Glossary

A see allelic diversity

Adaptive radiation The rapid diversification of an ancestral population into several ecologically different species, each of which is adapted to a specialized environmental niche

AFLP see amplified fragment length polymorphism allele A particular form of a given gene allele frequency The proportion of each allele at a given locus within a designated group such as a population allelic diversity (A) A measure of a population's genetic diversity, calculated as the average number of alleles per locus allopatric Two or more species that occur in non-overlapping geographical areas allopolyploid A polyploid that was created by hybridization between two different species. Compare with autopolyploid allozygous Two alleles at a locus that have not recently descended from a common ancestor (note that they may still be identical). Compare with autozygous allozymes Alternative forms of a protein that are encoded by different alleles at a particular locus amino acid One of a group of 20 organic molecules that contain an amino group and a carboxyl group; amino acids are the usual components of proteins amplified fragment length polymorphism (AFLP) A dominant molecular marker that genotypes individuals at multiple loci. Amplified DNA is digested with restriction enzymes, adapters are attached to the ends of amplified fragments, and a subset of fragments is then re-amplified to generate a multi-band pattern

Molecular Ecology Joanna Freeland © 2005 John Wiley & Sons, Ltd.

angiosperms Plants that produce seeds in reproductive organs that are called flowers; also known as flowering plants arithmetic mean The average of all the measurements within a data set, calculated by dividing the sum of all measurements by the total number of measurements assignment tests A method for quantifying dispersal by assigning each individual to the population in which its genotype has the highest probability of occurring, and from which it therefore most likely originated autopolyploid A polyploid that has more than two sets of homologous chromosomes, all of which came from the same species. Compare with allopolyploid autosomes Chromosomes other than sex chromosomes autozygous Two alleles that are identical by descent, i.e. they are copies of an ancestral gene (homologous). Compare with allozygous balancing selection A form of natural selection that favours the maintenance of multiple alleles within a population; includes heterozygote advantage and frequency-dependent selection

Bayesian A method of statistical inference that uses prior information to test the likelihood that various parameters can explain a particular data set benthic Living in or on the substrate (e.g. mud, sand, rocks) that underlies a body of water. Compare with planktonic bifurcating tree A phylogenetic tree depicting a series of events in which one ancestral lineage splits into two descendant lineages. Contrast with network biological species concept (BSC) A concept that places individuals within the same species if they are potentially capable of interbreeding and producing viable offspring biparental inheritance Genes and genetic elements that are inherited from both parents; applies only to sexually reproducing organisms bottleneck A severe, temporary reduction in the size of a population bounded hybrid superiority A force that maintains hybrid zones when hybrids have greater fitness within a limited geographical area than non-hybrids

BSC see biological species concept cDNA see complementary DNA

census population size (Nc) The number of individuals within a population chloroplast An organelle that occurs in large numbers in the cytoplasm of plant cells and some eukaryotic algae and is responsible for photosynthesis chloroplast DNA (cpDNA) A circular DNA molecule that constitutes the chloroplast genome. This is inherited maternally in most angiosperms and paternally in most gymnosperms cline A geographical gradient in one or more characteristics, such as a change in mean body size or allele frequencies. Clines are sometimes taken as evidence for natural selection along an environmental gradient chromosome A structure that is located in the nucleus of a eukaryotic cell on which nuclear genes are located co-adapted gene complex The group of loci that are involved in a beneficial epistatic interaction coalescent theory A theory in population genetics that starts with multiple contemporary samples and works backwards through time to identify the point at which alleles coalesce (come together in a common ancestor)

co-dominant markers Molecular markers that allow users to distinguish between heterozygotes and homozotyes codon Three consecutive nucleotides along an mRNA molecule that specify either a particular amino acid, or the end of protein synthesis complementary DNA (cDNA) A segment of DNA that is generated following reverse transcription of an RNA template conspecific brood parasitism (CBP) A behaviour in which a female lays an egg in the nest of another conspecific female (also known as egg dumping)

