Molecular Marker Glossary

Molecular Marker Glossary
Molecular
Marker Glossary
David McDonald, Fall 2008
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Index page
Glossary of terms in population
and molecular genetics, systematics etc.
+ a limited bibliography
Glossary of terms: (underlined terms
are hyperlinked cross-references)
Adaptive peak: Combinations of allele frequencies that result in high fitness in an adaptive landscape in the
shifting balance theory
of Sewall Wright (vs. mass selection theory of R.A. Fisher).
Adaptive radiation: divergence of members of a single taxon to fill a range of different ecological niches (often on islands).  Classic examples include the Galapagos finches and the Hawaiian honeycreepers.
Additive genetic variance: V
, a term in quantitative genetics.  The narrow-sense heritability (
) of a trait is given by the quotient of the additive genetic variance and the phenotypic variance,
. Hartl's (2000), Gillespie's (2004) or Wilson and Bossert's (1971) primers have good quick overviews of the highlights of core concepts in quantitative genetics.
: Effective number of alleles. The number of equally frequent alleles that would produce the same heterozygosity (gene diversity,
) as observed.  For example, if
= 0.9, A
= 10.  That is, ten equally frequent alleles would generate a
of 0.9.
AFLP: Amplified Fragment Length Polymorphism. A
sensitive method for detecting DNA polymorphism (as opposed to the relatively
coarse-grained resolution of
RFLP
).
Following
restriction enzyme
digestion of DNA, a subset of the DNA fragments are selected for
PCR
amplification and
visualization
.  Because one can screen many loci simultaneously, AFLP can be useful for detecting phylogenetic signal in poorly differentiated taxa. Because it is a dominant marker (vs.
codominant
), analysis requires some assumptions about heterozygote frequencies.
[See Mueller, U.G., and L.L. Wolfenbarger. 1999. AFLP genotyping and fingerprinting.
Trends Ecol. Evol. 14: 389-394].
Alignment: any of a series of techniques for juxtaposing
homologous
molecular sequences for phylogenetic analyses. Proper alignment of sequences
is a challenging problem.  (See Hillis et al., 1996, p. 374; Swofford
et al. p. 412 in Molecular Systematics, 2nd ed.).
Allele: a variant segment of
the genetic material. Diploid organisms will have two potential alleles
for any particular stretch (gene,
sensu
latu
) of DNA (e.g.,
a 'normal' and a 'mutant' allele for
Drosophila
trait such as eye
color). If the alleles are the same (or indistinguishable) on both chromosomes,
the individual is a homozygote, if the alleles differ, a heterozygote.
Bateson and Saunders (1902) originally coined the term for traits alternative
to one another in Mendelian inheritance (Gk.
Allelon
, one another;
morphe
form). Now used for alternative forms at a genetic
locus
Codominant
alleles are particularly useful as
genetic
markers
Allelic richness: a measure of genetic
diversity that takes account of sample size when considering the number
of alleles present.  Implemented in the software
FSTAT
2.9.3
(Sep-01) and introduced by El Mousadik and Petit (1996).
Allopatric: having non-overlapping
geographic ranges. Cf.
parapatric
sympatric
syntopic
vicariance
[See Cracraft (1984)].
Alu
: A short (approx. 300
bp
interspersed element, variants of which are found in many (approx. 500,000)
copies throughout the human
genome
Alu
variants alone account for approx. 7% of the entire human genome (0.07
X 3 X 10
approx. =  2 X 10
).
Alu
has been the source of a great deal of important work in molecular evolution.
Allozymes:
Codominant
protein variants (
alleles
that can be
visualized
by appropriate staining and starch-gel
electrophoresis
These were the first major molecular
genetic
markers
, developed in the late 1960�s.
Amplicon: amplified DNA product derived from
PCR
Anagenesis: evolutionary change through time.
Anagenesis refers to microevolutionary change (as opposed to
cladogenesis
which refers to macroevolutionary change, or the formation of clades/branches
of the "tree of life").  That is, anagenesis refers to evolutionary
change over time within a single continuous lineage, whereas cladogensis
implies branching events, speciation and the formation of new, distinct
clades.  [See Brooks and McLennan 1991, pp. 75-78].
Anastomosis: see
Reticulated evolution
Apomorphy: Derived
character
state -- that is, differing from the state present in the ancestor. Cf.
autapomorphy
plesiomorphy
synapomorphy
[See Avise, p. 116-117].
AP-PCR: Arbitrarily Primed
PCR
A technique for amplifying anonymous stretches of DNA using PCR. Related
to
RAPD
Assignment (test):  A method of assigning individuals
to the populations from which they were most likely to have originated
(regardless of where they dispersed to or were sampled).  A web-based
assignment calculator is at: http://www.biology.ualberta.ca/jbrzusto/Doh.html.
[See also Davies, N., F.X. Villablanca, and G.K. Roderick. 1999. Determining
the source of individuals: multilocus genotyping in nonequilibrium population
genetics. Trends Ecol. Evol. 14: 17-21; Waser, P.M., and C. Strobeck. 1998.
Genetic signatures of interpopulation dispersal. Trends Ecol. Evol. 13:
43-44].   J.M. Cornuet's software
GeneClass
does Bayesian
and other assignment tests: http://www.ensam.inra.fr/urlb/
Assortative mating: Nonrandom
mating systems in which like pairs with like. Cf.
Disassortative
mating
Random mating
Assumptions: A critical portion of any model of the
genetic structure of populations or taxa. Most models make simplifying
assumptions concerning drift, mutation or linearity that will be violated
to some degree by almost every actual data set. The key point is whether
the violations are sufficient to invalidate the conclusions of the model.
robust
analysis is one whose conclusions are insensitive to violations
of the assumptions.
Autapomorphy:
Apomorphy
unique to a single taxon (not useful for
cladistic
analysis). [See Avise, p. 116].
Autoclave: high temperature equipment for sterilizing
and cleaning lab. equipment such as beakers and flasks.
Autosome: chromosome other than a sex chromosome.
Bacteriophage: A viral
particle that infects bacteria. Widely used examples include M13 and
lambda
).
Basal: closer to the root of a phylogenetic tree.  See
Crisp and Cook 2004
for a common fallacy in designating taxa as "basal".
Bayesian approaches to phylogenetic or population
genetic inference.  See Lewis and Swofford (2001) and pp. 100-102
of Hall (2001) for phylogenies, and Pritchard et al. (2001) for a population
approach.  Also Shoemaker et al. (1999).
�Beanbag� genetics: An initially derogatory term
for the classical basis of population genetics founded by Sewall Wright,
J.B.S. Haldane, and R.A. Fisher. Manipulation of counts of gene and
genotype
frequencies based on the forces of mutation, drift,
migration
selection and non-
random mating
provide the basis for a theoretical understanding of evolution.
Blunt ends:
Restriction
enzyme
cut that produces even 5� or 3� ends. Cf.
sticky
ends
. Blunt ends are useful when no specificity
of
ligation
is possible,
but higher concentrations of DNA ligase are required.
Bottleneck: Reduction in population size that can
have major influence on genetic variation because of the relationship between
genetic drift and population size.
Bootstrapping: A statistical
technique, used increasingly frequently in population genetic and phylogenetic
analyses. The basic idea is that by repeated sampling (with replacement)
from an original sample, one can use the variance among a large number
of pseudoreplicates (often 2000 to 5000) to estimate variances and infer
confidence intervals). Each pseudoreplicate consists of a sample of size
equal to the original sample size, drawn randomly and
with replacement
bp: Abbreviation of 'base pairs'
(nucleotides).
Branch and bound: a method for reducing the number
of possible alternative trees that need to be evaluated during a phylogenetic
analysis. See Swofford et al. 1996, pp. 480-482 for an explanation of the
method.
cDNA: complementary DNA, which is produced by reverse
transcription from mRNA. {Usage note: compl
mentary is different
from compl
mentary}.
Centimorgan: (abbreviated
cM)  A �map unit� for DNA length based on
recombination
frequency (which varies among
loci
and taxa). One centimorgan is equal to a 1% chance per generation that
genetic marker
at one genetic locus will be separated from a marker at a second locus
due to crossing over. In humans, 1 centimorgan is equivalent, on average,
to 1 million
bp
(base pairs).
Characters: In phylogenetic
analysis a character is a genetically mediated, measurable trait that can
take on one of several states. Characters must be
homologous
� that is, all the states of characters in the taxa to be compared must
derive, with modification, from a corresponding state in the common ancestor.
Examples of characters include homologous anatomical features (e.g., eye
color, femur shape), nucleotide base pairs, or the order of genes along
chromosomes or
mtDNA
. Assessment
of homology can be difficult and controversial. [See Avise, p. 106].
Chronospecies: a portion of an evolving lineage preserved in the fossil record that differs sufficiently from descendants or antecedents to merit a distinct Latin binomial.
cis (vs. trans): A prefix meaning "on the same side
as."  In a molecular context, two non-allelic mutations (i.e., mutations
along different stretches of a chromosome) can be arranged either both
on the same chromosome (cis) or on different chromosomes (trans).  In biogeography, we talk of cis-Andean or cis-Alpine distributions (both
OTU
s occur on the same side of the mountain range) or
trans-Andean (the two OTUs occur on different sides of the mountain range).
Clade:
Monophyletic
group of taxa.
Cladistics: School of phylogenetic
analysis emphasizing the branching patterns of
monophyletic
taxa relying on
synapomorphies
(vs.
symplesiomorphies
to unite
sister taxa
Cf.
pheneticists
. [See
Avise, pp. 115-120].
Cladogenesis: formation
of evolutionary clades.  Often refers to macroevolutionary change,
as opposed to
anagenesis
, which refers to microevolutionary
change.
Cladogram: A diagram, in the form of a stylized tree,
showing inferred historical branching patterns among taxa.
Cline: The transition from one
form of a character (e.g., wing length or frequency of a genetic marker)
across a hybrid zone to a different form of the character in the other
hybridizing taxon.  The slope and overlap (e.g., steep and coincident,
versus shallow and offset) can tell us a great deal about the nature of
the evolutionary forces acting on the hybrid zone, such as the
tension
zone
between dispersal and selection.  [See Endler, 1977; for
a recent application using molecular markers on a manakin hybrid zone in
Panama, see Brumfield et al., 2001; Barton and Hewitt, 1985].
