Glossary for Ancient DNA and Human Evolution DNA STRUCTURE & ORGANIZATION INFORMATION ENCODED IN DNA Allele: Alternative variant forms at the same locus. Codon: A sequence of three nucleotides along a DNA or Heterozygotes: Have two different alleles at a locus. RNA chain encoding a single amino acid. Have two identical alleles at a locus. Homozygotes: CpG site: Locus where a cytosine nucleotide is followed Chromatin: DNA wrapped around histone proteins. by a guanine nucleotide in the linear sequence of bases. Euchromatin: Open, allowing information to be read. Cytosines in CpG dinucleotides can be methylated to Heterochromatin: Tightly wrapped and inactive. form 5-methyl cytosine, a common epigentic mark. Chromosomes: Discrete strands of packaged DNA. Enhancer: Short region of DNA that can be bound by Allosomes: Chromosomes that determine sex (XY, proteins to alter transcription of a gene. with Y-Chromosome inherited paternally). Epigenetic: Information not encoded directly in DNA. Autosomes: All other non-allosomal chromosomes. Do not differ between the sexes. Epigenome: Molecular modifications of the DNA and its Mitochondrial DNA (mtDNA): Maternally inherited associated histone proteins, affecting its function. DNA found only in the mitochondria. Functional DNA: Encodes biological information. DNA: The molecule of inheritance, consisting of ~2% of all DNA: Codes for proteins. sequences of the four nucleotide building blocks (ATGC). ~80% of all DNA: Regulates gene activity. Sequence: The linear order of the building blocks, Gene: DNA whose information encodes a function. which encodes individual form and function. Post-translation Modifications: Alter mature protein. Genome: All DNA in a cell. Also refers to the DNA Transcription: DNA sequence converted into RNA. sequence that typifies an individual or species. Translation: mRNA converted into a protein sequence. Genetics: The study of genes and their inheritance. Gene Regulation: Alterations of gene expression/activity. Genomics: The study of genome structure/function. lncRNA: Long non-coding RNA. Haplotype: A set of alleles at distinct positions in the miRNA: Short non-coding regulatory microRNA. genome which are inherited together. RNA Binding Proteins (RBP): Proteins that bind RNA. Individuals in Haplogroups share a given haplotype. Transcription Factor Proteins: Alter gene expression by binding directly or indirectly to DNA. Histones: Chief protein components of chromatin and can be chemically modified as part of epigenetics. Genotype: The two alleles at one or more diploid loci. Karyotype: Chromosome number in the cell nucleus. Mutation: Change of a DNA sequence. Diploid: Two sets of paired chromosomes. Indels: Insertions or deletions of DNA sequence. Haploid: One set of unpaired chromosomes. Single Nucleotide Polymorphisms (SNPs): Single nucleotide differences (e.g. A vs. T). A unique physical position on a Locus (pl. Loci): Silent Mutations: No change to the phenotype. chromosome. Synonymous/Non-synonymous Mutations: No Exons: Sequences at a locus that encode proteins. change to the protein; changes to protein, respectively. Introns: Sequences between exons, don’t encode proteins. Phenotype: Observable traits of an organism (result from interactions between genes and environment). Variant: DNA that differs among groups studied. Promotor: Region of DNA that initiates transcription of a Recombination: Exchanges between chromosomes particular gene. that causes independent inheritance of alleles. Linkage Disequilibrium: Non-random inheritance of Transposable Elements (TE): Sequences that replicate alleles at different loci (due to low recombination). in a genome by inserting copies of themselves at other loci (a type of “molecular parasite”).

DNA ORGANIZATION AND CHROMOSOME STRUCTURE Modified from www.wikipedia.org DNA DNA wound around histone protiens to from chromatin Chromatin packaged in tight coils to form chromosome

2 nm 11 nm 30 nm 300 nm 700 nm 1,400 nm METHODS OF GENOME ANALYSIS Genotyping: Characterizing genetic variants at one or more loci. Alignment: Arranging related sequences by position. CRISPR: A method that can mutate a specified locus. Cloning: Making a copy of an organism or sequence. Organisms are cloned by moving an entire genome PCR: A method of copying a specified locus. from a cell into an egg. DNA sequences are cloned by Sequencing: Reading the order of nucleotides in DNA. moving copies into a bacteria using a vector. Coverage: The number of reads for a given locus. Genome Wide Association Study (GWAS): An Shotgun: Sequencing cuts the genome into short approach for “gene mapping” in which hundreds of chunks that are read and reassembled by a computer. thousands of SNPs are tested statistically for genetic Vector: DNA molecule used to direct the replication of a associations with a phenotype. cloned DNA fragment (“insert”) in a host cell.

EVOLUTION OTHER TERMS Adaptation: Evolution of a phenotype by selection Admixture: Breeding between isolated populations. because it improved reproduction and/or survival. Archaic Admixture: DNA from ancient, divergent, and Coalescence: Time since common ancestor. now extinct populations found in current people. Coalescent Theory: Models evolution backward in time to infer historical population size, mutation rate, Atapuerca: An archaeological site in Spain with fossils allele age, and allele frequency change by selection and stone tools of the earliest known hominins in and drift. Western Europe. Divergence: Change in genetic content or phenotype Denisovans: A population of extinct hominins between isolated populations or species. contemporary with Neandertals. Our knowledge of Denisovan morphology is based on Effective Population Size (Ne): The size of an idealized two small fossils (a finger bone and a molar) found in population (random mating, no selection, mutation or the Eurasian Steppe. migration) with the same rate of genetic drift as the study population. Dental Calculus: Calcified dental plaque, provides information on diet, disease, health, microbiome and Genetic Drift: Loss of alleles by chance. protects the genetic information within the tooth from Homology: Similarity in DNA or phenotype because of degradation. shared evolutionary history from a common ancestor. Homo: The genus that comprises the species Homo Homoplasy: Similarity in DNA sequence or phenotype sapiens, which includes modern humans, as well as that has evolved independently. several extinct species classified as ancestral to or closely related to modern humans. Phylogeny: Historical relationships of species or loci. An extinct species of hominin with fossil Polymorphism: An allelic difference observed in more Homo erectus: than 1% of the population studied. evidence dating from 1.9 million (possibly earlier) to 70 thousand years ago and found from Africa to Indonesia. Allele Frequency: The proportion of all alleles within a population that are a particular type. May have been the first hominin to leave Africa. H. erectus DNA may be retrievable from other species Derived Alleles: Variants arising since last common ancestor. due to archaic admixture. Fixed Alleles: Replaced all other alleles in a Introgression: Transfer of alleles between species. population. Middle Pleistocene: A period of geological time Population: A defined group of similar individuals. (781-126,000 years ago). An important time for the Demography: Study of population size over time. diversification of hominins, including the emergence of Gene Flow: Movement of alleles between populations. Neandertals and Homo sapiens. Selection: Allele frequency change over time caused by Morphology: Shape or form (outward appearance) of the different replication rate of specific alleles. an organism. Species: A population whose individuals can mate Neandertals: An extinct Eurasian hominin species. with one another to produce viable and fertile offspring. Neandertals existed from over 500,000 to 30,000 (debated definition) years ago, and hybridized with ancient humans.

This ancient DNA glossary is the product of the Anthropogeny Graduate Specialization students, CARTA faculty and staff, and Stevan Springer at UC San Diego.