lecture 8 Flashcards
molecular phylogenies are used to
Gain insights into (molecular) evolution.
2) Predict gene functions.
3) Predict that gene functions diversify.
4) Detect various regimes of selective pressures (pharmacology).
5) Epidemiology
traditional objective of a phylogenetic
to represent the evolutionary
relationship between species.
Advantages of molecular sequences over morphological characters
DNA and amino acid sequences are strictly heritable units.
2) Unambiguous description of molecular characters and character states.
3) Amenability to mathematical modeling and quantitative analysis.
4) Homology assessment is easy.
5) Distant evolutionary relationships may be revealed.
6) Huge amounts of data available.
What is put into tree reconstructions
alignment of homologous genes
The phylogeny of the species can be transferred from the gene tree, if
genes
are orthologous.
homology vs orthologs vs paralogs
Homologous genes: that are similar genes due to their shared ancestor or common origin.
Orthologous genes: that are two genes in two different species that
share a common ancestor.
Paralogous genes: that are two genes in the same genome that are a
product of a gene duplication event of the original gene
horizontal gene transfer
exchange in hereditry info in prokaryotes
ex for HGT and its impact
B. subtilis obtained the gene encoding Glyclosyl Hydrolase (GH) from an E. coli strain.
not possible to
infer the species phylogeny based on the gene tree for Glycosyl Hydrolase
gene tree not equal species tree
The number of …..exchanges between hemoglobin’s of two species is approximately proportional to the
…..
amino acid
divergence time of the species.
probabilistic models usage
phylogenetic reconstruction, sequence alignment, molecular dating and
functional sites prediction.
Phylogenetics
is a study of branching patterns of descent among lineages.
Shift between population genetics and phylogenetics is often the
species
boundary.
…..are similar among all organisms.
replication and gene
expression
assumption of phylogenetic tree
organisms have evolved from common ancestors
evolutionary relationships are called…..
phylogeny
Molecular phylogenetics goal
reconstructing the tree of life
The evolutionary process may vary…
within groups of genes, among sites within a gene, between populations and among diverged species.
Evolutionary models must account for…
base pair substitutions insertion and deletion
DNA barcoding
few standardized universal molecular markers
for species identification
sequences must be..
applications..
protein coding
large-scale species inventories
global biodiversity assessments through
metabarcoding t
The Barcode of Life Data system
8 million barcode sequences representing more than 300,000 species.
Rules for DNA barcoding..
clear separation between intraspecific polymorphism and interspecific divergence
conserved,variable,orthology,amplificability,refrence data available
examples for DNA barcoding seq
mitochondrial cytochrome c oxidase I
chloroplast ribulose 1,5 bisphosphate carboxylase/oxidase
mutase k gene in plants
16S RNA in bacteria and archea
Ancestral Genome Organization helps know
conserved structures
functional gene clusters
patterns and processes of biodiversity
Ancestral Genome Organization how?
genetic map and polytene chromosomes analysis esp mutations
mutations??
large inversions/chromosomal translocations
small inversions/small indels/microsattellites
why mutations
structural and non coding regions causing alteration in gene organisation
muations are evidence for
adaptation/speciation/sex differentiation/polyploidization
