Lecture 18/19 :Phylogenetics part 2: Characters Flashcards
Characters used in phylogeny reconstruction
-Morphological Characters
-comparative Physiology, Histology, or Ethology
-Molecular Characters
Morphological characters used in phylogeny reconstruction (animals 3 plants 2)
-In animals, outer form and inner structure, such as:
* Number, structure, and position of bones in vertebrate forelimb, skull, etc.
* Teeth, feathers, heart chambers…
* Presence or absence of placenta, ruminant stomach
-In plants
* leaf venation, woody tissue
* pollen structure, arrangement of sepals, petals, bracts, cone scales
Comparative Physiology, Histology, or Ethology used in phylogeny reconstruction (2)
-Body temp regulation (Ethology = study of animal behavior)
-Cellular types and organization (histology = study of tissues)
Character
Character = structure or feature
Character states (2)
Character states = variant conditions of the character
e.g., Character = toe number vs Character state = 5 (humans) or 3 (guinea pigs)
Molecular Characters (4)
- Comes from molecular data
-Mutations accumulate as species diverge
-DNA is a “document of evo history” as it is highly sensitive (useful for closely related taxa) and includes silent mutations that would not result in phenotypic change
-Independent indicator of common ancestry
DNA (3)
-4 nucleotides or base pairs ( ACGT)
-Some regions (genes) code for proteins but most do note (rRNA, introns etc)
-Differences between sequences are called substitutions
Translation (3)
-DNA is first transcribed into mRNA (U replaces T)
-Then translated into proteins at the ribosomes
-Nucleotides groups into triplets called codons
Redundant genetic code (2)
-There are 64 different codons for only 20 amino acids = multiple codons code the same amino acid
-This allows mutations to be silent, where they happen but produce the same amino acid either way
Genome
They whole hereditary information of an organism that is encoded in their DNA (gene + chromosome)
Types of DNA Used in Phylogeny Reconstruction (3)
-Nuclear Genome
-Chloroplast Genome (cpDNA)
-Mitochondrial Genome (mtDNA)
Nuclear DNA (3)
-DNA found in the nucleus on the chromosome
-Inherited from both parents
-Encodes most traits that vary among taxa
Problems with Nuclear DNA (3)
-Large and complex in eukaryotes, but complete genomes are being sequenced in dozens of organisms
-Identifying actual gene regions takes even more time
-gene content varies a lot between species
Chloroplast Genome (3)
-In cytoplasm of plants and protists
-Chloroplast thought to have originated as endosymbiotic (one org lives in another) cyanobacteria which developed its Own small genome, originally bacterial genome
-Useful for plant phylogenies
Mitochondrial genome (6)
-In cytoplasm of most eukaryotes
- Also derived from endosymbiotic bacteria
- Own circular genome with own ‘machinery’ for protein synthesis (ribosomes, tRNAs)
- uses different genetic code than nuclear genome = contains very little noncoding DNA
-Smaller in animals more complex in plants = not as helpful in plants
*many many copies per cell from 1000-2000 in human liver cells
Mitochondrial Genome parts (4)
1) 13 protein-coding genes which produce Enzymes involved in oxidative phosphorylation
2) 22 tRNAs that transfer amino acids during translation
3) 2 rRNAs that are ribosomal RNA, not coding but not junk DNA either
4) Control region which is the most variable region. Contains the displacement loop (aka d-loop) which is the origin of replication
Using mtDNA for phylogenetics (4)
-mtDNA is well-characterized in 1000s of orgs which allows scientists to create “conserved primers” which amplify and sequence homologous regions in a wide range of taxa
-Different regions evolve at different rates! neutral mtDNA evolves 5-10x faster than a single cope of nuclear genes
-mtDNA is maternally inherited, so hybridization cannot be detected w/o data from nuclear genes as well
-only makes up a small proportion of the org’s total genome
Homology in molecular characters
Characters must be homologous so in order to correctly infer homology, scientists must ensure that when they compare species, they are looking at the same gene, with the nucleotides in the same position. Additionally, they must ensure that the character states are the same too! Because there are only 4 character states (A, T, C, G) in molecular characters, distinguishing homology from homoplasy has to be done by preponderance of evidence
Preponderance of evidence
In biology, “preponderance of evidence” generally refers to a strong body of evidence supporting a scientific claim or hypothesis. It’s about having more evidence that supports a particular view than it does that of a competing view, making it more likely to be true.
Ensuring correct nucleotide position in molecular characters (5)
-Sequences must be aligned to make sure they are comparing the same position of each gene
-Programs such as ClustalW can do this
-When looking at protein coding regions, because of the 3-nucleotide codons, insertions or deletions must be in multiples of 3 to maintain reading frame. In other words, due to differences in sequence length, sometimes they add “- - -“ as a blank between codons to ensure they line up.
-These blanks are called “Indels”
-When aligning non-protein coding regions (ex D-loop), Indels can be any number of bases. This varibility is very good when making intraspecific comparisons (comps between individuals of the same species) but bad when comparing different taxa, as the sequences can be so different no match looks aligned.
Ensuring homologous character state in molecular characters (4)
-Because of there only being 4 character states, there is a high change of indepentent mutations resulting in the same state. Things like converget and co evolution producing a A at a specific place is highly likley.
-There can also be multiple substitutions ending in the same result as well (T->C->T->A vs G->A->C->A)
-So to ensure the same character state, scientists look at both a large number of characters, as well as the complexity of these characters. Different mutations are more common than others and therefore are called more complex (ex A->T vs A-C)
-Transitions on the 3rd position of the codon receive less weight as they tend to result in the same AA being produced - but are still useful when comparing closely related species
