To cite adegenet:
Jombart T. (
2008)
adegenet: a R
package for the multivariate analysis of genetic markers.
Bioinformatics 24: 1403-1405. doi:
10.1093/bioinformatics/btn129
[
link
to a free pdf]
Related publications:
- a review of applications of multivariate analyses to genetic
markers data:
Jombart T, Pontier D, Dufour AB. (2009)
Genetic markers in the
playground of multivariate analysis.
Heredity
102: 330-341.
doi:10.1038/hdy.2008.130
. [
link
to the journal's pdf -
free
abstract -
email me
for a pdf]
- the paper presenting the
spatial
principal component analysis (
spca),
global and local tests (
global.rtest
and
local.rtest):
Jombart T, Devillard
S, Dufour AB, Pontier D
(2008)
Revealing
cryptic spatial patterns in genetic variability by a new multivariate
method.
Heredity 101: 92-103. doi:
10.1038/hdy.2008.34 [
link
on the journal's website -
free
abstract -
email me
for a pdf]
Publications in which
adegenet was used:
[1] Cohas A, Yoccoz NG, Bonenfant C, Goossens B, Genton C, Galan M,
Kempenaers B, Allainé D (2007) The
genetic similarity between pair members
influences the frequency of extrapair paternity in alpine marmots.
Animal Behaviour 76:
87-95.
[2] Satkoski JA, Malhi RS, Kanthaswamy S, Tito RY, Malladi VS,
Smith
DG (2008) Pyrosequencing as a method for SNP identification in the
rhesus macaque (
Macaca mulatta).
BMC
Genomics 9: 256.
[3] Kanthaswamy S, Satkoski J, George D, Kou A, Erickson BJ,
Smith DG. (2008). Interspecies hybridization and the stratification of
nuclear genetic variation of rhesus (Macaca
mulatta) and long-tailed macaques (Macaca fascicularis). Int J Primatol 29: 1295-1311.
[4] Kidd, AG, Bowman J, Lesbarrères D, Schulte-Hostedde AI
(2009). Hybridization between escaped domestic and wild American mink (Neovison vison). Molecular Ecology 18: 1175-1186.
[5] Cohas E, Bonenfant C, Kempaners B, Allainé D (2009).
Age-specific effect of heterozygosity on survival in alpine marmots, Marmota marmota. Molecular Ecology 18: 1491-1503.
[6] O'Brien J, Devillard S, Say L, Vanthomme A, Léger F, Ruette
S, Pontier D (2009). Preserving genetic integrity in a hybridising
world:
are European Wildcats (Felis
silvestris silvestris) in eastern France distinct from sympatric
feral domestic cats? Biodivers
Conserv 18: 2351-2360.
[7] Kanthaswamy S et al.
(2009). Canine Population Data Generated from a Multiplex STR Kit for
Use in Forensic Casework. Journal of
Forensic Sciences 54:
829-840.
[8] Lankau R A, Nuzzo V, Spyreas G, Davis A S (2009). Evolutionary
limits ameliorate the negative impact of an invasive plant. Proceedings of the National Academy of
Sciences 106:
15362-15367.