Clone: Asexually cultured cells
designed to produce multiple copies of a single gene or segment of DNA.
For
genetic markers
the process usually involves
cloning vectors
and a bacterial or yeast (
YAC
culture.
Cloning vector: DNA molecule
originating from a virus, a
plasmid
or the cell of a higher organism into which another DNA fragment of appropriate
size can be integrated without loss of the vector's capacity for self-replication;
vectors introduce foreign DNA into host cells, where it is replicated autonomously
in large quantities. Examples are plasmids,
cosmids
bacteriophages
(e.g.,
lambda) and
yeast artificial chromosomes (
YAC
).
Vectors are often recombinant molecules containing DNA sequences from several
sources. A vector must have the following properties:
Be able to replicate in a culturable host (yeast
or bacterium)
Have a dominant selectable marker that allows one
to detect its presence
(genes
for antibiotic resistance are a favorite)
Have >= 1 restriction site that allows cut-and-paste
insertion of the target DNA
[See Avise, p. 80 for simple diagram].
Coalescence: Looking backward at
allelic
diversity, one infers a coalescence at the common ancestor. Coalescence
theory is important in many areas of population genetics including inferences
about
effective population size
allele frequencies, selection intensity, mutation rate, and time since
common ancestry of alleles. [See Gillespie 2004 pp. 40-47; Hudson, 1990].
Codominant: expression of
heterozygote phenotypes that differ from either homozygote phenotype.
Microsatellites
are codominant
genetic markers
because one can distinguish a heterozygote (two bands) from each of the
homozygotes (single band).
Coefficient of relatedness
): A measure of the degree of relatedness between individuals,
ranging from �1.0 (no genes in common, at least over the
genetic
markers
assayed) to +1.0 (identical twins or clones).
In an outbred diploid population, siblings should have
= 0.5,
individuals chosen at random should have
= 0.0. This measure is
the foundation of Hamilton's (1964) theory of kin selection (
inclusive
fitness
), which sparked a revolution in the study
of animal behavior, behavioral ecology and the analysis of fitness. [See
Avise p. 232-233; Queller and Goodnight, 1989].
Coincident:  in hybrid zone theory, clines are
said to be coincident when their centers coincide.  Cf.
cline
tension
zone
Competent: Prepared for introduction of vector DNA.
One makes 'competent' cells (e.g., often
E. coli
) by increasing
membrane permeability with calcium chloride or other
transfection
reagents.
Complementary DNA: (cDNA) DNA that is synthesized from a messenger RNA template rather than a DNA template. Commonly used as a probe in physical mapping.
Congruence: Agreement among or within phylogenetic
data sets.
Consistency index (
CI
):
"A measure of the amount of
homoplasy
exhibited by a
character
or set of characters on a tree, defined as the sum of the minimum individual
character ranges divided by the observed number of changes. If there is
no homoplasy, these quantities will be equal, so that the consistency index
reaches its maximum value of one." [from Hillis et al. 1996]. One can compute
CI
for a single character or as an ensemble for all the characters
across a given tree.
To calculate the
CI
for a tree with
characters
(indexing from i = 1 to n) we need a measure of character weights,
a measure
MINi
(the minimum
number of steps possible) and
, the observed number
of steps. The
CI
is then given the sum of the
min
divided by the sum of the
{Formula below may be hard to read except in Mac-printed
hard-copy versions}.
Where there are
characters,
is the weighting (if any) given to the
th
character,
MIN
is the minimum conceivable number of
steps for the
th
character (on any tree with
the same number of
OTUs
),
and
is the observed number of steps for
the
th
character on the
given
tree.
The MacClade manual (Maddison and Maddison, 1992, pp. 267-271) has a useful
discussion of how the number of steps is computed. Cf.
Retention
Index
RI
),
Rescaled
Consistency Index
RC
).
Cosmid : Artificially constructed
cloning
vector
containing the
cos
gene of
phage
lambda
Cosmids can be packaged in phage particles for infection into the bacterium
Escherichia
coli
; this permits cloning of larger DNA fragments (up to 45 kb) than
can be introduced into bacterial hosts in
plasmid
vectors.
CpDNA: Chloroplast DNA.
Cryotube: cf.
Eppendorf
Small plastic vial (1.5 ml) with screw-top lid used for storing reagents,
samples, etc. Appropriate when leakage is more of a concern (but considerably
more expensive than eppendorfs).
Cytochrome: MtDNA contains several cytochrome genes
that have been important as sequences for molecular phylogenetic analyses.
Degenerate
primers
A mixture of
oligonucleotides
designed to allow for the degeneracy of the DNA triplet code (64 possible
combinations code for approx. 20 amino acids). That is, for a given set
of amino acids, the triplets could take any of several triplet forms (e.g.,
serine is UC*, where * can be any of the four RNA�s U, C, A or G). The
degeneracy is usually in the third codon position, producing a third-codon
synonymous
mutation bias. Two-fold degeneracy means that one of the three possible
substitutions will be synonymous (the other two will be non-synonymous),
four-fold degeneracy means that any substitution will be synonymous. The
degeneracy
or redundancy of the triplet code has other important implications such
as likelihood of persistence of mutation events in exons.
Deme: A group of interbreeding individuals (genetic
population).
Demographic stochasticity: for small population sizes, the unitary nature of individuals means that applying a probability (e.g. 0.5 survival) will have a 0/1 (integer) outcome per individual.  Demographic stochasticity can increase the extinction risk for small populations.  [Contrasted with environmental stochasticity].
Derived:  A
character
is said to have a derived condition when it differs from the state in the
presumed ancestor.  A derived character is
apopmorphic
(vs.
plesiomorphic
, meaning it is the same
as in the ancestor).  Cf.
polarity
DGGE: Denaturing Gradient Gel
Electrophoresis
As
PCR
product moves through
a denaturing
polyacrylamide gel
it will change from double-stranded to single-stranded. A single nucleotide
difference can change the location of the denaturation, allowing
visualization
of polymorphisms. The denaturation is usually die to increasing formamide/urea
concentration. Cf.
TGGE
SSCP
and
heteroduplex analysis
Dichopatric: vicariance of widespread ancestral populations following
the inception of a physiographic or ecological barrier [see Cracraft and
Prum (1988), Cracraft (1984)].
Diploid:  Having a double
complement of chromosomes (generally a paternal and a maternal set).
Many genetic analyses are conducted on taxa whose cells are usually diploid.
Exceptions to diploidy include haploid gametes, haplo-diploid males in
hymenoptera, polyploid species (particularly in plants, but a recent mammalian
example exists!), and haploid stages in some complex life cycles.
Disassortative mating:
Nonrandom mating system in which unlike individuals pair.
MHC
variation can be a basis for disassortative mating. Cf.
Assortative
mating
Random mating.
Disruptive selection: selection for two or more modal phenotypes and against intermediate form.  Also called diversifying selection.  Contrast with directional selection and stabilizing selection.
Distance matrix:  A way
of arranging
OTU
s by some measure of the distance between
them.  The distance metrics may be based on gene frequencies, numbers
of characters shared or other attributes.  Distance matrices can serve
as the input for phylogenetic tree-building algorithms such as
UPGMA
or
neighbor-joining
methods.
DNA-DNA
hybridization
A technique for assessing the similarity of DNA sequences by temperature-mediated
annealing of single strands. The temperature required to dissociate homoduplexes
(strands from the same
OTU
is related to that required to dissociate
heteroduplexes
(strands from two different OTUs) to obtain an index of relative similarity.
Sibley and Ahlquist�s (1990) phylogeny of birds is based on this technique.
[See Avise, p. 63-67].
dNTP: A deoxyribonucleotide (A,G, C, or T). Free
dNTPs in excess are an essential component of
PCR
Dollo parsimony: the assumption in phylogenetic analysis that character changes have asymmetric likelihoods of occurrence -- once gained, for example, a character may have a far lower (even zero) probability of recurring to the ancestral state.  [Avise p. 140]
Downstream: Toward the 3� end of a DNA sequence.
Drift: see
genetic drift
EDTA: Ethylene diamine tetra-acetate. A food preservative,
anticoagulant and common laboratory buffer component.
Effective population size: see
Ne
Electrophoresis: polarized
acetate, agarose or acrylamide gel through which one runs proteins or DNA.
The material then separates by weight or polarity and allows one to distinguish
variants (e.g.,
alleles
enzyme variants). [-
phoresis
; from the Greek for �to carry�]. [See
Avise, Fig. 3.2, p. 58, and elsewhere in Chapter 3].
Allozymes
refer to enzyme
variants used as
genetic markers
Endemism:  occurring in only one restricted
locality.  Island species are often endemic (not found on adjacent
mainland).  High levels of endemism (e.g., plants and invertebrates
in Florida sand-pine scrub habitats) suggest a history of geographical
isolation.  South American mountain ranges, for example, have very
high rates of endemism for plants and animals.
Endonuclease : Cf.
Restriction
Enzyme
exonuclease
EPF: extra-pair fertilization. Cases in which the
'behavioral' parent is not the true genetic parent. Demonstrated for numerous
species of birds. EPC (extra-pair copulation) may or may not result in
EPF.
Epistasis: Interactions among alleles (from different
genes) that affect the phenotype.  Epistasis can be additive, multiplicative
or synergistic.  [See mentions in Gillespie text, and Fenster, C.B.,
L.F. Galloway, and L. Chao. 1997. Epistasis and its consequences for the
evolution of natural populations. Trends Ecol. Evol. 12: 282-286].
ESS: an evolutionarily stable strategy.  A strategy that can resist invasion by alternative strategies.  A concept developed by John Maynard Smith in a game theory context.  Highly influential concept in evolutionary theory.
ESU: cf. Evolutionary significant units.
Eppendorf: cf.
Cryotube
Small (<= 1.5 ml) flip-top plastic vial for storing reagents, samples
etc. Less expensive than cryotubes but also more subject to leakage.
Evolutionary forces:  Five major forces can
cause evolutionary change:
MEMORIZE
THESE!