cpDNA see chloroplast DNA

cytonuclear disequilibrium In hybrids, the coexistence of cytoplasmic markers (mitochondria, chloroplasts) from one parental species or population, and nuclear markers from another cytotypes Alternative levels of polyploidy within a single species deoxyribonucleic acid (DNA) A nucleic acid macromolecule that contains the bases adenine, cytosine, guanine and thymine and carries the genetic information of all cells and many viruses diapause A time of dormancy between periods of activity during which physiological activity is temporarily suspended dideoxyribose A deoxyribose sugar that lacks the 3' hydroxyl group and can therefore be used to terminate the extension of a DNA sequence during a sequencing reaction dioecious Plant or animal in which individuals have either male or female reproductive organs, but not both. Compare with monoecious diploid An organism that has two complete sets of homologous chromosomes (2«)

directional selection Selection that favours either a higher or lower value of a particular characteristic relative to its current mean within a population displacement loop A loop that is formed during DNA replication when the origin of replication is different on the two strands of DNA. Also known as a D-loop, this is the most variable region of sequence in many animal mitochondrial genomes disruptive selection Natural selection that favours two or more extreme phenotypes that are both fitter than the intermediate phenotypes that lie between them. Also known as diversifying selection distance methods Methods of phylogenetic reconstruction that are based on the evolutionary (genetic) distances between all pairs of taxa diversifying selection see disruptive selection

D-loop see displacement loop

DNA see deoxyribonucleic acid

DNA barcode see genetic barcode

DNA polymerase An enzyme that catalyses the synthesis of new DNA strands using a template DNA sequence

DNA replication Duplication of a DNA molecule using the original DNA sequence as a template for the synthesis of a new DNA sequence dominance A mechanism that promotes inbreeding depression, so-called because the favourable alleles at a locus are usually dominant whereas deleterious alleles are recessive (masked). The increased homozygosity that results from inbreeding means that deleterious recessive alleles are more likely to be expressed dominant markers Molecular markers that do not allow us to distinguish between homozygote and heterozygote individuals effective population size (Ne) The theoretical size of an ideal population (one with an even sex ratio, random mating and no variation in reproductive success) that will lose genetic variation through drift at the same rate as an actual population. If an actual population of 500 individuals is losing genetic variation at a rate that would be found in an ideal population of 100 individuals, then this population would have Nc = 500 but Ne = 100

electrophoresis see gel electrophoresis environmental sex determination Occurs when certain environmental variables such as temperature play a major role in determining the sex of an organism. Compare with genetic sex determination enzyme A protein that catalyses a specific biochemical reaction epistasis The interaction of genes from multiple loci and their collective influence on particular traits eukaryote Found in higher animals and plants, fungi, protozoa and most algae, eukaryotic cells have a membrane-bound nucleus that contains chromosomes and proteins. Other cell components include membrane-bound organelles eusociality A form of social breeding that is characterized by overlapping generations, cooperative care of young, and specialized castes that do not reproduce; most common in social insects evolutionarily significant units (ESU) In conservation biology, these are populations that show enough genetic differentiation (monophyletic mtDNA and significantly different nuclear allele frequencies) to warrant their management as distinct units exon The part of a gene's DNA sequence that codes for amino acids and is retained in mRNA after introns are removed expected heterozygosity (He) A commonly used measure of genetic diversity that reflects the level of heterozygosity that would be expected if a population was in Hardy-Weinberg equilibrium. Compare with observed heterozygosity extra-pair fertilization (EPF) Achieved when an individual is fertilized by a mate that is outside its social pair bond

F see FIS

FIS The inbreeding coefficient (also designated F). In diploid species, the probability that an individual has two alleles at a particular locus that recently descended from a single common ancestor

Fit An overall inbreeding coefficient that compares the heterozygosity of an individual to that of the total population under consideration; influenced by both FIS and FST

fitness The relative ability of an individual to survive and reproduce compared with other members of its population fitness value (w) The fitness of an individual with a particular genotype (and phenotype) relative to the genotype that has the maximum fitness within the population fixation An allele reaches fixation when it has attained a frequency of 100 per cent within a population founder effect The changes in allele frequencies, relative to the source population, that are often evident in populations that have been founded by a small number of individuals frameshift mutation A mutation that inserts or deletes one or more pairs of nucleotides within a gene and, in so doing, shifts the reading frame of all subsequent codons frequency-dependent selection If the fitness of a genotype depends on its frequency within a population, it will be selected for or against following frequency-dependent selection

