit.ly/NoW89i) ($ 200)
IGenea (Switzerland) offers these same tests at http://bit.ly/1pSjhDX
If you are a man, there are tests that determine both the haplogroup of your mtDNA and that of your Y chromosome:
23andMe http://bit.ly/1uohNkC ($ 200)
Geno2 or Geno3 (http://bit.ly/143lmi8) ($ 160)
The BritainsDNA company at http://bit.ly/1pSj0Rr offers several mtDNA and yDNA tests.
Before ordering, make sure that the results of the test will indicate the haplogroup of belonging. The tests of some companies do not always provide the membership haplogroup.
Pre-Columbian origins of Amerindian origin (i.e. existing in America before it was discovered by Christopher Columbus) will be attested if your mt-DNA belongs to one of the following haplogroups: A2, B2, C1, D1, X2a or one of their Subclades, which are subdivisions. The status of haplogroup X2b remains uncertain.
Warning! The fact of belonging to the haplogroup A, B, C, D does not necessarily imply Amerindian origins. Indeed, these haplogroups all exist elsewhere in the world, in Eurasia, in Asia, in Polynesia. Only the subclades A2, B2, C1, D1 are considered of Amerindian origin. The X2b could be native Amerindians but it is still impossible to distinguish it from the X2b Europeans.
The Catalogue of Ancestral Signatures validated at www.triangulations.ca contains some founding mtDNA Amerindian signatures. About 5% of Quebecois of French colonization carry Amerindian mitochondria.
If your documentary genealogy indicates that your matriarch in the line of mothers was an Amerindian but your mtDNA test does not confirm Native Amerindian founder, various explanations are possible:
A documentary error could have slipped into your genealogy; It is necessary to rigorously check all your documentary sources. Do not rely on searches made by other users.
A mtDNA transmission discontinuity in your matriline due to a non parental event or NPE (maternal). In the case of mtDNA, an NPE (m) is introduced as an adoption or a silent assimilation. Have you been adopted? Has a woman in your line of mothers been adopted?
Your matriarch could be a native Indian culturally but descending from a non-native Indian mother. For example, a  girl or a woman of European origin may have been abducted by Amerindians and assimilated.  Some Europeans also adopted the manner of living of native Americans at the beginning of the colony and their descendants were assimilated.
(B) If you are a man and your Native American ancestor was also a man and is part of your direct lineage of fathers (also called patriline: your father, father, and so on),  then the appropriate test is a test on your Y chromosome. Only men have a Y chromosome. This chromosome is transmitted from father to son. If you are a woman, your father, brother or even a paternal cousin will be able to provide the DNA sample that will be used for the Y-DNA test.

The tests for determining the haplogroup of a Y-DNA are:
Y-DNA12 / 25/37/67/111 markers FTDNA (from $ 60 to $ 340) followed by the appropriate SNP Pack or by a Big-Y ($ 700)
A Geno2NextGen  (http://bit.ly/143lmi8) ($ 160)
IGenea offers these same tests at http://bit.ly/1pSjhDX
The BritainsDNA company at http://bit.ly/1pSj0Rr offers several DNA-mt and DNA-Y tests.
Before ordering a test from a company other than FTDNA, make sure that the test result will include the haplogroup of your Y-DNA.
Which Y-DNA haplogroups attest to an indigenous origin of strain?
Only the following three Y-DNA haplogroups appear clearly as founding Amerindians:
P-M45 *
C-P39 C-M217 (former C-M130, and subclades)
Q1a and more downstream (Q-L53, Q-L54, Q-L55, Q-L213, Q-M3, Q-L804)
If your ancestor in patriline was Native American based on the documentary evidence but your membership DNA-Y haplogroup does not find among those listed above, you are not of Native American ancestry.
Your patriarch could be a native Amerindian culturally but from a  non-native father. Many Amerindians carry a Y chromosome of European origin.

It may be thought that very few lines of Quebecois (or Acadian) men possess a Y chromosome of founding Amerindian origin. They represent only one man in a thousand. The line of Germain DOUCET II is the only well established to date by DNA. See the Triangulation Catalog at http://bit.ly/1xuiHMs
(C) If the mtDNA or Y-DNA results do not reveal native American origins,  it is always possible to examine your Amerindian metissages through AIMs (Ancestry-informative markers) . AIMs are SNPs that show significant differences in the frequency of alleles between different populations tested. The selected motifs are found in our DNA of chromosomes 1 to 22.  This DNA is generally called autosomal.
Thus, a team of researchers develops and validates a battery composed of several hundred markers that correlate significantly with membership of an ethnic group or with a particular geographical origin. Companies that develop tests use these partitioning tools borrowed from researchers. In the case of Geno2, over 75,000 AIMs were selected covering more than 450 global populations. Once these references have been established, a computer program then makes it possible to recognize the presence of these discriminating motifs in the autosomal DNA of a person who has been tested and to weight these reasons according to their importance. Thus, scores of admixture are obtained.
Omnibus tests covering at least partially autosomal DNA include * Amerindian strain markers *. However, their validity often rests on Amerindians from Central and South America. It is also difficult to distinguish between Amerindian and Asian markers.
The most important tests are:
23andMe (Ancestry composition) http://bit.ly/1uohNkC ($ 200)
Family Finder FTDNA http://bit.ly/1uohMgr ($ 100)
Geno2NextGen (http://bit.ly/143lmi8) ($ 160)

There are also third party softwares that analyze the results that were provided to us by the autosomal DNA testing companies. These programs use their own markers to describe our admixtures.
For more information on admixture analysis, see the ISOGG Wiki at http://bit.ly/1uoobZa (search for * Admixture analyzes *)
The figure at the end of this section is an example of crossbreeding results for a Quebecois from Sorel, Québec, whose maternal uncle is from the Odanak reserve (Pierreville, Québec). The test enabled him to discover that he also had some fairly recent African origins.
What is the * best * test?

The * best * test is actually one that allows both to know:
The haplogroup of your mitochondrial DNA from your matriline;
The haplogroup of your Y chromosome DNA of your patriline;
To get a representation of your admixtures.

Two tests are clearly applicable:
23andMe http://bit.ly/1uohNkC ($ 200)
Geno2NextGen (http://bit.ly/143lmi8) ($ 160)
If, in addition, you are interested in your health susceptibilities, breast, colon and prostate cancer, then the test offered by 23andMe is appropriate.