Natural selection
Genetic drift
Mutation
Non-random mating
Migration (in the genetic sense of permanent
movement of genes from one location to another)
The presence of any of these forces can generate gene frequency changes and violates assumptions of the
Hardy-Weinberg
Equilibrium (HWE).
Evolutionary significant units: [See Moritz, C. 1994. Defining "evolutionary
significant units" for conservation. Trends Ecol. Evol. 9: 373-375].
Exact test: A statistical test developed by Fisher (yes, that Fisher), Irwin and Yates that calculates an exact probability from the marginal totals.  In population genetics, exact tests have been developed for assessing genetic differentiation and implemented in programs such as
Genepop
.  [Goudet et al. 1996] http://www.bmj.com/collections/statsbk/9.shtml
Exon: Section of the DNA that
codes for amino acids. See
intron
Exonuclease: An enzyme
that can attack DNA from the ends without needing a recognition site. The
non-specificity means that they are almost always undesirable in a molecular
biology context.
Fitch-Margoliash method: Algorithm for building phylogenetic
trees from
genetic distance
data.
Fitness: Easiest to encapsulate in its population
genetics sense as the relative rate of increase of a
genotype
under viability selection alone. Metz et al. (1992) discuss the concept
in a TREE article, Grafen (1982) discusses
inclusive
fitness
, Danchin et al. (1995) and McGraw and Caswell
(1996) discuss measuring fitness from real-world data. For many cases,
the matrix population parameter
can be taken as a measure of fitness (Caswell, 1989, p. pp. 163-171). [If
> 1 then the genotype increases, if
< 1 then it decreases].
Fixation index:  see
-statistics.
Flanking region: for
microsatellites
the flanking regions are the stretches of DNA outside the simple sequence
tandem repeat. These sequences are used as
primer
pairs. The flanking regions are usually invariant across a population or
species, but mutations in the flanking region can be a cause of
null
alleles
as well as a potentially serious source
of
homoplasy
(see Pemberton
et al. 1995).
Forensic: Of or relating to
courts or legal matters. Molecular markers are increasingly common in the
context of forensics, both in wildlife and human cases involving identity
or relatedness.
Founder effect: the effect caused by the establishment of a small subset of the genetic variation from a larger subset in a new context (as on islands).  The resulting
genetic drift
may lead to rapid evolution and speciation.  (Mayr, 1954; Templeton, 1980 transilience; Slatkin, 1996)
Frameshift mutation: Insertion or deletion of nucleotides,
such that an
exon�s
genetic
code is read in a different frame (i.e., the amount of change is not a
factor of three).
-statistics: a
measure of genetic structure developed by Sewall Wright (1969, 1978). Statistically
related to
ANOVA
ST
is the
proportion of the total genetic variance contained in subpopulations (the
subscript) relative to the total genetic
variance (the
subscript). Values can range
from 0 to 1. High
ST
implies a
considerable degree of differentiation among populations.  Also called
the fixation index (because high
ST
implies high degree
of local fixation of different alleles).
IS
(inbreeding
coefficient) is the proportion of the variance in the subpopulation contained
in an individual. High
IS
implies
a considerable degree of inbreeding.  Values can range from -1 (outbred)
to +1 (inbred).
Related measures:
(theta) of Weir and Cockerham (1984),
ST
of Nei (1973, 1978) and
ST
of Slatkin (1995 a,b). [See
Weir, 1996; Avise, Box 6.3, p. 252].
Gene conversion: Process by which one sequence replaces
another at an
orthologous
or
paralogous
locus
Gene diversity: A measure
of genetic variation in a population. It is calculated from the squared
gene (= allele) frequencies. See Weir (1996) p. 124 for the formula.
Gene frequencies: The term
used in population genetics for
allele
frequencies.
Gene trees (vs. species
trees): The concept that gene (allele) divergence can predate speciation
events (e.g., at
MHC
alleles
),
making it difficult to make phylogenetic inference from gene phylogenies.
Deep nesting of allelic ancestors is known as
lineage
sorting
.  Two other processes that can cause disagreement between
gene trees and species trees are gene duplication/extinction, and horizontal
transfer of genes.  Most species trees will consist of a modal version
of the underlying gene trees, ignoring the cloud of other links that comprise
a variance.  [See Avise pp. 143-157, Fig. 4.11; Maddison. 1996. Ch.
3 In Molecular Zoology, Figs. 7-9].
Genetic distance: various
statistics for measuring the 'genetic distance' between subgroups or populations.
Major distance measures include Nei's distance (1972, 1978), Reynold's
distance (Reynolds et al. 1983) and new distance measures that incorporate
the
stepwise mutation
process in
microsatellites
ST
of Slatkin 1995a, b;
of Shriver
et al.,
delta mu
of Goldstein et al. 1995).
Genetic drift: a force that reduces heterozygosity
by the random loss of alleles.  Drift is inversely related to population
size.  Infinitely large populations (an assumption of the Hardy-Weinberg
equilibrium) will not experience drift, whereas small populations will
experience major effects of drift.  Drift is one of the major forces
of evolutionary change (along with natural selection, mutation, genetic
migration, and non-random mating).  The equilibrium/balance between
drift and mutation is a major focus of much of population genetics.
Genetic load: reduction
in mean fitness resulting from fixation of many
alleles
with small detrimental effects. Genetic load largely impacts populations
with long-term small size.  [See Avise, p. 24 for a historical perspective;
Hedrick, 2001 for conservation implications]. Cf. i
nbreeding
depression
Genetic markers: any
trait used as a marker of genetic variation with in and among individuals
and taxa. Traits used include phenotypic traits (eye color), protein products
allozymes
, albumin),
and segments of the DNA. One might use a particular genetic marker as a
diagnostic trait [is this meat a legal elk or Rancher Smith's prize bull?;
does this person have a heritable genetic disorder?], as a tool for management
(how different are trout in Wyoming from trout in Colorado?), as an aid
to systematic analyses, or in a huge variety of ways in basic evolutionary
biology. Different genetic markers (e.g.,
microsatellites
mtDNA
allozymes,
RAPD's
) have different
scopes (fine-grained vs. coarse-grained analyses), and different advantages
and disadvantages (e.g., specificity, cost, ease of analytical interpretation
of the resulting data).
Genetic swamping: the obliteration of local genetic variation by invasion or migration of individuals from another population.  Often a concern in conservation.  [See Hedrick, 2005]
Genome size: The genome is the
collective term for all the complement of hereditary material found in
an organism (e.g., all the DNA in the set of chromosomes in eukaryotes).
Genome size ranges from approximately 10
base pairs (
bp
) in some viruses
to approximately 10
10
in many angiosperm plants, to > 10
10
in some salamanders and fishes. Mammals have approximately 2-3 X 10
bp. Although polyploidy can increase genome size, most increase seems to
be due to relatively small duplication events (because genome sizes within
taxa tend to be approximately normally distributed around an intermediate
modal size. [See Ayala, 1982, pp. 219-22].
Genomic library : See
Library
(genomic).
Genotype: The set of DNA variants
found at one or more
loci
in an individual. The information from which genotypes are developed could
include
allozyme
alleles
sequence information, or
RFLP
variants.
GTR: General Time Reversible model for DNA substitution.
[See Molecular Systematics text, Fig. 11, p. 434-437; or Hall, B.G. 2001.
Phylogenetic Trees Made Easy. Sinauer. pp. 91-93].
Haldane�s rule: "When in the F1 offspring of two
different animal races one sex is absent, rare, or sterile, that sex is
the heterozygous [
heterogametic
sex." [See Avise, p. 378-379].
Haploid: having a single complement of chromosomes.
See
diploid
Haplotype: a variant sequence
in a haploid genome.  Variant mitochondrial haplotypes are the basis
for many molecular phylogenetic analyses.
Hardy-Weinberg
principle: (Hardy-Weinberg Equilibrium is abbreviated HWE)
Given certain simplifying assumptions such as no genetic drift (= infinite
population size),
random mating
non-overlapping generations, no selection and no (genetic)
migration
the
genotype
frequencies
in an infinite population can be predicted from the gene frequencies,
and
by the formula:
+ 2
pq
A population will achieve Hardy-Weinberg equilibrium
(HWE) in a single generation (unless one of the assumptions listed above
is violated). We test for HWE by comparing observed and expected genotype
frequencies.  An amazing proportion of the subject matter of population
genetics is centered on how/why populations deviate from HWE.
Heritability:
= narrow-sense
heritability in quantitative genetics =
where
is the additive genetic variance and
is the phenotypic variance.  Heritability (in the narrow sense) enters
into the response to selection
where
, and
is the intensity of selection.  Broad sense heritability includes dominance variance,
and epistatic variance,
, in the numerator, so that
(V
)/V
.  See Gillespie (2004) p. 165, Hartl
(2000) pp. 166-167.
Heteroduplex: A hybrid DNA-DNA or RNA-DNA molecule
formed between (presumably
homologous
sequences from two different sources (
loci
individuals or
OTU
s). Heteroduplexes
are presumed to be the primary cause for the �shadow bands� commonly seen
on
microsatellite
gels. Cf.
heteroduplex analysis
Heteroduplex
analysis: Analysis of
heteroduplex
mobility under
polyacrylamide gel
electrophoresis
Reduced mobility of heteroduplexes relative to homoduplexes is presumed
to be proportional to the degree of sequence divergence.
Heterogametic sex: the
sex whose sex chromosomes are different from each other. In mammals, most
other vertebrates and most insects, males are the heterogametic sex (XY),
whereas in birds, lepidopterans, and some fish it is females (WZ). Chromosomal
sex determination is not universal (alternatives are phenotypic and
allelic
sex determination).
Heterologous: Homologous sequences from a species
other than the one being analyzed.
Heteroplasmy: Containing more than one type of a
particular organellar DNA (e.g.,
mtDNA
or cpDNA).
Heterosis: The hypothesis that
multilocus
heterozygosity
will be associated with fitness or a fitness component. See Coulson et
al., 1998 for a recent application using
microsatellite
DNA.  [See also Goudet, J., and L. Keller. 2002. The correlation between
inbreeding and fitness: does allele size matter? TREE 17: 201-202. and
Tsitrone, A. et al. 2001. Heterosis, marker mutational processes and population
inbreeding. Genetics 159: 1845-1859. for the view that the allele size
diff. method of Coulson et al. PRSLB 265: 489-495. may be flawed].
