Biology Reference
In-Depth Information
using universal primers, “suggesting that numts may be widespread in other taxo-
nomic groups.” Increased primer specificity reduced numt coamplification in some
species, but only eliminated it in one species tested.
Moulton et al. (2010)
con-
cluded, “numt coamplification is a serious problem for DNA barcoding and more
quality control measures should be implemented to identify and eliminate numts
before using mitochondrial barcodes for species diagnoses.”
Blacket et al. (2012)
found that the Queensland fruit fly
Bactrocera tryoni
also had a numt that could
be coamplified. However, they designed an alternative primer that allowed them
to amplify the COI gene rather than the numt.
13.5.12 Single Nucleotide Polymorphism (SNP) Markers
cDNAs from species can be sequenced using next-generation sequencing meth-
ods, and large numbers of transcripts can be sampled (
Helyar et al. 2011
).
Genetic variation within these expressed sequence tag (EST) libraries can be
detected and used to study population genetics in insects or for breeding pro-
grams. SNPs have been used in assays for pesticide resistance genes (
Brun-
Barale et al. 2005
). Selection of honey bees for resistance to
Varroa
mites could
involve breeding for hygienic behavior;
Spotter et al. (2012)
obtained 70,000
SNPs obtained from the honey bee genome project and validated them by using
next-generation sequencing of pooled DNA samples of bees resistant to
Varroa
and of DNA from bees that are susceptible. Approximately 44,000 SNPs were val-
idated that could be used to select for multiple desirable traits in honey bees.
The traditional methods for identifying SNP markers is time-consuming and
expensive, but
Black and Vontas (2007)
describe methods for obtaining SNP
markers from insects that do not involve genome sequencing.
13.6 Analysis of Molecular Data
Molecular ecology is a rapidly changing field of study (
Ferraris and Palumbi
1996, Symondson and Liddell 1996
). Methods of analyzing molecular popula-
tion data are being developed and improved. For reviews and overviews of
methods, see
Weir and Cockerham (1984)
,
Slatkin and Barton (1989)
,
Doolittle
(1990)
,
Lynch and Crease (1990)
,
Weir (1990)
,
Hoelzel and Dover (1991)
,
Hoelzel
and Bancroft (1992)
,
Ferraris and Palumbi (1996)
,
Bossart and Pashley-Prowell
(1998)
,
Estoup and Angers (1998)
,
Howard and Berlocher (1998)
,
Rieseberg
(1998)
,
Schnabel et al. (1998)
,
Templeton (1998)
,
Davies et al. (1999a,b)
,
Bohonak (1999)
,
Cornuet et al. (1999)
,
Goodnight and Queller (1999)
,
Schwartz
et al. (1998)
,
Black et al. (2001)
, and
Hewitt (2001)
. Computer software pack-
ages for molecular population genetic analyses are available from several
sources (e.g.,
Rozas and Rozas [1997]
and the Felsenstein website:
www@evolu
