Genetics
Allele
Different versions of the same gene.(Different as they have some different nucleotides when compared to each other).
Diversity
In genetics:
A term that describes genetic variation.
E.g genetic diversity describes the difference in DNA sequence from the same gene sequenced from different individuals.
Individual 1: ATCGTGCTGAG
Individual 2: ATCGTGCAGAG
Individual 3: ATCGTGCCGAG
Genetic diversity is the difference between the three sequences.(At site 8 they differ)
*diversity is also used to describe how many species are present in a given geographical area. (also called biodiversity).
Gene
The basic heritable unit in biology. A gene is a sequence of DNA that performs a biological function as either protein coding or non-coding.
Genome
All of the genetic material (genes and non-coding DNA) from a cell, stored in chromosomes.
Genetic polymorphisms
A gene is called polymorphic if there is more than one version or allele in a population. Also each allele must occur in the population at a rate of at least 1%. E.g ABO blood group system.
Genome phylogeny or ‘genome tree’
A phylogeny built from genome data.The more genes the more power you have to build the correct tree however not all genes are informative. A phylogeny created from all of the orthologs between genomes that occur only once (1:1 Orthologs) should represent the evolutionary relationship of species, these are also called species trees.
Gene phylogeny or ‘gene tree’
Before we had genome data we sequenced individual genes and then identified if they represent good evolutionary markers. This way genes were used as ‘molecular markers’. So a gene tree is a phylogeny built from a single gene that is hypothesised to give the same tree as a species tree.
Haplotype
A combination of genes inherited together from the same chromosome.
Heteroplasmy
When two or more mtDNA variants exist within the same cell.
Haplotype network
Network diagram of allele ancestry that incorporates frequencies and predicts extinct haplotypes. (Note, not a phylogeny!).
Nucleotide/base/site
DNA bases that make up the structure of the DNA molecule. They are represented in DNA sequence data as ‘A’ , ‘T’ , ‘C’, and ‘G’ which stands for Adenine, Thymine, Cytosine and Guanine.
Molecular evolution
The mechanisms of evolution that occur at the molecular level i.e DNA, RNA and protein evolution. Fundamentally evolution occurs physically at this level. Molecular evolution is studied through looking at changes in the DNA, RNA and protein sequences over time.Sequences change over time
Mitochondrial haplotype
Specific regions of mitochondrial DNA that cluster with other mitochondrial sequences to show the phylogenetic origins of maternal lineages.
Mitochondrial haplogroup
A group of organisms that share similar mtDNA sequence (or have similar mtDNA sequence changes or polymorphism)
Mutation
A change in the DNA sequence, caused by errors in DNA replication process or environmental damage.
Mutation rate
The rate of new mutations occurring in a gene or genome over time.This varies across the tree of life (all species that exist) e.g in viruses mutation rate is much higher than in animals.
Ortholog
Gene copies that arise from a speciation event. Their phylogeny is hypothesised to follow the pattern of species descent.
Substitution
Type of mutation where one nucleotide base is replaced with another. There are two different types of substitutions: transitions and transversions. See diagram below
Sequence alignment
Phylogenetic trees are built from sequence alignments.An alignment is where DNA sequences are lined up so that they can be compared in a biologically meaningful way.
In biology we use alignments to study genes that perform the same function in different species or populations.
If we want to measure evolutionary change that has happened to the same region in a gene we must first line them up. Alignments with more than two sequences are called multiple sequence alignments.
Example:
There are a number of different alignment algorithms – these are very important – if the alignment is bad you will get a bad tree! (i.e the relationships shown in the tree will not represent the true evolutionary history).