Cf.
transgressive segregation
Heterozygosity: An individual
or population-level parameter. The proportion of
loci
expected to be heterozygous in an individual (ranging from 0 to 1.0).
(observed
heterozygosity) is the observed proportion of heterozygotes, averaged over
loci.
(expected
heterozygosity) is also known as
gene diversity
(=
; preferred, less ambiguous term) and is calculated as 1.0 minus
the sum of the squared
gene frequencies
[See Weir, 1996, p. 124 for the multi-locus, multi-allele formula].
HLA:
uman
eukocyte
ntigen.
Term used in biomedical field for human
MHC
Homology: having the same
origin (used for genes,
characters
deriving from a common ancestor).
Homeobox: Sets of regulatory genes important in development.
Key area of developmental biology, particularly the evolution of segmentation/appendages.
[See Galis, F. 1996. The evolution of insects and vertebrates: homeobox
genes and homology. Trends Ecol. Evol. 11: 402-403].
Homoplasy: similarity of
traits or genes for reasons other than coancestry (e.g., convergent evolution,
parallelism, evolutionary reversals, horizontal gene transfer, gene duplications).
Homoplasy violates a basic assumption of the analysis of
genetic
markers
--variants of similar phenotype (e.g., base
pair size) are assumed to derive from a common ancestor. Homoplasious characters
will be identical by state (IBS) in unrelated taxa, but will not be
identical
by descent
(IBD).  See
synapomorphy
[See Sanderson, M., and Hufford. 1996. Homoplasy: The Recurrence of Similarity
in Evolution. Academic Press, NY ISBN 618030-X].
HWE: see
Hardy-Weinberg
Hybridization : In
molecular
biology
, the process of joining two complementary strands of DNA or
one each of DNA and RNA to form a double-stranded molecule. One strand
is often labeled and used as a
probe
to detect the presence of the second strand.  In
speciation
and evolution, the interbreeding of distinct species.  See Allendorf
et al. (2001) for an overview of the conservation importance of hybridization.
Hypervariability: High
degree of variation among individuals within local populations at a given
genetic
marker
. Examples of hypervariable markers include
minisatellites
and
microsatellites
Identical by descent (IBD): phylogenetic
characters (e.g., alleles) derived
from a common ancestor
and having
the same state.  Characters  can be identical in state (IBS)
without being IBD, in which case they exhibit
homoplasy
Inbreeding depression: reduced
fitness due to increased homozygosity (therefore expression of recessive
deleterious alleles) from inbreeding.  Inbreeding depression is mostly
a problem for large populations at drift-mutation equilibrium.  See
Hedrick and Kalinowski (2000) for conservation implications.  Cf.
genetic load
Inclusive fitness:
Measure of fitness that includes not only an individual�s own progeny but
the representation of its genes in the descendants of relatives (�kin selection�).
Calculation of inclusive fitness requires measurement of the
coefficient
of relatedness
Indel: Insertion or deletion event in a molecular
sequence.
Independent assortment: During gamete formation segregating
pairs of unit factors (e.g., genes controlling color or shape traits) assort
independently of each other.  As a result, one can use multiplicative
probabilities to compute multi-trait or multigene phenotypes or genotypes.
Linkage
disequilibrium can prevent the expected probabilities from being realized.
Individualization: buzzword (largely restricted to forensics applications)
to embrace the idea that molecular markers can facilitate distinguishing
individuals.
Infinite alleles model (IAM): a model for the mutation process, used
to derive measures of genetic distance or differentiation.  A major
alternative is the
stepwise mutation
model (SMM).
Ingroup: A group of taxa presumed
to be
monophyletic
and which form the primary focus of a phylogenetic analysis. Cf.
Outgroup
Introgression: Movement of genes (or traits) between
species or between well-differentiated populations. Introgression zones
are useful in the study of speciation and hybridization. [See Parsons et
al., 1993, and Brumfield et al. 2001, for an example of nuclear and mtDNA
markers used to illuminate hybrid and introgression zones in Neotropical
manakins].
Intron: DNA sequences within
the protein-coding sequences of a gene; introns are transcribed into mRNA
but are cut out of the message before it is translated into protein. Introns
may contain sequences involved in regulating expression of a gene. See
exon
Isolate breaking: Excess
heterozygosity (over
Hardy-Weinberg
expectation) observed when divergent
populations or subpopulations establish secondary contact.  The opposite
of the
Wahlund effect
Isolation by distance:  genetic differentiation that increases as a function of geographic distance between populations.  Deviations from isolation by distance suggest special circumstances impinging on the pattern of genetic variation.  Because points (pairs of populations) will not be independent, it is usual to test for isolation by distance with a nonparametric Mantel test.
Isozymes: Enzyme variants with the same functional
role, but differing in 1°, 2°, 3° or 4° structure. In some
cases, isozymes may be multimers produced by multiple genes. They may,
therefore, not qualify as
codominant
allozymes
for use as
genetic markers
Jackknifing: A statistical procedure based on sequential
omission of one item at a time from a data set, in order to estimate variances
and confidence intervals from small samples.
Bootstrapping
performs much the same function, often better, and with the power of modern
computers, jackknifing is less frequently used.
Jukes-Cantor distance: an algorithm
for computing distances among sequences based on the number of substitutions
among them.  It is computed as
= -3/4 ln(1-4/3
), where
is the proportion of sites with different nucleotides [see MEGA software help file]. A slightly more complex model is the
K2M
Kimura 2-parameter Model
Karyotype:  the complement of chromosomes (e.g.,
= 46 in humans) that constitute the genetic material of a eu
karyote
Kimura 2 parameter model (K2M):
a commonly used model for the probability of base pair changes in DNA sequences.
Often used as the basis for phylogenetic analyses.  Cf.
Jukes-Cantor
distance
. Other models one might see include F84 and HKY85[See Molecular
Systematics text, Fig. 11, p. 434-437; or Hall, B.G. 2001. Phylogenetic
Trees Made Easy. Sinauer. pp. 91-93].
Ladder: A series of known-size
fragments run in a gel to allow sizing of fragments of target DNA run in
other lanes. One commonly used ladder is
phage
lambda
cut with
Pst
[yields fragments
of 216, 211, 200, 164 and 150
bp
].
Ladderized:  a way of depicting a phylogenetic tree so that, in an unbalanced tree, the species-poor sister group is placed on the same side at every node.
Lambda: Lambda (
phage
DNA is a useful tool in molecular biology. Because its entire sequence
is known (= 50Kb double-stranded), it is often used to create a
ladder
of known-size fragments for sizing bands on gels. It is also a useful
cloning
vector
Library (genomic): a set of
clones
made from a set of randomly generated overlapping DNA fragments (usually
incorporated in
cloning vectors
representing the entire
genome
of an organism. DNA is cut into fragments with
restriction
enzymes
and then cloned. Clone number necessary
is a function of genome size, and DNA fragment size. [See Avise, Fig. 3.11,
p. 80; Freifelder: Molecular Biology p. 824].
Ligation: Enzyme-mediated
procedure for joining segments of DNA. Variants include
blunt
end
ligation (both strands of DNA end at the same
point, so that any other blunt end can be ligated onto it) or
sticky
end
ligation (one strand overhangs by a few base
pairs; this requires a specific enzyme to recognize and initiate ligation/synthesis).
Lineage sorting: The inevitable
�pruning� of evolutionary trees due to differential reproduction. In lineage
sorting, an ancestral polymorphism was maintained through more than one
speciation event, and therefore the common ancestors of sampled gene copies
are found deep in ancestral species (not at the nearest internal node).
Lineage sorting raises the issue of
gene trees vs.
species trees
.  [See Avise, Fig. 4.9, p. 144, Fig. 4.12, p. 147;
Maddison. 1996. Ch. 3 of Molecular Zoology, Figs. 7-9]
Linkage : An association in
inheritance between traits, such that the parental trait combinations appear
among the progeny more often than the non-parental. The proximity of two
or more
genetic markers
(e.g. genes,
RFLP
markers)
on a chromosome; the closer together the markers are, the lower the probability
that they will be separated during DNA repair or replication processes
(binary fission in prokaryotes, mitosis or meiosis in eukaryotes), and
hence the greater the probability that they will be inherited together.
Cf.
recombination
Linkage disequilibrium:
loci
not in random association. The linkage disequilibrium parameter for a one-locus,
two-
allele
model is given
by
11
22
12
21
= (1 -
where
is the
recombination
frequency and
is the number of generations since
Speed of approach to linkage equilibrium depends on the magnitude of
Decrease of linkage disequilibrium,
, is given by:
= (1-c)
* d
where
is the starting level of disequilibrium,
is number of generations,
and
is the recombination rate (<= 0.5). [See Ayala, 1982, p.
138].
Locus: from the Latin for 'place'.
A stretch of DNA at a particular place on a particular chromosome � often
used for a 'gene' in the broad sense, meaning a stretch of DNA being analyzed
for variability (e.g., a
microsatellite
locus).
Long branch attraction: Also called the "Felsenstein
zone". Phenomenon whereby
parsimony
will select the wrong tree given certain data configurations (when short
basal branches lead to distinct long branches, parsimony will tend to cluster
the long branches). [See Swofford et al. 1996 pp. 426-428 for a well-worked
out example].
Lyophilize: Freeze-dry.
M13: A filamentous
bacteriophage
of
E. coli
that is widely used in molecular biology.
Map unit: See
Centimorgan
Marker: see
Genetic
marker
Maxam-Gilbert sequencing:
A chemically based technique for deducing DNA sequences. Cf.
Sanger
sequencing
. [See Avise, 1996, Fig. 3.21, p. 99;
Russell, 1992, pp. 458-462].
MAX
(maximum number of steps): measure used in calculating the
Consistency
Index
and
Retention
Index
for phylogenetic trees. Heuristically (a heuristic
is a 'rule of thumb'), one takes the worst-case fit to a dichotomous tree.
Imagine analyzing fifteen taxa (see Figure). Seven of the taxa have State
0, the other eight have State 1 (e.g., this might be a presence/absence
character
).
The worst fit would be to match State 0 taxa with State 1 taxa on each
possible tip of the tree.
