Molecular Phylogenetics
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What is
phylogenetics?
– Phylogenetics is the study of
evolutionary relationships
among biological entities –
often species, individuals or
genes (which may be
referred to as taxa).
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Phylogeneticists study one of the following
types of question:
– What are the evolutionary relationships or histories among my
species/individuals/genes of interest?
– How do sequences evolve?
– Can I better describe processes of sequence evolution with a mathematical
model?
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Why use molecular data?
– Today, almost all evolutionary relationships are inferred from molecular
sequence data. This is because:
– DNA is the inherited material
– We can now easily, quickly, inexpensively and reliably sequence genetic material
– Sequences are highly specific and are often information rich
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Cont..
– In rare cases, where it is not possible to obtain genetic material (e.g. in the case
of certain ancient fossil samples), morphological measurements can be used to
infer evolutionary relationships.
– This approach is less reliable than using molecular data because we know that
sometimes the same morphological trait can arise from multiple independent
evolutionary lineages (i.e. occurrences of the trait are analogous).
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Why is phylogenetics
important?
– Enriches our understanding
of:
– How genes, genomes, species
(and molecular sequences
more generally) evolve?
– How the sequences came to
be the way they are today?
– Enable us to predict how they
will change in the future?
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Applications of phylogenetics
Classification: Phylogenetics based on sequence data provides us with more
accurate descriptions of patterns of relatedness than was available before the
advent of molecular sequencing. Phylogenetics now informs the Linnaean
classification of new species.
Forensics: Phylogenetics is used to assess DNA evidence presented in court cases
to inform situations, e.g. where someone has committed a crime, when food is
contaminated, or where the father of a child is unknown.
Identifying the origin of pathogens: Molecular sequencing technologies and
phylogenetic approaches can be used to learn more about a new pathogen
outbreak. This includes finding out about which species the pathogen is related to
and subsequently the likely source of transmission.
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Applications of phylogenetics
Conservation: Phylogenetics can help to inform conservation policy when
conservation biologists have to make tough decisions about which species
they try to prevent from becoming extinct.
Bioinformatics and computing: Many of the algorithms developed for
phylogenetics have been used to develop software in other fields.
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What is a phylogeny?
– A phylogeny, also known as a tree, is an explanation of how sequences evolved,
their genealogical relationships, and therefore how they came to be the way they
are today.
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Aspects of phylogenies
– Topology
– Branches
– Nodes
– Tips
– Internal nodes
– Root
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Major stages in
phylogenetic analyses
– There is no recipe available to
complete a phylogenetic analysis
– The approaches that you take are
highly context and situation specific,
and ultimately depend upon your
biological question of interest.
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Phylogenetics resources at EMBL-EBI
– Ensembl: is a vast resource for vertebrate genome data, where (among other things) you
can download nucleotide sequence data and run BLAST searches to inform the
identification of homologous sequences. For many genes, you can also download the
orthologous sequences that we have identified, as well as interspecific alignments that
we have pre-computed. To do so, simply search for your favourite gene (e.g. ADH1B),
and explore the ‘genomic alignments’ options within the comparative genomics menu.
– Ensembl genomes: extends Ensembl across the tree of life, making genome data
publically available for Bacteria, Plants, Fungi, Protists and Metazoa. This includes pre-
computed alignments and orthologues.
– Ensembl compara: offers pre-computed phylogenies for visualisation and download.
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Phylogenetics resources at EMBL-EBI
– ClustalW2 Phylogeny: is a basic tool for estimating evolutionary trees from
multiple sequence alignments. By default, it uses the Neighbour Joining method
with the option of a very simple model of sequence evolution, or UPGMA
(Unweighted Pair Group Method with Arithmetic Mean) can be chosen instead.
– Clustal Omega and Prank: are multiple sequence alignment programs which are
useful as part of a phylogenetics workflow.
– EMBOSS Seqret: is a file format conversion tool that can be useful at multiple
stages of a phylogenetics workflow
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More Advanced Tools
– Phylip
– MEGA
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Aligning Sequences
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Estimating Evolutionary Distances Using
Pairwise Distance
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Bootstrap Testing for a Neighbor-Joining Tree
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