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From: "Bernard SECHER" <>
Subject: Re: [DNA] New mtDNA sequences from Newfoundland (18-FEB-2011)
Date: Sun, 20 Feb 2011 15:07:32 +0100
References: <C55CC9D6083F49B5A4561FEFEC17E2E9@IanPC>


Thanks Ian,

Oddly, the U6a7 sample HQ287880 has not the 3 following mutations: T1193C,
A2672G and T8473C
In the U6 mtDNA project at FTDNA, all the acadian U6a7 samples have these
three mutations. So I expect there is an error somewhere...

Best
Bernard Secher

----- Original Message -----
From: "Ian Logan" <>
To: "Genealogy" <>
Sent: Sunday, February 20, 2011 10:47 AM
Subject: [DNA] New mtDNA sequences from Newfoundland (18-FEB-2011)


> List
>
> A set of 27 mtDNA sequences has appeared on GenBank.
>
> They are to accompany this paper (which I haven't seen as yet) :-
>
> Pope,A.M., Carr,S.M., Smith,K.N. and Marshall,H.D.
>
> Mitogenomic and microsatellite variation in descendants of the
> founder population of Newfoundland: high genetic diversity in an
> historically isolated population
>
> Genome 54 (2), 110-119 (2011)
> Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9,
> Canada
> ----
> Abstract
> The island of Newfoundland, the first of England's overseas colonies, was
> settled
> from the 17th century onward by restricted numbers of English, Irish, and
> French
> immigrants, in small "outport" communities that have maintained
> geographic,
> religious, and linguistic isolation to the latest generations. To measure
> the extent
> of modification and loss of genetic variation through founder effect,
> drift, and
> inbreeding in this historically isolated population, we analyzed the
> complete
> mitochondrial DNA (mtDNA) genomes and 14 microsatellite loci from each of
> 27 individuals with matrilineal ancestries extending to the colonial
> period.
> Every individual has a unique mtDNA genome sequence. All but one of these
> genomes are assignable to one of five major (H,J,K,T, and U) or minor (I)
> European haplogroups. The possibility of homoplasy at single nucleotide
> polymorphism (SNP) sites that define subtypes within the H haplogroup is
> discussed. Observed haplogroup proportions do not differ significantly
> from
> those of western Europeans or between English and Irish Newfoundlanders.
> The exceptional individual is a member of haplogroup A2, who appears to be
> the descendant of a Mi'kmaq First Nations mother and a French father,
> a common marriage pattern in the early settlement of Newfoundland.
> Microsatellite diversity is high (HE = 0.763), unstructured with respect
> to mtDNA
> haplotype or ethnicity, and there is no evidence of linkage
> disequilibrium.
> There is a small but significant degree of inbreeding (FIS = 0.0174).
> Collection
> of whole mtDNA genome data was facilitated by the use of microarray
> sequencing,
> and we describe a simple algorithm that is 99.67% efficient for sequence
> recovery.
> ---
>
> They belong to haplogroups :-
> A2f1, H, H1c1, H1c3, H3, H5, H5a, H16, I2, J1c5, J1c5a,
> K1a, T2, T2b, U5b1d1, U6a7a
> and the sequences do contain a number of distinctive mutations
> - which raises the question as to whether, or not, the DNA samples