MAX
is therefore
the smaller number of the two state distributions for a given character.
For example, if nine taxa had State 0 and six had State 1, then
MAX
= 6; if twelve had State 1 and three had State 0, then
MAX
Illustration of
MAX
for case where
15 taxa have a binary character with a 7-8 split (seven taxa have State
0, shown with a solid circle, eight have State 1, shown with unmarked branches).
Because each of the seven State 0 taxa is paired at a tip with a State
1 taxon, the tree requires seven steps. The numbers refer (in arbitrary
order, from left to right) to the places where steps are required. Thus
(using alphabetical designations for the taxa, from left to right) Taxa
b, d, f, h, j, l, and n each force a step. Dashes between the alphabetical
labels for taxa indicate the taxa that are paired at tips. When we place
the 15 taxa on our calculated tree we will be likely to get fewer steps
(this number will be the
in the
consistency
index
and the
retention
index
). That is, it is unlikely that the computed
tree will produce the worst-case pairing shown in the tree above.
MHC: major histocompatibility complex.
Controls antigen response in the immune system. May be involved in mate
choice in some species (e.g., work by W.K. Potts and J.T. Manning on mice).
[Hedrick-P Loeschcke-V. 1996. MHC and mate selection in humans. Trends
Ecol. Evol. 11: 24-24; Potts, W.K., and E.K. Wakeland. 1990. Evolution
of diversity at the Major Histocompatibility Complex. Trends Ecol. Evol.
5: 181-187; Potts, W.K. and E.K. Wakeland. 1993. Evolution of MHC genetic
diversity: a tale of incest, pestilence and sexual preference. Trends in
Genetics 9: 408-412. ].
Microsatellites: Short
tandem repeats (e.g., AC
, where
8) of nucleotide sequences--the tandem units can be dinucleotides, trinucleotides
or tetranucleotides. The apparent mutation process is by
slippage
replication
errors, where the repeats allow matching via excision or
addition of repeats. Because this sort of slippage replication is more
likely than point mutations, microsatellite
loci
tend to be
hypervariable
The usual procedure is to use an
oligo
(e.g., AC
10
) as a
probe
screen a
genomic library
and then sequence positive
clones
to develop
primer
pairs
that can be used to amplify the target DNA with the
PCR
Strassmann et al. (1996) provides a useful set of laboratory protocols.
Another set of protocols is available by anonymous ftp at the Smithsonian
(see the Web page guide at the end of this glossary). Alternative name
is SSTR (simple sequence tandem repeat). [See also McDonald and Potts (1997),
or 1-page intro. at http://www.uwyo.edu/a&s/zoology/McDONALD.HTM].
Migration: In population
genetics, migration means the (permanent) movement of genes into or out
of a population. Thus, a 'migrating' warbler does not cause any migration
(in the genetic sense) by moving from breeding grounds in Wyoming to wintering
grounds in Mexico and then returning to breed in the same Wyoming locale.
Minimum viable population size:  See Nunney,
L., and K.A. Campbell. 1993. Assessing minimum viable population size:
demography meets population genetics. Trends Ecol. Evol. 8: 234-239.
Minisatellites: [see
VNTR]. Segments of repeated DNA often used as
genetic
markers
for individual identification (
forensic
DNA 'fingerprinting') or analyses of relatedness. Can be either single-
or multi-
locus
. Minisatellite
technology relies on
probe
-based
hybridization
Advantages include lack of need for specific
primers
and
hypervariability
Disadvantages include inability to use
PCR
amplification, the need for
Southern blotting
and, for multi-locus minisatellites, the lack of locus-specificity (making
population genetic analyses difficult). [See Avise, Fig. 3.15, p. 86].
MLE: Maximum Likelihood Estimation.
Mathematical technique based on the premise that best explanation is the
most likely (as opposed to the most parsimonious). In phylogenetic analyses,
MLE has been championed by such authors as J. Felsenstein in PHYLIP. Advances
in computer algorithms and hardware have made feasible the calculation
of Maximum Likelihood Estimators for complex underlying equations. Cf.
parsimony
Eliason (1993) is a general primer on MLE.
Molecular clock hypothesis:
Hypothesis that molecular change is linear with time, and constant over
different taxa and in different places. If that is so, then the sequence
difference between homologs in different taxa can be used to estimate time
since divergence. [See Avise text, pp. 120-132].
Monophyletic group (
clade
):
Evolutionary assemblage of taxa that includes a common ancestor and all
of its descendants. [See Avise, p. 117]. Cf.
Paraphyletic
polyphyletic
Morgan: a map unit for genomes, defined as that distance along which one crossing over is expected to occur per gamete per generation.  In humans one centiMorgan is about 1,000 kb.
MtDNA: mitochondrial DNA. Sequencing
of variant mtDNA
haplotypes
is a widely used technique
in systematics. The mostly maternal, clonal transmission of mtDNA provides
both opportunities and problems for phylogenetic analysis. [See Avise,
p. 73].
Muller�s ratchet: Hypothesis that lack of
recombination
in clonally reproducing organisms will lead to buildup of deleterious mutations.
Multiplexing: Using several pooled samples simultaneously,
thereby greatly speeding the analysis of
genetic
markers
. The samples must be distinguishable (i.e.,
either the range of fragment lengths does not overlap or the dyes used
fluoresce at different wavelengths).
Mutational meltdown: as deleterious alleles become fixed in small populations, they may drive population decline, leading to enhanced likelihood of extinction as a positive feedback loop.  [See Lynch et al. 1995; empirical counterexample in Gilligan et al. 1997].
Mya: Millions of years ago.
Effective population size. Many factors include fluctuating population
size, sex ratio (
= (4
)/(
),
age of reproduction (overlapping generations), the spatial dispersion of
the population (
= 4
ps
and family size can affect
. Usually,
will be less than
(the census population size) in natural populations.
If, however, the distribution of family sizes is more uniform than
Poisson
then
can be >
is
a fundamental component of many population genetics formulations.
Often, however, it is found in the term 4
or 4
m (mutation or migration respectively) and hence cannot be
estimated by itself.  See Crow and Kimura (1970) for an overview;
Ewens (1982), Harris and Allendorf (1989), Caballero and Hill (1992), and
Nunney and Elam (1994) also discuss the concept.  Hartl's (2000) primer
of population genetics has a useful summary on pp. 96-98.
Negative control: . In the context of
PCR
amplification this means running a reaction in which water replaces DNA
so that when the product is
visualized
the expectation is no signal. If the negative control shows a signal, then
one suspects contamination of the PCR amplification cocktail or of reagents
used in the amplification or
visualization
procedures.
Neighbor-joining: A method for building
an evolutionary tree from a
matrix of distances
among
OTU
s (see Avise, pp. 136-139 or Hillis et
al., 1996, p. 488).
Neutrality test: test of the assumption that a haplotype or allele is selectively neutral.
Nick translation: at a single-stranded break, replacement
of the old strand occurs in the 5' to 3' direction. [See Freifelder: Molecular
Biology p. 273].
Node: Branch points in a cladogram
(phylogenetic branching pattern diagram).
The point at which two sister groups descend from a common ancestor.
Non-
synonymous
substitution: A nucleotide substitution (mutation) that results in a different
amino acid. More likely for first and second position codons.
Nucleotides: the building blocks of DNA (and RNA).
DNA nucleotides comprise a nitrogenous base, a deoxyribose sugar and a
phosphate group.
Null allele: allele that fails
to become
visualized
under the analytical conditions (can happen with
allozymes
microsatellites
et al.). See Pemberton et al. 1995 for discussion of the potential problem
of
homoplasy
caused
by null
alleles
OD: Optical density as measured in a photospectrometer.
Used to assess the purity and concentration of DNA.
Oligo(nucleotide): short chain
of nucleotides. Synthesized in the lab. as a starting point for developing
primers
or for use as a
probe
Ordered (characters): States 0, 1, 2....
form an ordered sequence, such that a change from 0 to 2 requires two steps,
a change from 2 to 3 one step, etc.  the ordering does not tell us
about the ancestral state (i.e., does not inform us on
polarity
).
[See pp. 411-412 of Mol. Syst., 2nd edn.; also, Maddison and Maddison 1992
MacClade manual p. 52, which helps distinguish polarity from ordering]
Orthology: Homology (of a
molecular sequence) that arises from a speciation event. Cf.
Paralogy
[See Avise, p. 18].
OTU: Operational taxonomic unit.
Examples include populations, species, genera, and families. For phylogenetic
analyses, the OTUs will be terminal taxa (i.e., occur at the branch tips
of the tree).
Outbreeding depression (OD):  reduced fitness
resulting from hybridization between divergent taxa.
Intrinsic
OD results from genetic incompatibility between the two taxa (e.g. chromosome
differences that disrupt meiosis), whereas
extrinsic
OD results
from reduced adaptive fit of the hybrid to the environment.
Outgroup: Taxon phylogenetically
outside the
clade
of interest
(the
ingroup
). When one
uses an outgroup in phylogenetic inference, the ingroup is implicitly assumed
to be
monophyletic
.  Best reference point
for determining
polarity
(direction of
character
change/whether a character is or isn't ancestral). [See Avise, p. 116; p.
416 of Molecular Systematics, 2nd edn.].
Overdominance: same as heterozygote advantage. Fitness
of heterozygote
genotype
is greater than fitness of either homozygote genotype.
PAGE: PolyAcrylamide Gel
Electrophoresis
A technique for separating DNA fragments based on differential mobility
in a gel.
Panmixia: Absence of any differentiation among subpopulations
(because of high levels of gene flow, creating effectively one single large
population with no internal structure).  The adjective is
panmictic
Paralogy: "Homology that arises
via gene duplication" [from Hillis et al. 1996]. (Cf.
Orthology
Pseudogene
).
[See Avise, p. 18].
Paranome: the complete set of all duplicated genes in a genome.
Ref:

Vandepoele, K.,  W. De Vos, J.S. Taylor, A. Meyer, and Y. Van de Peer. 2005. Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc. Natl. Acad. Sci. USA 101: 1638–164.
Parapatric: adjacent but
non-overlapping distribution (as opposed to
sympatric
allopatric
).
{A more obscure term is
peripatric
speciation).