FST The probability that two random gametes, drawn from the same subpopulation, will be identical by descent, relative to gametes taken from the entire population; developed by Wright (1951), this is the most common measurement used to describe the genetic differentiation of populations

F-statistics A series of measurements (FIS, FST and FIT) that use inbreeding coefficients to describe the partitioning of genetic variation within and among populations gamete A mature reproductive cell such as sperm, egg or pollen; also known as a germ cell gel electrophoresis The separation of molecules (DNA or proteins) through a gel medium along an electrical field geminate species Pairs of morphologically similar, closely related species that share a recent common ancestor gene conversion A genetic process in which one sequence replaces another at a homologous locus; leads to genotypic ratios that deviate from those expected under normal Mendelian inheritance gene diversity (h) A measure of genetic diversity based on the probability that two alleles chosen randomly from the population will differ; often equivalent to expected hetero-zygosity when calculated for nuclear loci gene expression A process involving numerous steps that convert the information encoded in a gene into a protein gene flow The transfer of genetic material from one population to another following the dispersal and subsequent reproduction of individuals, propagules or gametes gene genealogy The evolutionary history of a particular gene; usually represented as a branching tree or network that shows the historical relationships of multiple lineages genetic barcode A sequence of DNA that is specific to, and hence an identifier of, a particular species. Also known as a DNA barcode genetic code A set of 64 codons, 61 of which specify one of the 20 amino acids and three of which signal the end of translation genetic diversity The amount of genetic variation that is contained within a population or species genetic drift A process that changes the allele frequencies within a population from one generation to the next because of the random sampling of gametes genetic load The decrease in the mean fitness of a population due to the presence of genotypes that confer relatively low rates of survival and reproduction genetic rescue A reduction in inbreeding depression following the introduction into a population of new alleles via immigrants genetic sex determination Occurs when sex chromosomes play a major role in determining the sex of an organism. Compare with environmental sex determination genome The full set of DNA in a cell or organism. In eukaryotes, the nuclear, mitochondrial and plastid genomes may be considered separately genomics The branch of genetics that studies the genomes of organisms and the functions of different genes genotype The set (or subset) of genes possessed by an individual germ cell see gamete good genes hypothesis A hypothesis in behavioural ecology that states that an individual will choose its reproductive partner on the basis of some measure of phenotypic superiority

Gst An analogue of FST, GST is equivalent to FST when there are only two alleles at a locus, and is the weighted average of FST for all alleles when there are multiple alleles gymnosperms Vascular plants in which the seeds develop on the scales of a cone or conelike structure; include conifers, Gingko and cycads

Haldane's rule A rule stating that hybrids are less likely to be viable in the heterogametic sex compared with the homogametic sex haploid Having only one set of chromosomes haploid diversity A measure of gene diversity (h) that describes the numbers and frequencies of different haplotypes. Most commonly applied to mitochondrial and chloroplast data haplotype A particular form of a gene or DNA sequence. In molecular ecology this is most commonly used in reference to the haploid genomes of organelles (mitochondria, chloroplasts)

Hardy-Weinberg equilibrium (HWE) A predictable ratio of genotype frequencies in a sexually-reproducing population of infinite size with random mating and no selection; represented as p2 + 2pq + q2 = 1

