Teeling L3 & L4: Cladistics and Phylogenetic

Phylogenetic tree

Diagram showing evolutionary relationships among species.

Homologous characters

Traits derived from a common ancestor.

Cladistics

Classification of organisms based on common descent.

Clade

Group including an ancestor and all descendants.

Monophyletic group

A clade consisting of a common ancestor and all its descendants.

Paraphyletic group

Grouping consists of an ancestral species with some, but not all, descendants.

Polyphyletic group

Grouping consists of various species from different ancestors, doesn’t include recent common ancestry

Shared ancestral character

Trait originating in an ancestor of the taxon.

It is used in cladistics to help construct phylogenetic trees, indicating common ancestry among species.

Shared derived character

Novel trait unique to a specific clade.

eg Hair is a shared derived character that identifies mammals and distinguishes them from other vertebrates.

Character status

Relative classification of traits in phylogenetic analysis.

Evolutionary relationships

Connections between species based on shared traits.

Outgroup

An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied

• The outgroup is a group that has diverged before the ingroup

• Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics

• Characters shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor

Vertebral column

Backbone distinguishing vertebrates from invertebrates.

Hinged jaws

Derived character present in some vertebrates.

Four walking legs

Derived trait in certain tetrapods.

Amnion

Membrane surrounding embryo in amniotes.

Character table

Matrix displaying presence/absence of traits across taxa.

Phylogenetic analysis

Study of evolutionary relationships using shared traits.

Taxon

Group of one or more populations of organisms.

Evolutionary novelty

New trait that appears in a clade.

Branch point

Node in a phylogenetic tree indicating divergence.

Nested clades

Clades contained within larger clades.

Cladogram

Tree diagram representing clades and their relationships.

Outgroup

Species related to ingroup, diverged earlier.

Ingroup

Group of species being studied in analysis.

Shared derived characters

Traits evolved in a common ancestor, unique to a group.

eg the backbone is a shared derived character that at branch point distinguishes vertebrates from invertebrates

Shared ancestral characters

Traits present in both outgroup and ingroup.

eg backbone is shared by all members in the ingroup but not the outgroup (lancelet)

Cladistic analysis

Method to study evolutionary relationships among species.

Maximum parsimony

Tree requiring fewest evolutionary events is preferred.

Maximum likelihood

Tree reflecting most probable evolutionary sequence is preferred.

Character table

Matrix displaying traits across different taxa.

Chordata

Phylum including vertebrates and lancelets.

Vertebral column

Backbone structure present in vertebrates.

Hinged jaws

Jaw structure allowing movement, found in some vertebrates.

Four walking legs

Limbs adapted for terrestrial locomotion in some species.

Synapomorphy

Shared derived trait used to define a clade.

Convergent evolution

Independent evolution of similar traits in different species.

Reversal evolution

Return to an ancestral trait after divergence.

Lancelet

Outgroup species lacking a backbone, member of Chordata.

Lamprey

Jawless fish, part of vertebrate ingroup.

Bass

Type of fish within the vertebrate ingroup.

Turtle

Reptile with a shell, part of vertebrate ingroup.

Leopard

Mammal with hair, part of vertebrate ingroup.

Phylogenetic Hypotheses

Proposed explanations for evolutionary relationships among species.

Parsimony

Method minimizing the number of evolutionary changes.

Molecular Systematics

Study of genetic data to understand evolutionary relationships.

Ancestral Sequence

Original DNA sequence from which species diverged.

Phylogenetic Trees

Diagrams representing evolutionary relationships among species.

Branch Length

Indicates genetic changes or chronological time in trees.

Phylogenetic Bracketing

Predicting ancestor features from descendant characteristics.

Orthologous Genes

Genes diverged due to speciation events and retain the same function in different species. They are used to study evolutionary relationships between species.

Paralogous Genes

Genes diverged within the same species via duplication where they acquire different functions over time.

Gene Duplication

Process increasing gene number for evolutionary opportunities.