Paraphyletic group: Artificial
assemblage of taxa that includes a common ancestor and some but not all
of its descendants. Cf.
monophyletic
polyphyletic
, reciprocal monophyly [See Avise, p. 116, Fig. 4.11, p. 146].
Parsimony: Idea that simplest
explanation is best. In phylogenetic analysis, the phylogeny that involves
the fewest changes in
character
states when considering alternative branching patterns for a phylogeny.
Championed by such people as D. Swofford in the software PAUP (Phylogenetic
Analysis Using Parsimony). See
MLE
PAUP: Phylogenetic Analysis Using
Parsimony
Software program (and associated manual) by Dave Swofford of the Laboratory
of Molecular Systematics at the Smithsonian. See Swofford, 1996.
PCR: polymerase chain reaction.
Technique for amplifying nucleic acids in a
thermal
cycler
. Involves use of forward and reverse
primer
pairs that start off the reaction. End yield is many orders of magnitude
more DNA of the target sequence than one started with. The resulting amplified
DNA can then be
visualized
with stains or radioactive labeling, or sized with fluorescent markers
in a sequencer. [See Avise, p. 87, Fig. 3.16, p. 88].
Penetrance: the frequency with which an
allele
manifests itself (i.e., the proportion of the population that shows the
influence of the allele). See Cooke and Buckley 1987 p. 14.
Peripatric speciation: Speciation
resulting from "long-distance dispersal across a pre-existing barrier".
The idea that small, peripheral populations may be particularly prone to
speciation.  See Ödeen and Florin (2002), Cracraft and Prum (1988),
Mayr (1954, 1982).  The term is slightly unfortunate because 1) it
sounds a lot like parapatric, 2) it has not received wide enough use to
generate recognition, even among people who deal with speciation and phylogenetic
systematics fairly regularly.  Although Cracraft and Prum (1988) dismiss
the possibility of long distance dispersal, a recent Nature paper on chameleons
provides at least one good counterexample [Raxworthy, C.J., M.R.J. Forstner,
and R.A. Nussbaum. 2002. Chameleon radiation by oceanic dispersal. Nature
415: 784-787].
Phage: A type of virus that infects
bacteria. Phages are often used as a
cloning
vector
, because one can incorporate DNA into them,
then produce multiple copies by culturing the bacterial host. Can have
2-strand DNA (most common), 1-strand DNA, 1-strand RNA and 2-strand RNA
(least common). See Freifelder: Molecular Biology 18-23.
Lambda
is a widely used phage.
Pheneticists: School of phylogenetic
analysis focusing on statistical criteria for clustering taxa (numerical
taxonomy). See
cladistics
PHYLIP: Phylogenetic Inference Package (Version 3.5c,
as of October 1996). Joe Felsenstein, Univ. of Wash. Suite of phylogenetic
analysis software programs for various platforms (PC, UNIX, and Mac/PowerMac).
Neighbor-joining
UPGMA
Fitch-Margoliash and other tree-building methods. Available on the WWW
via
ftp://evolution.genetics.washington.edu/pub/phylip/.
Phylogeography: Study of the patterns of genetic
differentiation across landscapes (phylogenetic biogeography). Pioneered
by John Avise.
Plaque: hole in bacterial lawn (in agar). Used in
counting
phage
-- one hole
or plaque = 1 phage.
Plasmid: Autonomously replicating,
extrachromosomal circular DNA molecules, distinct from the normal bacterial
genome and nonessential for cell survival under nonselective conditions.
Some plasmids are capable of integrating into the host genome and are used
as a
cloning vector
for small pieces of DNA (typically 50 to 5000 base pairs) inserted into
the plasmid. A number of artificially constructed plasmids are used as
cloning vectors. Cf.
cosmid
YAC
plasmids
sex plasmid. Can transfer chromosomal genes
and also transfer F to a cell lacking F.
R plasmids: antibiotic resistance plasmids.
Col plasmids: synthesize colicins that kill closely
related bacterial
strains lacking the Col plasmid.
Pleiotropy: the phenomenon whereby a single gene has several different phenotypic effects.
Plesiomorphy: Ancestral
character
state (present in the ancestor of the taxa under study). Cf.
apomorphy
symplesiomorphy
synapopmorphy
[See Avise, p. 116].
Poisson distribution: a discrete distribution used to describe randomness in time or space.
In calculating
effective population size
), the distribution of family sizes is expected to follow a Poisson distribution.
By breeding so that family sizes are more even, one can make the effective size larger than the census size. A Poisson has the property that the mean equals the variance -- var > mean means clumped, var < mean means uniform.
Polarity: Direction of change
of a
character
(whether
a character is ancestral or
derived
), usually assessed
by referring to an
outgroup
Polarity determines whether shared characters represent
synapomorphies
symplesiomorphies
or
homoplasy
Global polarity (meaning that character evolution is irreversible) is a
desirable condition but difficult to demonstrate conclusively.  [See pp.
411-412 of Mol. Syst., 2nd edn.; also, Maddison and Maddison 1992 MacClade
manual p. 52, which helps distinguish polarity from ordering]
Polyacrylamide: See
PAGE
Polymerase chain reaction: See
PCR
Polymorphism:  the presence of two or more variants of the DNA at a given locus.  Often applied to variants of an expressed gene.
Polyphyletic group: Artificial
assemblage of taxa derived from two or more common ancestors. Cf.
monophyletic
paraphyletic
[See Avise, p. 116].
Polyploid: having more than two sets of homologous
chromosomes.  A common route to speciation in plants.  Recently,
a South American rodent has been found to be tetraploid (Gallardo et al.,
1999).
Polytomy (hard vs. soft): A branching point in an evolutionary tree
with more than two upward branches.
Soft
polytomies result from data that are
insufficient to fully resolve a phylogeny.
Hard
polytomies occur when several lineages split essentially simultaneously.
Positive control: In the context of
PCR
amplification, this means running a DNA sample that we know, from previous
experience, has amplified with the given set of
primers
and been
visualized
If our PCR batch plus the positive control don't show up, then we can assume
that something was wrong with: the PCR amplification reaction, the gel
loading, the staining or something else in that particular 'run'--such
as the pH or reagents.
Primer: Short, preexisting single-stranded
polynucleotide chain to which new deoxyribonucleotides can be added by
DNA polymerase (to 'prime'
PCR
amplification). The primer anneals to a nucleic acid template (DNA of the
organism of interest) and promotes copying of the template, starting from
the primer site. To amplify
microsatellites
one uses a forward and reverse primer pair:
agctcagtccctagtcagtact
]acacacacacacacacacacac[
ggtacttcggagctatccgaattccct
In this example the italicized
bp
are the forward and reverse primers (should not differ among individuals),
whereas the unitalicized 'ac' repeat is the microsatellite. By running
back and forth across the repeat one can amplify a few copies of the microsatellite
region by orders of magnitude, yielding sufficient DNA to allow
visualization
of the amplified product on an acrylamide gel by staining with ethidium
bromide.
Some primer sequences may be conserved across wide
taxonomic gaps (e.g., across families), while others may differ even among
congeners.
Private alleles:  alleles found only in

a single population.  Used by Slatkin (1985) to assess gene flow.  Neel, J. V. 1973. “Private” genetic variants and the frequency of mutation among South American Indians. Proc. National Acad. Sci. USA 70: 3311–3315.
Probe : Single-stranded DNA or
RNA molecules of specific base sequence, labeled either radioactively,
immunologically, or by other means, that are used to detect the complementary
base sequence by
hybridization
Some
genetic markers
(e.g.,
minisatellites
depend on probe-based techniques.
Pseudogene: "A usually non-functional
copy of a protein-coding gene inserted at another location in the genome.
Most pseudogenes result from retroposition of processed mRNA's, and therefore
typically lack
introns
and the regulatory sequences necessary for expression." [from Hillis et
al. 1996] (See
Paralogy
Pst: A
restriction
enzyme
. Used, for example, to create known-size
fragments of the
phage
lambda
for use as a
ladder
on
acrylamide gels.
QTL: Quantitative Trait
Loci
Molecular advances provide a relatively new opportunity to link quantitative
genetics (which is largely phenotype-based) to its molecular basis.
See Rieseberg et al. (2002) for an application of QTLs to the problem of
whether speciation is driven largely by selection or drift.
: See
Coefficient
of relatedness
Random mating: A fundamental
simplifying assumption for many population genetics models. Non-random
mating may be
assortative
(birds of a feather),
disassortative
(opposites attract) or skewed (hotshots). For example, for
Hardy-Weinberg
equilibrium, random mating is required.
RAPD (pronounced 'rapid'): Randomly
Amplified Polymorphic DNA. A
genetic marker
technique using
PCR
amplification
from short (= 10
bp
) segments
of arbitrary sequences to look for polymorphisms. Quick (no development
time for
primers
!) but
can be problematic in terms of interpretability within the framework of
population genetics theory. RAPD's may work very well in certain cases
(e.g., Ode et al., 1995).
Reciprocal monophyly: two sister taxa are reciprocally monophyletic when all alleles within each taxon are genealogically closer to one another than to any alleles in the other taxon.  See Avise Fig. 4.12.  Reciprocal monophyly is a "good thing" when resolving phylogenies.  Alternatives ("bad things") are paraphyly and polyphyly.
Recombination: Exchange
of gene segments by crossing over at chiasmata (exchange of material between
non-sister chromatids). The exchanged sections are usually homologous.
The likelihood of recombination increases with increasing physical distance.
Cf.
linkage
Reinforcement: an increase in reproductive isolation between populations.  Where somewhat divergent forms come into secondary contact and hybrids are less fit than either parental form, reinforcement will lead to enhanced prezygotic isolating mechanisms.
Relatedness:  See
coefficient
of relatedness
Rescaled Consistency Index
RC
): A phylogenetic index (range 0 to 1) used to assess the congruency
and fit of
characters
within a given tree. It is computed as:
CI
RI
where
CI
is the
Consistency
Index
and
RI
is the
Retention
Index
. A higher value of
RC
indicates that
the characters in the data set are more congruent with each other and the
given tree.
Restriction enzyme (or
endonuclease):
[From http://www.ultranet.com/~jkimball/BiologyPages]
DNA-cutting enzymes found in bacteria (and harvested
from them for use). Because they cut within the molecule, they are often
called restriction endonucleases.