harmonic mean A method for calculating the mean of a set of numbers that is expressed as the reciprocal of the arithmetic mean of the reciprocals of the numbers hemizygous A diploid individual who has only one allele at a particular locus; usually refers to sex-linked genes in heterogametic individuals, such as X-linked genes in male mammals heterogametic Having two different sex chromosomes, e.g. male mammals (XY) or female birds (ZW). Compare with homogametic heteroplasmy The state of a single individual having two or more genetic variants of mitochondria or plastids heterosis The superiority of hybrids compared with either parental type with respect to one or more traits such as increased growth rate or higher fertility; also known as hybrid vigour heterozygote An individual that has more than one type of allele at a particular locus heterozygote advantage The condition that results when a heterozygote has a higher fitness than either homozygote at a particular locus. Also known as overdominance hitch-hiking effect If an allele at one locus is linked to an allele at another locus then the frequency of that allele will deviate from the expected frequency of an unlinked allele homogametic Having only one type of sex chromosome, e.g. female mammals (XX) or male birds (ZZ). Compare with heterogametic homology Describes a characteristic present in two or more individuals or species that is similar because it was inherited from a recent common ancestor. Compare with homoplasy homologous chromosomes Two or more chromosomes within a single individual that bear the same genes and pair up during meiosis homoplasy Describes a characteristic present in two or more individuals or species that is similar for reasons other than inheritance from a recent common ancestor. Compare with homology homozygous An individual that has only one type of allele at a particular locus horizontal transfer The transfer of genes from one species to another, most commonly following hybridization

HWE see Hardy-Weinberg equilibrium hybrid The offspring that results from mating between a male and a female from two different species or populations (hydridization)

hybrid vigour see heterosis hybrid zones Restricted geographical areas in which the members of two different species come into contact and hybridize with each other hybridization see hybrid identical by descent Alleles that are copies of a single allele that existed in a recent ancestor inbreeding coefficient see FIS

inbreeding depression A reduction in the fitness of offspring that result from matings between close relatives inclusive fitness A fitness value that reflects the extent to which an individual's genes are transferred from one generation to the next, either through its own offspring or through the offspring of its relatives indel The collective term given to mutations that involve nucleotide insertions or deletions infinite alleles model A mutation model that assumes that the number of possible alleles at a given locus is infinite and therefore any new allele must be different from all other alleles that are already present in the species in question introgression The movement of genes from one species or population into another following hybridization intron Part of a gene's DNA sequence that does not code for amino acids and is spliced out of mRNA before transcription occurs; mostly restricted to eukaryotic genes isolation by distance A pattern of population differentiation in which the genetic dissimilarity of populations is correlated with the geographical distance that separates them karyotype The complement of chromosomes in a cell kin selection Selection that acts on an individual's inclusive fitness, i.e. it factors in both the fitness of an individual and the fitness of its kin lineage sorting The process in which multiple populations or species that are recently descended from a common ancestral population or species, but are now reproductively isolated from one another, each acquires a single genetic lineage linkage disequilibrium Occurs when the alleles at two or more loci co-occur more often than is expected on the basis of their frequencies. Usually involves two loci that are close together on a chromosome linkage equilibrium Occurs when the alleles at two or more loci co-occur to an extent that is expected on the basis of their frequencies locus The location of a particular gene or region of DNA on a chromosome (plural is loci)

major histocompatibility complex (MHC) A large multigene family in vertebrates that controls several aspects of the immune response management units (MU) In conservation biology, these are populations that have very low levels of gene flow and can therefore be genetically differentiated from other populations

Mantel test A statistical procedure that uses permutations to test the null hypothesis that two variables are independent of each other. In molecular ecology this is most commonly used to compare the geographical distance and genetic differentiation among populations, i.e. to test for isolation by distance maximum likelihood (ML) An analytical method that provides an explanation for a particular data set by maximizing the probability of observed data under an explicit model meiosis Cell division in which a diploid parent produces four haploid daughter cells (gametes). Compare with mitosis messenger RNA (mRNA) RNA that acts as a template for protein synthesis metapopulation A group of populations that is prone to local extinctions and recolo-nizations and is interconnected by gene flow

