Comprehensive Guide to Phylogenies, Molecular Evolution Models, and Epigenetics

Molecular clocks

Dating events with molecular clocks and fossils.

Ancestral traits

Reconstructing ancestral traits and character history.

Epidemiology and forensics

Tracking outbreaks in epidemiology and forensics.

Trait evolution

Testing adaptation and comparing trait evolution.

JC69 model

All substitutions are equally likely.

K80 model

Distinguishes transitions from transversions.

K81 model

Separates the three substitution classes more finely than K80.

Strengths of molecular systematics

Uses many characters, often from DNA.

Fine-scale differences

Can detect fine-scale differences.

Neutral sites

Can focus on neutral sites.

Statistical models

Works well with statistical models.

Weakness of molecular systematics

Homoplasy can mislead trees.

Gene trees vs species trees

Gene trees may not match species trees.

Complex models

Complex models can take longer and require more data.

Phylogenetically independent contrasts (PIC)

PIC corrects for shared ancestry by comparing differences between sister lineages.

Use of PIC in research

PIC helps test whether a trait evolved in association with an environmental factor.

Epigenetics

Control of gene expression 'above' the DNA sequence.

DNA methylation

Addition of a methyl group to cytosine, creating 5-methylcytosine.

DNA methyltransferases

Enzymes that write DNA methylation.

Demethylation processes

Erased by processes such as TET/APOBEC activity.

CpG sites

Most methylation occurs at CpG sites.

Transcription regulation

Methylation in promoter/CpG island regions usually represses transcription.

Inheritance of DNA methylation

DNA methylation can be inherited through cell division.

Biological aging biomarkers

Methylation patterns often increase or change with age.

Cancer and methylation

Abnormal promoter hypermethylation can silence important genes.

Bisulfite treatment

Key method for measuring DNA methylation.

High-throughput methylation profiling

Can be linked to traits and diseases at scale.

Decitabine and 5-azacitidine

Therapies that target DNA methylation.

Nucleosome

Basic unit of chromatin, made of about 200 base pairs of DNA wrapped around a histone octamer.

Histone code

Combination of chemical marks on histone tails that regulate gene activity.

Chromatin Immunoprecipitation (ChIP)

Technique used to determine where specific histone marks are located across the genome.

Topologically associated domains (TADs)

Self-associating genome neighborhoods that facilitate transcription.

Insulators

Barriers that define transcriptionally independent domains.

Deregulation of TADs

A hallmark of cancer that can miswire gene regulation.