A restriction enzyme recognizes and cuts DNA only
at a particular sequence of nucleotides. For example, the bacterium
Hemophilusaegypticus
produces an enzyme named
HaeIII
that cuts DNA wherever it encounters
the sequence
5'GGCC3'
3'CCGG5'
The cut is made between the adjacent G and C. This particular
sequence occurs at 11 places in the circular DNA molecule of the virus
phiX174. Thus, treatment of the DNA with the enzyme produces 11 fragments,
each with a precise length and nucleotide sequence. These fragments can
be separated from one another and the sequence of each determined.
HaeIII
and
AluI
cut straight across
the double helix producing
blunt ends
However, many restriction enzymes cut in an offset fashion. The ends of
the cut have an overhanging piece of single-stranded DNA. These are called
sticky
ends
because they are able to form base pairs with
any DNA molecule that contains the complementary sticky end. Any other
source of DNA treated with the same enzyme will produce such molecules.
Mixed together, these molecules can join with each
other by the base pairing between their sticky ends. The union can be made
permanent by another enzyme, DNA ligase that forms covalent bonds along
the backbone of each strand. The result is a molecule of recombinant DNA
(rDNA).
The ability to produce recombinant DNA molecules
has not only revolutionized the study of genetics, but has laid the foundation
for much of the biotechnology industry. The availability of human insulin
(for diabetics), human factor VIII (for males with hemophilia A), and other
proteins used in human therapy all were made possible by recombinant DNA.
[McDonald] Over 400 such enzymes have been developed
that recognize and cut over 100 different DNA sequences. Most endonucleases
are palindromic [same letters backwards or forwards], so that they can
be recognized along either strand. The longer the recognition sequence,
the lower the probability of encounter and therefore the fewer cuts per
size of DNA. Major classes are 6-cutters, 5-cutters and 4-cutters. For
example, the 6-cutter
Eco
RI (isolated from
Escherischia
coli
cuts non-methylated 5'-GAATTC-3'. These enzymes serve bacteria as a protection
against foreign DNA (they methylate their own DNA). They have been of revolutionary
importance as a tool in molecular biology (along with
PCR
).
They are also known as endonucleases (cf.
Exonucleases
).
1 unit of restriction enzyme is the amount required
to digest completely 1 µg of substrate DNA (usually
lambda
phage
DNA). [See Avise, pp. 67-70].
[Enzyme: A molecule, largely or wholly protein,
that acts as a catalyst, speeding the rate at which a biochemical reaction
proceeds but not altering the direction or nature of the reaction].
Restriction fragment length polymorphism: See
RFLP
Retention Index (
RI
):
A phylogenetic index (range: 0 to 1) computed as the ratio of a given tree's
observed length (number of steps) to the minimal possible length.
The ensemble
RI
across all
characters
on a tree is given by (the weighted sum of the
MAXi
minus the weighted sum of the si), divided by (the weighted sum of the
MAX
minus the weighted sum of the
MIN
). [Formula below may
be hard to read except in hard copy Mac printout]:
Where
is the number of characters,
is the weighting (if any),
MAX
is the maximum possible
number of steps, and
is the observed number
of steps. [All values indexed for the
th
of
characters].
Verbally,
RI
is the (weighted) sum of the
maximum conceivable number of steps in
any
tree minus the observed
sum in the
given
tree, divided by the maximum minus the minimum.
[In contrast the
Consistency Index
is simply the minimum over the observed]. The MacClade manual (Maddison
and Maddison, 1992, pp. 267-271) shows how to compute the number of steps.
Cf.
Rescaled Consistency Index
RC
),
MAXi
(maximum
number of steps).
Reticulate evolution:  (From the Latin
for "net").  When paths of ancestry cross and intersect repeatedly,
the pattern of inheritance is reticulate (as opposed, for example, to strictly
dichotomous branching).  Hybridization, recombination and horizontal
gene transfer can all cause reticulations (anastomoses) that can cause
problems for phylogenetic inferences.  See Avise p. 4; MacClade
manual by Maddison and Mison 1992 also discusses reticulate evolution
well.
Retrovirus: small single-stranded
RNA viruses that use reverse transcriptase as part of their arsenal of
self-replication (HIV/AIDS is the most famous example).
RFLP (pronounced 'riflip'): Restriction
Fragment Length Polymorphism. A
genetic
marker
technique using variants in the DNA exposed
by cutting with
restriction enzymes
Variants are
visualized
by running through
electrophoretic
gels. [See Avise, pp. 67-87].
Root:  In a phylogenetic tree, the root is the
location of the common ancestor.  Many trees are unrooted.  [See
p. 410 and Fig. 2a vs. 2b of Mol. Syst., 2nd edn.]
ST
: a measure of genetic differentiation
related to
-statistics
, but incorporating
stepwise mutation
model (Slatkin 1995 a, b)
Sanger/dideoxy sequencing: A
technique for deducing DNA sequences. The technique relies on using modified
nucleotides, which terminate the synthesis reactions at specific base pairs
(A,G, C, or T). The resulting DNA fragments are then
visualized
on a
polyacrylamide gel
Sanger sequencing is the basis for automated sequencer techniques. [See
Avise, 1996, Fig. 3.21, p. 99; Russell, 1992, pp. 458-462].
Saturation: In phylogenetic analyses, the idea that
multiple
transitions
or
transversions
can obliterate the information content of a DNA sequence.  For coding
genes, the third position in codons can become saturated, meaning that
so much change has occurred that any systematic pattern is obscured.
scnDNA: Single-copy nuclear DNA.
Segregating site: If two sequences of a
homologous
stretch of DNA have different nucleotides at a given position, the spot
is called a segregating site.
Selection coefficient (s): a measure of relative
fitness of alleles, given as
= 1 - (w
/ w
) where
is the relative fitness of the
allele and is arbitrarily
given a relative fitness of 1.  See Gillespie 2004 Chapter 3 or Hartl
(2000) pp. 75-88 for introductory treatments.
Selection differential: shift in the mean value of
a trait. Due both to direct selection and indirect selection (via selection
on correlated traits).
Selection gradient: partial regression of relative
fitness on a trait, holding all other traits constant. Measures direct
force of selection on a trait.
Sequencing: Molecular techniques for deducing the
nucleotide composition of the DNA. The two major alternatives are
Maxam-Gilbert
sequencing, and
Sanger
/dideoxy
sequencing. [See Avise, 1996, Fig. 3.21, p. 99; Russell, 1992, pp. 458-462;
Miyamoto and Cracraft, 1991].
Shadow bands: Secondary bands formed, for example,
on
microsatellite
gels. They probably represent
heteroduplex
events.
Shifting balance theory:  Sewall Wright's concept of a shifting balance between drift and selection whereby populations can cross the valleys between peaks of fitness in an adaptive landscape.  Contrasts with Fisher's theory of mass selection championed by Coyne et al. (2000). [See O'Fallon and Adler, 2006 and references therein; ].
Sidereal: Determined or measured by means of the
stars. Sidereal time is 'true' clock time, as opposed to
molecular
clock
time.
Silent substitution: mutation in a coding/expressed
region of the DNA that produces no change in the amino acid coded for (because
of the redundancy of the genetic code).  Also known as
synonymous
substitution
Simple sequence tandem repeat: See
microsatellite
Single strand conformational polymorphism: See
SSCP
Singleton bands: bands that occur in only a single sample of a genotypic fragment-based analysis.
Sister taxa: Taxa stemming
from the same
node
in a phylogeny.
[See Avise, p. 116].
Slippage replication:
A mutation process whereby a simple sequence tandem (
microsatellite
repeat grows by addition or subtraction of the "beads" of simple units
that make up the "necklace".  A dinucleotide AC repeat would grow
by addition or subtraction of AC units.
SNP: Single nucleotide polymorphism.  In genome
sequencing projects, attention is now often focusing on detection of single
base-pair changes in the DNA sequence.
Southern blotting : Transfer
by absorption of DNA fragments separated in
electrophoretic
gels to membrane filters for detection of specific base sequences by radiolabeled
complementary
probes
. Method
to reveal information about identity, size and abundance of the DNA. Southern
blotting is used in
visualization
of
minisatellites
and
RFLP's
. [See Avise, p.
69-70]. Originally described by E.M. Southern [Western blotting is a pun
of sorts].
SSCP: Single strand conformational
polymorphism. A technique for detecting polymorphisms using
electrophoresis
of single-stranded DNA whose conformation differs due to point substitutions,
deletions, or insertions. [See Hillis et al., 1996, p. 252, 262; Orita
et al., 1989]. Cf.
DGGE
TGGE
and
heteroduplex analysis
SSTR: See
microsatellite
Stepwise mutation:
Microsatellite
variation appears to result from
slippage
in replication,
which is most likely to add or delete a single repeat unit (steps of one).
As a result,
alleles
more
similar in size will presumably be more closely related. This additional
'phylogenetic' information can be used in assessing genetic differentiation
or
genetic distance
The stepwise mutation model (SMM) is an alternative to the infinite alleles
model (IAM) as the basis for deriving measures of genetic differentiation.
Sticky ends:
Restriction
enzyme
cut that produces overhanging 5� or 3� ends.
Cf.
blunt ends
. Sticky ends
tend to be more useful when specificity of
ligation
is desirable.
Stoichiometric: Having a definite proportion of chemical
constituents by weight.
Stringency: "conditions
of
hybridization
(such as temperature and concentration of chemical additives) that determine
the degree of similarity that will result in formation of hybrid molecules."
[from Hillis et al. 1996]. In hybridization, a stringent wash of a membrane
leaves very little bound DNA. For
plasmids
= low copy number vs. relaxed = high copy number.
Sympatric: occurring in the
same geographic area. A less stringent criterion for overlap than
syntopic
Cf.
parapatric
allopatric
Symplesiomorphy: shared
ancestral
character
Cf.
synapomorphy
[See Avise, p. 116].
Synapomorphy: Shared derived
character
state, useful for
cladistic
analysis. Cf.
apomorphy
autapomorphy
homoplasy
plesiomorphy
symplesiomorphy
[See Avise, p. 116].
