ABBA–BABA test: a test that uses the genome-wide average of shared mutations to determine whether there is evidence for admixture. This is achieved by comparing the amount of shared mutations with a possibly admixed population to the amount of shared mutations with a population that is hypothesized not to be admixed (or at least has less admixture).
Adaptations: phenotypes or genotypes that enhance the survival and reproductive success of individuals.
Admixed population: a population that contains genes from at least two distantly related populations or species as a result of interbreeding between populations or species that have been reproductively isolated and genetically differentiated.
Admixture: the formation of novel genetic combinations through the hybridization of genetically distinct groups.
Allele: one version of a gene that has two or more versions.
Allele frequency spectrum: the distribution of the frequencies of alleles at a given set of loci (often single nucleotide polymorphisms) in a population sample.
Allometric: the growth of body parts at different rates, resulting in a change of body proportions.
Ancient: before 1800 (when describing North American canids).
Ancient DNA: DNA isolated from ancient specimens.
Anthropogenic: resulting from the influence of human activities.
Approximate Bayesian Computation (ABC): A statistical framework that uses simulation modeling to approximate the Bayesian posterior distribution of parameters of interest. It is far faster computationally than fully Bayesian approaches, but generally slightly less accurate and precise.
Autosome: any chromosome that is not a sex chromosome. In mammals, females (XX) have two copies of the X chromosome, and males (XY) have one copy of the X chromosome and one copy of the Y chromosome. The X chromosome is much larger than the Y chromosome. The members of the autosome pairs are identical in size and contain a full complement of the same genes.
Base-pair: a pair of complementary bases in a double-stranded DNA consisting of a purine in one strand linked by hydrogen bonds to a pyrimidine in the other. Cytosine (C) always pairs with guanine (G), and adenine (A) with thymine (T).
Basicranium: the inferior or lower region of the skull.
Breeding unit: a group of individuals who breed together.
Canids: the taxonomic family that includes wolves, coyotes, jackals, foxes, and wild dogs.
Cline: a gradual directional change in a characteristic across a geographic or environmental gradient.
Coding sequence: the portion of a gene’s DNA that codes for protein.
Common ancestor: an ancestor that two or more descendants share in common.
Consensus sequence: a sequence that contains the most frequent base-pair or amino acid found at each position in a sequence alignment.
Coprolite: a piece of fossilized dung.
De novo genome assembly: the construction of genomes from a large number of (short- or long-) DNA fragments, with no a priori knowledge of the correct sequence or order of those fragments.
Dental calculus: calcified dental plaque that form deposits on teeth; also known as tartar.
Derived: when referring to a characteristic found in an organism that is not present in the common ancestor of a group of organisms being studied.
DNA library: a collection of DNA fragments that were cloned in vectors so they can be identified and isolated for further study.
Endemic: found only in a particular geographic location, such as an island, country, or other defined area; organisms that are native to a place are not endemic to it if they are also found elsewhere.
Evolutionary lineage: a continuous line of individuals related by descent, from ancestor to descendant.
Extant: still in existence; surviving.
Extirpation: the loss of a species or subspecies from a particular area, but not from its entire range.
F1 hybrid: a first-generation hybrid.
F2 hybrid: a second-generation hybrid.
Fitness: the ability of an individual or genotype to survive and produce viable offspring. Fitness is quantified as the number or relative proportion of offspring contributed to the next generation.
Founder effect: the loss of genetic variation in a population established by a small number of individuals that carry only a fraction of the original genetic diversity from a larger population.
Gene: a segment of DNA whose nucleotide sequence codes for protein or RNA, or regulates other genes.
Gene flow: the movement of genetic material from one population into another population.
Genetic drift: random changes in allele frequencies in a population between generations due to sampling individuals that become parents and binomial sampling of alleles during meiosis. Genetic drift is more pronounced in small populations.
Genetic incompatibilities: the situation in hybrids where genes or chromosomes originating in different genetically divergent parental populations or species do not function well together in combination.
Genome: the complete sequence of DNA in an organism.
Genotype: an individual’s genetic identity.
Ghost alleles: alleles present in historical populations that were thought to have been lost over time, but have been rediscovered in living individuals.
Haplotype: continuous region of DNA inherited from a recent common ancestor.
Heterozygosity: a measure of genetic variation that estimates the proportion of individuals in a population that are expected or observed to be heterozygous at a particular locus or over the entire genome.
Historical: between 1800 and 1920; the period before extensive deforestation in the eastern United States, the alteration of the landscape, and hunting of wolves.
Homozygosity: the proportion of individuals in a population that are expected or observed to be homozygous, that is, having the same two alleles or forms of a gene. It can be estimated for a single locus or for the entire genome.
Hybridization: mating of individuals from genetically distinct populations, or species, that results in offspring with mixed ancestry.
Hybrid lineage: a group of individuals descended from a hybridization event.
Hybrid swarm: a population of individuals that are all hybrids by varying numbers of generations of backcrossing with parental types and matings among hybrids.
Hybrid zone: a region where the ranges of two interbreeding species or populations meet and mate together.
Hybrids: offspring produced by hybridization. Hybrids can be either first-generation (F1) hybrids or the offspring of hybrids themselves.
Inbreeding: mating between related individuals that results in an increase of homozygosity in the progeny because the individuals possess alleles that are identical by descent derived from the same common ancestor of both parents.