> were actually sequenced.
> So are these microarray results ? And the sequences constructed ?
>
> As usual I have added the sequences to my Checker program
> - to ensure against typographical errors.
>
> Ian
>
> --------------------
>
> HQ287872(Newfoundland) Pope Haplogroup A2f1 18-FEB-2011
> C64T A73G T146C A153G A235G A263G 309.1C C522- A523- A663G
> A750G A1438G A1736G T1809C T2638C A2706G G3316A T4248C A4769G A4824G
> C7028T G7897A G8027A C8794T A8860G G11719A G12007A C12705T T12714C G12940A
> C14766T C14911T A15326G T15670C T15850C C16111T C16192T C16223T C16290T
> G16319A
> T16362C
>
> HQ287873(Newfoundland) Pope Haplogroup J1c5 18-FEB-2011
> A73G T146C G185A G228A A263G C295T 309.1C C462T T489C C522-
> A523- A750G A1438G A2706G G3010A T4216C T4688C A4769G A5198G C7028T
> A8860G A10398G A11251G G11719A A12612G A13434G G13708A C14766T T14798C
> A15326G
> C15452A C16069T T16126C
>
> HQ287874(Newfoundland) Pope Haplogroup J1c5a 18-FEB-2011
> A73G G185A G228A A263G C295T C462T T489C A750G A1438G T2387C
> A2706G G3010A T4216C A4769G A5198G C7028T A8860G C10192T A10398G A10598G
> A11251G G11719A A12612G G13708A C14766T T14798C A15326G C15452A C16069T
> T16126C
>
> HQ287875(Newfoundland) Pope Haplogroup T2b 18-FEB-2011
> A73G A263G 309.1C 309.2C G709A A750G G930A A1438G A2706G T4216C
> A4769G A4917G G5147A C7028T A7245G A8860G T10253C T10463C A11251G G11719A
> A11812G G13368A A14233G C14766T G14905A A15326G C15452A A15607G G15928A
> T16126C
> C16294T C16296T T16304C T16325C T16519C
>
> HQ287876(Newfoundland) Pope Haplogroup T2b 18-FEB-2011
> A73G A263G 309.1C 309.2C G709A A750G G930A A1438G G1888A A2706G
> T4216C A4769G A4917G G5147A C7028T A7245G G8697A A8860G T10253C T10463C
> A11251G G11719A A11812G G13368A A14233G C14766T G14905A A15326G C15452A
> A15607G
> G15928A T16126C C16294T C16296T T16304C T16325C T16519C
>
> HQ287877(Newfoundland) Pope Haplogroup T2 18-FEB-2011
> A73G T195C A263G G709A A750G A1438G G1888A A2706G T4216C A4769G
> A4917G T5277C C6489A C7028T G8697A A8860G T10463C A11251G G11719A A11812G
> G13368A A14233G C14766T G14905A C15028A G15043A A15326G C15452A A15607G
> G15928A
> T16126C A16182- A16183- C16184T T16189C 16193.1C 16193.2C C16294T C16296T
> T16298C
> T16519C
>
> HQ287878(Newfoundland) Pope Haplogroup U5b1d1 18-FEB-2011
> A73G C150T A263G A750G A1438G A2706G T3197C A4769G C5437T A5656G
> C7028T A7768G G7912A A8860G G9477A A11467G G11719A A12308G G12372A T13191C
> T13617C T14182C C14766T A15326G A15631G T15721C C16192T C16218T C16270T
> C16320T
>
> HQ287879(Newfoundland) Pope Haplogroup U5b1d1 18-FEB-2011
> A73G C150T T199C A263G 309.1C A750G A1438G C2225A A2706G T3197C
> C3507T A4769G C5437T A5656G C7028T A7768G 8276.1C 8276.2C 8276.3C T8277C
> A8860G G9477A T10084C A11467G G11719A T12136C A12308G G12372A T13617C
> C13947T
> T14182C C14766T A15326G T15721C C16218T C16270T
>
> HQ287880(Newfoundland) Pope Haplogroup U6a7a 18-FEB-2011
> A73G T152C A263G A750G T794A A1438G A1692T A2706G A3348G A4769G
> A5120G G5471A C7028T G7805A A8860G A11467G G11719A T11929C A12308G G12372A
> A14179G C14766T G15043A A15326G T15530C C15632T T16172C A16219G C16278T
>
> HQ287881(Newfoundland) Pope Haplogroup K1a 18-FEB-2011