Synonymous substitution:
A nucleotide substitution that does not result in a different amino acid
(e.g., any codon beginning CC will code for proline, regardless of the
codon in the third position). Also known as a "silent" substitution.
Synonymous substitutions result from the
degeneracy
(redundancy) of the genetic code at the third codon position. A non-synonymous
substitution changes the amino acid coding. [See Avise, Fig. 4.2, p. 122].
Syntenic: located on the same chromosome.
Syntopic: occurring in the
same macrohabitat and therefore presumably having the opportunity to interbreed.
Taq
polymerase: A thermostable DNA polymerase
from Thermus aquaticus, a hot springs bacterium. Used in
PCR
amplification because it does not degrade during the high heat cycles generated
by a
thermal cycler
Taxon (plural taxa): Group of
organisms linked by common ancestry.  Taxa can range in scale from
populations to kingdoms.
TE: Tris-EDTA, a common laboratory buffer.
Tension zone:  hybrid
zones often exhibit a balance between the homogenizing force of dispersal/gene
flow on the one hand, and the divergence-promoting force of selection on
the other hand.  See Barton and Hewitt (1985).  Cf.
cline
Terminal nodes:  The
taxa
at the tips of a phylogenetic tree [See p. 410 of Mol. Syst., 2nd edn.].
TGGE: Thermal Gradient Gel
Electrophoresis
A technique for separating DNA fragments for
visualization
based on differential mobility under increasingly denaturing conditions
due to increasing temperature. Cf.
DGGE
SSCP
and
heteroduplex analysis
Thermal cycler: the 'engine'
or
PCR
machine, in which the
PCR is performed.
Topology: the study of the properties of geometrical figures that are subjected to defomations such as twisting or bending.  In systematics, the "shape" of phylogenetic trees.  Two trees have the same
topology
if rotating (without reattaching) branches shows that the pattern of relationships among the
OTU
s are identical.
Transfection: Entry of
purified viral nucleic acids into cells, followed by activity or replication
of the incorporated nucleic acids.
Transgressive segregation:  in hybrid zones, phenotypes of offspring outside the range of variation found in the parental forms, are said to be transgressive.  Ref: Rieseberg et al. 1999.
Transformation : A process
by which the genetic material carried by an individual cell is altered
by incorporation of exogenous DNA into its genome. Griffith (1928) first
described the phenomenon in
Diplococcus
pneumoniae
Transgenic: Having DNA incorporated from an external
source, usually via
retroviral
transfection
Transgenic techniques can be used to �mass-produce� biocompounds, and to
test for gene function.
Transilience: rapid but temporary inbreeding without depletion of genetic variation leading to speciation. Templeton's (1980) mechanism for
founder effect
speciation.
Transition: a point mutation
in the DNA in which replacement is by a similar nucleotide. I.e., a purine
(A and G) by a purine or a pyrimidine (C or T) by a pyrimidine. Transitions
happen more often than
transversions
The dissimilar rates of mutation can be incorporated in phylogenetic inference
by various weighting schemes.  [See pp. 432-438 of Mol. Syst., 2nd
edn.].
Transversion: a point
mutation in the DNA in which replacement is by a dissimilar nucleotide.
I.e., a purine (A or G) is replaced by a pyrimidine (C or T) or vice versa.
Cf.
transition
UPGMA: unweighted pair-group
method of arithmetic averages. Tree-building technique for phylogenetic
analysis. Data required are distances (
genetic
distance
or other distance measure) between taxa, arranged
in a matrix form. [See Avise, pp. 134-136].
Upstream: Toward the 5� end of a DNA sequence.
Vicariance biogeography:
proposition that most speciation events occur by geological separation
of the range of species (e.g., rise of mountain ranges, submersion of continents,
etc.) rather than by any form of dispersal. That is, under a vicariant scenario, the range of a formerly unitary OTU is split by the rise of a geological barrier such as the Andean uplift.  Under a dispersal scenario, an OTU colonizes a suitable but formerly unoccupied area.  [See Avise, pp. 418-429].
Vicariance biogeography was developed by Leon Croizat.  A major champion of vicariance is Joel Cracraft [Cracraft and Prum
(1988), Cracraft (1984)].  See
allopatric speciation
Visualization: technique
for assessing variation among DNA segments (
genetic
markers
). Methods include radiolabeling (exposure
of gels to x-ray film) and various stains (ethidium bromide, silver stains
etc.).
VNTR (variable number tandem repeat): Segments of
repeated DNA. Short base unit repeats (2-6
base pairs
are
microsatellites
longer repeats (100s of
bp
are
minisatellites
The short length of the microsatellites (<= 300 bp) allows one to amplify
the DNA with the
PCR
and is
a key factor making microsatellites preferable to minisatellites (which
require radioactively labeled
probes
).
Wagner distance method: Criterion for obtaining a
phylogenetic tree from molecular distance data. Path lengths in Wagner
trees equal or exceed corresponding observed distances (unlike
UPGMA
or
neighbor-joining
methods).
Wagner
parsimony
a criterion for determining the most parsimonious tree in a phylogenetic
analysis. [See Hillis et al., 1996, p. 416].
Wahlund effect: Reduction in
heterozygosity
(increase in
homozygosity)
when distinct taxa are analyzed jointly.
Whenever subpopulations vary in gene frequency, the population as a whole
will show a Wahlund effect.  The opposite effect, known as
isolate
breaking
, occurs when divergent populations intermix.  In that
case, the interbreeds will show an increase in heterozygosity over the
Hardy-Weinberg expectation.
Xenologous:  having separate evolutionary origins.
Cf.
homologous
paralogous
YAC (yeast artificial chromosome)
: A
cloning vector
used to
clone
DNA fragments
(up to 400 kb); it is constructed from the telomeric, centromeric, and
replication origin sequences needed for replication in yeast cells. The
inserts can be much larger than those accepted by other vectors such as
plasmids
or
cosmids
����������������������������������������������������������������������
Useful reference texts:
(*
means copy in McDonald library)
*Avise, J.C. 2004. Molecular Markers, Natural
History and Evolution (2nd edn.). Chapman and Hall, New York.
*Brooks, D.R., and D.A. McLennan. 1991. Phylogeny,
Ecology, and Behavior. Chicago Univ. Press, Chicago.
*Ferraris, J.D., and S.R. Palumbi (eds.). 1996. Molecular
Zoology: Advances, Strategies, and Protocols. Wiley-Liss, NY. 580 pp.
*Gillespie, J. H. 2004. Population Genetics: A
Concise Guide (2nd edn.). The Johns Hopkins University Press, Baltimore, Md. On Reserve
ISBN  0-8018-8009-2 $19.95
*Hall, B.G. 2004. Phylogenetic Trees Made Easy:
A How-to Manual (2nd edn.). Sinauer, Sunderland, MA.
ISBN 0-87893-312-3
*Hartl, D.L. 2000. A Primer of Population Genetics
(3rd ed.). Sinauer Associates, Sunderland, MA.
*Hartl, D.L., and A.G. Clark. 1989. Principles of
Population Genetics. Sinauer Associates, Sunderland, MA. [3rd edition is
now available]
*Hillis, D.M., C. Moritz, and B.K. Mable (eds.).
1996. Molecular Systematics (2nd ed.). Sinauer Associates, Sunderland,
MA.
[Has useful Glossary]
Hoelzel, A.R., and G.A. Dover. 1991. Molecular Genetic
Ecology. IRL Press, Oxford U. Press, Oxford
SCI QH 455.H64 1991.
Kendrew, J.C. 1994. The Encyclopedia of Molecular
Biology . Blackwell Science, Oxford
SCI REF CALL #: QH506 .E53 1994
*Li, W. 1997. Molecular Evolution. Sinauer Associates,
Sunderland, MA.
*Maddison, W.P., and D.R. Maddison. 1992. MacClade:
Analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland,
MA. V. 3.
Martins, E.P., and T.F. Hansen. 1997. Phylogenies
and the comparative method: a general approach to incorporating phylogenetic
information into the analysis of interspecific data. Am. Nat. 149: 646-667.
Rieger, R, A. Michaelis, and M.M. Green. 1991. Glossary
of Genetics : Classical and Molecular, 5
th
edn. Springer-Verlag,
Berlin
SCI REF CALL #: QH427.R54 1991
Russell, P.J. Genetics, 3
rd
Edition. Harper, Collins, New York.
UW Science library call # QH 430.R87 1992.
*Weir, B.S. 1996. Genetic Data Analysis II: Methods
for discrete population genetic data (2nd ed.). Sinauer Assoc., Sunderland,
MA.
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Literature cited:
Allendorf, F.W., R.F. Leary, P. Spruell,
and J.K. Wenburg. 2001. The problems with hybrids: setting conservation
guidelines. Trends Ecol. Evol. 16: 613-6622.
Avise, J.C. 2004. Molecular Markers, Natural History and Evolution, 2nd Ed. Sinauer Associates, Sunderland, MA.
Ayala, F.J. 1982. Population and Evolutionary
Genetics: A Primer. Benjamin/Cummings, Menlo Park, CA.
QH 455.A94 1982
Barton, N.H., and G.M. Hewitt. 1985.
Analysis of hybrid zones. Ann. Rev. Ecol. Syst. 16: 113-148.
Brooks, D.R., and D.A. McLennan. 1991.
Phylogeny, Ecology, and Behavior. Chicago Univ. Press, Chicago.
Brumfield, R.T., R.W. Jernigan, D.B.
McDonald, and M.J. Braun. 2001. Evolutionary implications of divergent
clines in a manakin (
Manacus
; Aves) hybrid zone. Evolution 55: 2070-2087.
Caballero, A., and W.G. Hill. 1992.
A note on the inbreeding effective population size. Evol. 46: 1969-1972.
Callen, D.F., A.D. Thompson, Y. Shen,
H.A. Phillips, R.I. Richards, J.C. Mulley, and G.R. Sutherland. 1993. Incidence
and origin of "null' alleles in the (AC)n microsatellite markers. Am. J.
Human Genetics 52: 922-927.
*Caswell, H. 1989. Matrix Population
Models. Sinauer Associates, Sunderland, Mass.
*Cooke, F., and P.A. Buckley (eds.).
1987. Avian Genetics: a Population and Ecological Approach. Academic Press,
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