MHC see major histocompatibility complex microarray A two-dimensional array of DNA sequences that is set up on a glass, filter or silicon wafer. Typically used as a high-throughput method for simultaneously measuring the expression of many genes under different conditions in order to deduce the functions of these genes microsatellite A stretch of DNA that consists of a short tandem sequence of up to five base pairs that is repeated multiple times, e.g. (AG)10 represents a microsatellite in which the sequence AG is repeated ten times minisatellite Repetitive DNA sequences that are each 10-100 bases long and are dispersed throughout the genome. Also known as VNTRs (variable number of tandem repeats)

mitochondria Organelles that occur in large numbers in the cytoplasm of eukaryotic cells and are central to the production of ATP

mitochondrial DNA (mtDNA) A circular molecule of DNA that is located within the mitochondrion; usually inherited maternally mitochondrial pseudogenes Non-functional copies of mitochondrial genes that are located in the nuclear genome. Also known as numts mitosis The replication of genetic material in eukaryotic cells that involves the segregation of chromosomes and subsequent nuclear division. Following mitosis, a diploid parental cell will become two diploid daughter cells. Compare with meiosis mixed stock analysis A type of analysis that uses data from molecular markers to determine the relative proportions of various stocks in a mixed-stock fishery

ML see maximum likelihood molecular clock A theory that uses a calibration date to calculate the rate of sequence divergence, and then applies this rate to pairs of sequences to determine the amount of time that has passed since they diverged from one another monoecious Plants that have unisexual flowers, i.e. a single plant is effectively both male and female. Compare with dioecious monogamy A mating system in which a single female is partnered with a single male monogynous colony A social insect colony that has a single queen monomorphic A locus that has only one allele in a population and is therefore lacking in genetic variation monophyletic A group of organisms (e.g. a population or species) that all share a common ancestor and in which all of the descendants of that ancestor can be found most recent common ancestor (MRCA) Going back in time, this refers to the most recent ancestor of two or more genetic lineages mRNA see messenger RNA

mtDNA see mitochondrial DNA

multifurcating tree see network mutation An alteration in the structure of a gene or a chromosome mutational meltdown The potentially irreversible decline in the fitness of a small population that follows the fixation of numerous mildly deleterious alleles

Nc see census population size

Ne see effective population size negative selection see purifying selection

Network A phylogenetic reconstruction that depicts a series of events in which at least some of the ancestral lineages have split into three or more descendant lineages. Also known as multifurcating tree. Compare with a bifurcating tree non-synonymous substitution A nucleotide substitution that alters a codon so as to cause one amino acid to be replaced with another nuclear DNA The complement of DNA that is arranged in chromosomes and located in the nucleus of a cell nucleotide diversity (p) A measure of genetic diversity that quantifies the mean sequence divergence among several haplotypes by factoring in both the frequencies and the pairwise divergences of different sequences nucleotide substitution A mutation that results in the substitution of one nucleotide for another null alleles Alleles that fail to amplify during a PCR reaction. Microsatellite null alleles can lead to the erroneous identification of homozygotes numts see mitochondrial pseudogenes observed heterozygosity (Ho) The actual level of heterozygosity within a population, usually averaged across several loci. Compare with expected heterozygosity oligonucleotide primer A short segment of single-stranded DNA or RNA that is used as a starting point for copying template sequences, e.g. in PCR. Often referred to simply as a primer organelle A membrane-bound structure found in the cytoplasm of a cell. Organelles have specialized functions and include mitochondria and plastids (including chloroplasts)

outbreeding depression A reduction in fitness following the hybridization between members of two genetically distinct populations or species overdominance see heterozygote advantage p see nucleotide diversity

P see proportion of polymorphic loci panmixia Random mating; within a panmictic population there is the potential for any male to reproduce with any female paraphyletic A group of organisms (e.g. a population or species) that includes some, but not all, of the descendants of a recent common ancestor parthenogenesis The development of an individual from an egg without the contribution of a paternal genotype patrilineal descent In sexually reproducing organisms, the transmission of genes through the male line of descent, e.g. the Y chromosome in mammals

PCR see polymerase chain reaction phenotype The physical, observable properties of an organism that result from an interaction between its genotype and its environment phenotypic plasticity The ability of a particular genotype to develop into one of several different phenotypes, depending on environmental conditions philopatric The tendency to return to, or remain at, a particular location. A philopatric animal may never leave its birthplace or, if it does disperse, will later return for breeding purposes phylogenetic species concept (PSC) A concept that defines species as groups of individuals that share at least one uniquely derived characteristic and constitute mono-phyletic groups phylogeny A branching diagram, usually depicted as a tree, that shows the evolutionary relationships among different genetic lineages (e.g. species or genera)

