Biology Reference
In-Depth Information
presence of functionally similar forms of enzymes (
isozymes
). Protein electro-
phoresis provides a relatively inexpensive method for analyzing several genes
from individuals at the same time (
Hames and Rickwood 1981, Pasteur et al.
1988, Murphy et al. 1996
). This technique is useful for analyzing mating systems,
heterozygosity, relatedness, geographic variation, hybridization, species bound-
aries, and phylogenetic analyses of divergences within the last 50 million years
and is inexpensive and rapid.
Immunological analyses were used in the 1960s, but they are rarely used
today. Immunological techniques provided qualitative or quantitative estimates
of amino-acid sequence differences between homologous proteins (
Maxon and
Maxon 1990
). Cytogenetic analyses of variation in chromosome structure and num-
ber have been used for studies of hybridization and species boundaries (
White 1973
).
Specific DNA sequences can be localized by
in situ
hybridization and new stain-
ing techniques can reveal the fine structure of chromosomes by revealing banding
patterns. However, cytogenetic analyses are less useful for phylogenetic analyses,
gene evolution, heterozygosity, and relatedness studies (
Hillis et al. 1996
).
Differences in single-copy DNA sequences revealed by
DNA-DNA hybridiza-
tion
have been used for analysis of phylogenies since the late 1960s (
Powell and
Caccone 1990, Werman et al. 1996
). DNA-DNA hybridization is used for analyses
of species and higher taxa relationships up to the family and order level but is
used relatively infrequently for arthropods, so it is not discussed further.
Protocols of molecular methods for systematics and evolutionary studies were
provided by
Hillis and Moritz (1990)
, including guidelines for sampling, collec-
tion and storage of tissues, protocols for isozyme electrophoresis, immunologi-
cal techniques, molecular cytogenetics, DNA-DNA hybridization, restriction site
analysis, Sanger sequencing of nucleic acids, and analytical methods for intra-
specific differentiation and phylogeny reconstruction.
Pasteur et al. (1988)
and
Murphy et al. (1996)
described protocols and methods of isozyme analysis.
Weir
(1990)
provided guidelines on analyzing population structure, phylogeny con-
struction, and diversity by using molecular and morphological data. Protocols
are readily available for the PCR and nucleic-acid sequencing and data analy-
sis (
Howe and Ward 1989, Doolittle 1990, Hillis et al. 1990, 1996, Gribskov and
Devereaux 1991, Palumbi 1996, Green 2001, Gibson and Muse 2002, Hall 2011
).
Updated methods for molecular phylogenetics analyses are available:
Hall (2011)
provides the fourth edition of
Phylogenetic Trees Made Easy: A How To Manual
,
and
Wiley and Lieberman (2011)
provide the second edition of
Phylogenetics:
Theory and Practice of Phylogenetic Systematics.