> A73G T195C A263G C497T 523.1C 523.2A 523.3C 523.4A A750G T1189C
> A1438G A1811G A2706G A3480G A4769G C5300T C7028T A8860G G9055A G9477A
> T9951C A10398G A10550G T11299C A11467G G11719A A12308G G12372A C14167T
> C14766T
> T14798C A15326G G16048A T16093C T16224C C16291T T16311C T16519C
>
> HQ287882(Newfoundland) Pope Haplogroup I2 18-FEB-2011
> A73G T152C T199C T204C G207A T250C A263G 573.1C 573.2C 573.3C
> A750G A1438G G1719A A2581G A2706G A4769G C7028T T7561C G8251A A8860G
> T10034C T10238C A10398G G11719A G12501A A13780G C14766T G15043A A15326G
> A15758G
> A15924G G16129A C16223T G16391A
>
> HQ287883(Newfoundland) Pope Haplogroup H16 18-FEB-2011
> A263G A750G A1438G A4769G A8860G C10394T A15326G T16189C T16519C
>
> HQ287884(Newfoundland) Pope Haplogroup H16 18-FEB-2011
> A263G A750G A1438G A4769G G4820A A8860G C10394T A15326G C16291T T16311C
> T16519C
>
> HQ287885(Newfoundland) Pope Haplogroup H1c1 18-FEB-2011
> A263G 309.1C T477C A750G A1438G G3010A A3744G A4769G A8860G A9150G
> A15326G T16263C T16519C
>
> HQ287886(Newfoundland) Pope Haplogroup H1c1 18-FEB-2011
> A263G T477C A750G A1438G G3010A A4769G C5945T A8860G A9150G A15326G
> T16263C T16519C
>
> HQ287887(Newfoundland) Pope Haplogroup H1c3 18-FEB-2011
> G107A A257G A263G 309.1C 309.2C T477C C522- A523- A750G A1438G
> G3010A A4769G G5997A T8473C A8860G A8981G A15326G A16183- T16189C 16193.1C
> T16249C T16362C T16519C
>
> HQ287888(Newfoundland) Pope Haplogroup H16 18-FEB-2011
> A263G A750G A1438G A4769G A8860G C10394T A15326G T16189C T16519C
>
> HQ287889(Newfoundland) Pope Haplogroup H3 18-FEB-2011
> T152C A263G 309.1C A750G A1438G A4769G T6776C A8860G A11590G A14587G
> A14687G A15326G T16189C T16519C
>
> HQ287890(Newfoundland) Pope Haplogroup H3 18-FEB-2011
> A263G 309.1C A750G A1438G C3757T A4769G T6776C A8860G A15326G G16129A
> T16519C
>
> HQ287891(Newfoundland) Pope Haplogroup H1a 18-FEB-2011
> A73G A263G 309.1C A750G A1438G G3010A A4769G A8860G A9341T A15326G
> A15655G A16162G T16519C
>
> HQ287892(Newfoundland) Pope Haplogroup H1a 18-FEB-2011
> A73G A263G 309.1C A750G A1438G G3010A A4769G A8860G T9951C T10416A
> A14978G A15326G A16051G A16162G T16519C
>
> HQ287893(Newfoundland) Pope Haplogroup H1a 18-FEB-2011
> A73G A263G 309.1C A750G A1438G G3010A A4769G A8860G A15326G A16162G
> T16519C
>
> HQ287894(Newfoundland) Pope Haplogroup H5 18-FEB-2011
> 309.1C C456T 523.1C 523.2A A750G A1438G A4769G G5471A G7269A G7897A
> A7941G A8860G A10972G C13516T T14319C A15326G T16304C
>
> HQ287895(Newfoundland) Pope Haplogroup H5a 18-FEB-2011
> T146C A263G 309.1C C456T A750G A1438G T4336C A4769G T6076G T8588A
> A8860G G9912A A15326G A16302G T16304C
>
> HQ287896(Newfoundland) Pope Haplogroup H 18-FEB-2011
> A263G 309.1C A750G A1438G A4769G A6060G G8572A A8860G A15326G C16278T
> C16290T T16311C T16519C
>
> HQ287897(Newfoundland) Pope Haplogroup H 18-FEB-2011
> A263G 309.1C A750G A1438G A4769G A8860G C11788T C14129T A15326G G16129A
> T16519C
>
> HQ287898(Newfoundland) Pope Haplogroup H 18-FEB-2011
> T152C A263G A750G A1438G A4769G A8860G C9391T G11719A A15326G T16093C
> G16129A G16274A A16316G T16519C
>
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