phylogeography A field of study that compares the evolutionary relationships of genetic lineages with their geographical locations in an attempt to understand which factors have most influenced the current distributions of genes, populations and species planktonic Living in open water. Compare with benthic plastid A family of membrane-bound cytoplasmic organelles (including chloroplasts) that contain DNA and are found in plant cells and some protists polyandry A mating system in which one female is socially bonded with multiple males polygynandry A mating system in which multiple males are socially bonded with multiple females polygynous colony A social insect colony that has multiple queens polygyny A mating system in which one male is socially bonded with multiple females polymerase chain reaction (PCR) A procedure that uses template DNA sequences to produce numerous copies of a specific segment of DNA. The reaction typically consists of 30-40 cycles that each have three parts: denaturation of DNA, annealing of primers, and extension of sequences polymorphic A locus that has multiple alleles in a population polypeptide A linear chain of amino acids that is smaller than a protein polyphyletic A group of organisms (e.g. a population or species) that do not all share the same recent common ancestors polyploid Having three or more complete sets of homologous chromosomes population A potentially interbreeding group of individuals that belong to the same species and live within a restricted geographical area population bottleneck see bottleneck positive selection A form of directional selection that selects for a particular mutation that increases the fitness of carriers primary sex ratio The sex ratio of a brood at the time of conception. Compare with secondary sex ratio primer see oligonucleotide primer probability of identity (PI) The likelihood that two individuals chosen at random from a population will have the same genotype probe A length of RNA or single-stranded DNA that is labelled (usually either radio-actively or fluorescently) and then used to locate complementary sequences from a pool of DNA through hybridization with the target sequence prokaryotes Unicellular organisms that lack a nucleus promiscuity Mating in the absence of any social pair bonds proportion of polymorphic loci (P) A measure of genetic variation that reflects the proportion of loci at which two or more alleles have been identified

PSC see phylogenetic species concept pseudogenes Non-functional copies of genes purging The elimination of deleterious alleles from an inbred population following natural selection purifying selection Selection that eliminates deleterious mutations from a population or reduces their frequencies. Also known as negative selection purines Two types of bases (adenine and guanine) that are found in DNA and RNA

pyrimidines Two types of bases that are found in DNA (cytosine and thymine) and RNA (cytosine and uracil)

qualitative traits Discrete traits that are controlled by one or a few loci, such as eye colour or blood type. Compare with quantitative traits quantitative PCR see real-time PCR

quantitative trait locus (QTL) A locus that affects a quantitative trait quantitative traits Continuous traits such as height and weight that are influenced by several different genes and also tend to be influenced by environmental factors. Compare with qualitative traits quasi-parasitism (QP) Behaviour in which a female lays an egg in a nest that is shared by the male with whom she mated and his social partner random amplified polymorphic DNA (RAPD) Dominant molecular marker that generates multiple DNA fragments through the random PCR amplification of multiple regions of the genome using single arbitrary primers real-time PCR A method of PCR that allows users to monitor the amplification reaction and, in so doing, quantify the DNA (or cDNA, if the aim is to quantify RNA) that is present in the original sample. Also known as quantitative PCR

reciprocal monophyly The situation that arises when two populations or species become monophyletic with respect to each other recombination The exchange of DNA segments between DNA molecules or chromosomes restriction enzymes Bacterially-derived enzymes that digest DNA sequences at specific locations; each restriction enzyme recognizes and cuts a particular sequence of 4-8 nucleotides restriction fragment length polymorphism (RFLP) Dominant molecular marker that generates multiple fragments of DNA by digesting an entire genome or a pre-selected stretch of DNA with one or more restriction enzymes. The resulting band patterns will vary depending on the underlying DNA sequences, because these will determine the number of restriction sites that are found in each individual reticulated evolution The fusing of separate branches on an evolutionary tree, e.g. following hybridization between previously distinct lineages

RFLP see restriction fragment length polymorphism ribonucleic acid (RNA) A single-stranded nucleic acid macromolecule with ribose sugar that contains four bases: adenine, cytosine, guanine and uracil ribosomal RNA (rRNA) RNA molecules that, along with proteins, make up the structures (ribosomes) where protein synthesis occurs