Incomplete lineage sorting: a characteristic of phylogenetic reconstruction in which the tree produced by a single gene differs from the population or species level tree because a polymorphism present in the ancestral species is retained in the descendant species.
Intergradation: area of connection between distinct subspecies where populations are found that have the characteristics of both subspecies.
Introgression: movement of alleles from one population or species into another through hybridization and repeated backcrossing (the reproduction of hybrids with individuals of the parental species).
Locus (plural loci): the position (location) of a gene or other marker on a chromosome.
Meiosis: the cellular division process that is involved in sexual reproduction in which gametes are produced having half the number of copies of each chromosome as the parents.
Midden: an old dump for domestic waste associated with past human occupation.
Migration: in the genetic literature, the movement of individuals from one genetically distinct population to another, resulting in gene flow. In the ecological literature, migration is the movement, often seasonal, of populations, groups, or of individuals across geographic space.
Mitochondrial DNA (mtDNA): a small, circular, maternally inherited, haploid DNA molecule found in the mitochondria of eukaryotes.
Monophyletic: an adjective used to describe a group of taxa that all descend from a common ancestral taxon (i.e., a group of organisms that share a common ancestor to the exclusion of all other entities).
Morphological marker: a morphological difference between individuals or species.
Multivariate: having more than one independent mathematical or statistical variable.
Mutation: a change in the DNA sequence in the transmission of genetic information from parent to progeny.
Natural selection: differential contribution of genotypes to the next generation due to differences in survival and reproduction.
Next-generation sequencing (NGS): high-throughput sequencing of DNA.
Non-metric trait: a discrete trait or a discontinuous morphological trait.
Nuclear DNA: the DNA contained within the nucleus of a cell.
Parapatric: occupying geographic ranges that are partially overlapping or have a partial barrier between them.
PCR crossover: the formation of molecules that are hybrids of two original molecules arising through “recombination” during polymerase chain reaction, or PCR.
Petrous: an exceptionally dense region of the temporal bone, located at the base of the skull.
Phenotype: the observable traits of an organism (e.g., appearance, physiological function, or behavior).
Phylogenetic tree: a diagram showing the evolutionary relationships of taxa.
Phylogeny: the evolutionary history of the relationships among species.
Pleistocene: the epoch that began about 2.6 million years ago and lasted until about 11,700 years ago. The most recent ice age occurred during this time, as glaciers covered huge parts of the planet Earth.
Polymerase chain reaction (PCR): a technique to rapidly make billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to an amount that is large enough to study in detail.
Population: all of the individuals of a given species within a defined ecological area.
Population structure: the pattern of genetic differentiation among a group of populations.
Post-mating isolation: reproductive isolation that prevents successful fertilization and development even though mating may have occurred.
Pre-mating isolation: reproductive isolation that stops production of an F1 by preventing mating.
Quantitative trait loci: genes that affect continuous phenotype traits such as weight or height. These traits are controlled by dozens to hundreds of such loci as well as environmental factors. The locations of quantitative trait loci are diagnosed through statistical associations between genetic markers and varying values of the phenotypic traits.
Read depth: the number of separate reads that include a given genomic region in a reconstructed sequence.
Recent: since 1920, when coyotes invaded the eastern United States, until the present (when describing North American canids).
Recombination: the process that generates a haploid product of meiosis with a genotype differing from both the haploid genotypes that originally combined to form the diploid zygote.
Reference genome: a representative genome from one individual organism used to represent the genome of its species.
Reproductive isolation: the separation of distinct gene pools as a result of genetic differences that prevent successful interbreeding.
Reticulating: the exchange of genes between different species, as in the formation of a new species through hybridization.
Sexual dimorphism: differences in size or appearance or other characteristics between the sexes in addition to the differences between the sexual organs themselves.
Shotgun sequencing: a sequencing method that involves breaking up DNA randomly into many smaller pieces—in a “shotgun fashion”—with each of those pieces then sequenced individually. The resulting sequences are then analyzed by a computer program, looking for stretches of sequence from different reads that are identical with one another. When identical regions are identified, they are overlapped with one another, allowing the two sequence reads to be stitched together.
Single nucleotide polymorphism (SNP): a nucleotide site in a DNA sequence that is variable within a population and can be used as a marker to assess genetic variation within and among populations.
Social structure: the pattern of social relationships among the individuals in a population.
Species: a group of organisms with a high degree of physical and genetic similarity that naturally interbreed among themselves and can be differentiated from members of related groups of organisms.
Species concepts: ways to define a species.
Stable hybrid zone: a hybrid zone that does not move over time—a situation that results from a balance between the dispersal of parental types and selection against hybrids.
Substitution: the replacement in the genome of one nucleotide by another.
Subspecies: a taxonomically defined subdivision within a species that is physically or genetically distinct and often geographically separated from other members of the species.
Suture: an immovable joint, especially between the bones of the skull.
Targeted DNA capture: an efficient and sensitive means for sequencing specific genomic regions in a high-throughput manner.
Taxonomy: the branch of biology concerned with the classification of organisms.
Tension zone: a persistent hybrid zone in which the transition between the two parental types is maintained by the conflicting effects of dispersal of parental forms and selection against hybrids.
Whole-genome sequencing: the process of determining the complete DNA sequence of an organism’s genome. This entails sequencing all of an organism’s chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. In practice, genome sequences that are nearly complete are also called whole-genome sequences.
Zygoma (plural zygomata): the bony arch of the cheek formed by connection of the zygomatic and temporal bones.