• Repeated gene duplications result in gene families

• Like homologous genes, duplicated genes can be traced to a common ancestor

Gene Families

Groups of related genes from repeated duplications.

Pseudogenes

Non-functional genes that have lost coding ability.

Can be formed from paralogous genes through mutation or gene duplication, often resulting in sequences that are similar to functional genes but do not produce proteins.

They will have relatively high rates of mutation and may provide insights into evolutionary history.

Morphological Data

Physical characteristics used in phylogenetic analysis.

Molecular Data

Genetic information utilized to infer evolutionary relationships.

Fossil Record

Historical evidence of past life forms and evolution.

Common Ancestor

Most recent species from which multiple species evolved.

Evolutionary Changes

Alterations in genetic makeup over generations.

Speciation

Formation of new species through evolutionary processes.

Natural Selection

Process where advantageous traits become more common.

Mutation Rates

Frequency of changes in DNA sequences over time.

Chronological Time

Time scale used to represent evolutionary history.

Genetic Changes

Alterations in DNA sequences across generations.

Divergence of Genes

Evolutionary process where genes evolve differently.

Gene Duplication

Process increasing gene number in genomes.

Olfactory Receptor Genes

Largest gene family in mammalian genomes.

OR Gene Count

Approximately 1000 intronless genes, each 1kb.

Class I OR Genes

Over 51 genes for waterborne odors.

Class II OR Genes

1-50 genes for airborne odors.

Functional OR Gene Repertoires

Comparison across 50 mammalian genomes.

Ecological Traits

Factors influencing OR gene repertoires.

Heatmap Analysis

Visual representation of functional gene distribution.

Ecotype Partitioning

Grouping OR genes by ecological categories.

Terrestrial Environment

Land-based ecological group for OR genes.

Aquatic Environment

Water-based ecological group for OR genes.

Semi-Aquatic Environment

Mixed habitat for OR gene adaptation.

Volant Environment

Airborne habitat influencing OR gene variation.

Loss of Function

Evolutionary reduction in gene functionality.

Single-Nucleotide Polymorphisms (SNPs)

Variations at single base pairs in genomes.

Haplotype

Specific set of SNPs & other genetic variations on a chromosome.

Linkage Disequilibrium

Non-random association of alleles at loci.

Genome-Wide Association Studies

Research linking SNPs to traits or diseases.

Nonsynonymous SNPs

Variants altering amino acids in proteins.

What disease is associated with variation in a gene ?

Miller Syndrome - Rare disorder linked to DHODH gene mutations:

• Causes distinctive craniofacial and limb abnormalities / malformations

DHODH Mutations

• 10 different non-synonymous (AA- altering) mutations associated with Miller Syndrome that are not found in other mammals

• 50% of mutations are found at completely conserved positions in over 46

  vertebrates.

• These sites evolve 40% slower than sites in DHODH associated with non-

  disease polymorphism

Visual Impairment Statistics

314 million affected globally, 45 million blind.

Hearing Impairment Statistics

1 in 1000 newborns affected, >50% elderly.

Genetic Disorder Awareness

Only 10% of affected individuals know causes.

Genotype

Genetic constitution of an organism.

Phenotype

Observable characteristics resulting from genotype.

Disease Prediction

Forecasting disease risk using genetic data.

Evolutionary Conservation

Preservation of genetic sequences over time.

Horseshoe Bat

Species used in comparative genetic studies.

Philippine Tarsier

Another species in comparative genetic studies.

Non-synonymous SNPs

Mutations that alter amino acid sequences.

How can we predict what SNPs will cause disease?

Fine-tuned disease prediction:

• Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome eg Subramanian and Kumar 2009

• 541 genes analysed in human, mouse, chicken, fungi

• Disease-Associated Mutations: in conserved regions

• Non-synonymous SNPs in regions under positive/relaxed selection

• Comparative studies can help categorizing SNPs into benign, possibly-damaging, and probably- damaging categories

Positive Selection

Natural selection favoring advantageous mutations.

Relaxed Selection

Reduced selection pressure on genetic variations.