RNA see ribonucleic acid rRNA see ribosomal RNA

Rst An analogue of FST that assumes a stepwise mutation model and in some situations may be more appropriate than FST for quantifying population differentiation on the basis of microsatellite data s see selection coefficient scn DNA see single-copy nuclear DNA

secondary sex ratio The sex ratio of a brood once the eggs have hatched. Compare with primary sex ratio selection coefficient (s) A measurement of the reduced probability of survival associated with an individual's fitness value (w); calculated as s = 1 — w self-fertilization Fertilization involving male and female gametes from the same individual. Also known as selfing selfing see self-fertilization sex-biased dispersal Occurs in a species when one sex is more likely that the other sex to disperse and subsequently reproduce at a location away from their birthplace sex chromosome A chromosome that is at least partially responsible for the determination of an individual's sex, e.g. X and Y chromosomes in mammals and Z and W chromosomes in birds single-copy nuclear DNA (scnDNA) A DNA sequence that occurs only once in each haploid nuclear genome single nucleotide polymorphism (SNP) A variation between two sequences of DNA that is caused by a single nucleotide substitution size homoplasy A phenomenon that describes microsatellite alleles that are the same size for a reason other than recent descent from a common ancestor slipped-strand mis-pairing An imperfect re-alignment of DNA strands following slippage of DNA polymerase and temporary displacement of strands during DNA replication

SNP see single nucleotide polymorphism somatic cell Any cell other than germ cells stabilizing selection A process of natural selection that favours individuals that have the mean form of a particular character, and selects against extreme phenotypes standard deviation The square root of the variance of a data set statistical parsimony network A graphic representation of a network in which haplo-types are linked to one another through a series of evolutionary steps that require the fewest mutations possible statistical phylogeography A relatively new analytical approach in studies of phylogeo-graphy; uses models based on coalescent theory to generate statistics that provide a basis for accepting or rejecting specific hypotheses that may explain the current distributions of species and their genes stepwise mutation model A microsatellite mutation model that assumes that mutations involve either the gain or loss of a single microsatellite repeat sympatric Two or more species that occur in the same geographical area synonymous substitution A nucleotide substitution that, because of redundancy in the genetic code, does not change the amino acid that is encoded taxa see taxon taxon A taxonomic unit such as a subspecies, species or genus; plural = taxa tension zones Hybrid zones that are maintained by a balance between dispersal of parental genotypes into the zone and selection against hybrids within the zone theta (0) An estimate of population subdivision (analogue of FST) that takes into account the effects of uneven sample size and the number of sampled populations transcription The process in which the information contained within a DNA sequence is copied into an RNA molecule transfer RNA (tRNA) An RNA molecule that translates a codon into an amino acid during protein synthesis. Each tRNA molecule recognizes a specific codon on the mRNA molecule transgressive segregation The generation of extreme phenotypes in segregating hybrid populations relative to the phenotypes that are found in either parental form transient polymorphism The temporary polymorphic state of a locus that is being driven to fixation following selection or drift transitions Nucleotide substitutions in which one purine (A or G) is changed into the other purine, or one pyrimidine (T or C) is changed into the other pyrimidine translation The generation of a specific polypeptide from messenger RNA

transposable elements A DNA sequence that can move from one location to another in the genome transversions Nucleotide substitutions in which a purine (A or G) is changed into a pyrimidine (T or C), or vice versa tRNA see transfer RNA

uniparental inheritance Genes and genetic elements that are inherited from only one parent. This term is most commonly applied to the inheritance of mitochondrial and plastid genomes plus some sex chromosomes in sexually reproducing organisms variance The average squared deviation that a set of measurements show from the arithmetic mean variation in reproductive success (VRS) The variation in the number of offspring that each individual within a population manages to produce throughout its lifetime vicariance The splitting of formerly continuous populations by a geographical or ecological barrier

VRS see variation in reproductive success w see fitness value

Wahlund effect The reduction in heterozygosity values, relative to expectations under Hardy-Weinberg equilibrium, that arises when data from two or more subpopulations with different allele frequencies are combined

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