Chapter 25:Phylogeny and Systematics

phylogeny – evolutionary history of a species or group of species

systematics – analytical approach to understanding the diversity and relationships of present and past

organisms

Phylogenies based on common ancestors using fossil, morphological

and molecular evidence

the fossil record – based mostly on the sequence in which fossils have

accumulate in sedimentary rock strata (layers)

Sedimentary rock forms when silt builds up on bottom of waterway. More deposited on top, compress

older sediments into rock.

morphological and molecular homologies

• organisms with similar morphology or similar DNA closely related

analogy is not homology; analogy is a similarity due to convergent evolution

(organisms adapting to similar environment/niche but no common

ancestor)

• distinguishing analogy from homology critical to constructing phylogenies

homoplasies – analogous structures that have evolved independently

Marsupial mole(Australia)

eutherian mole(North America)

No recent common ancestor

molecular homologies

• compare nucleic acids of two species; if very similar, organisms closely related

• a hard to tell how long ago they shared a common ancestor; must also look at fossil record

• mathematical tools can distinguish between distant homologies from coincidental matches

Systematics connects classification with evolutionary history

taxonomy – ordered division of organisms

into categories

bionomial nomenclature – scientific name

• binomial – 2- part scientific name developed by Linnaeus “Linnean system”

• genus – first part of name• specific epithet – second part of name

Homo sapiens = humans, means “wise man”

Heirarchical classification

• Domain• Kingdom• Phylum• Class• Order• Family• Genus• Species

mnemonic to help you remember:

“Dreadful King Phillip Came Over From Great Spain”

Linking classification with phylogeny

phylogenetic trees – branching diagrams that depict hypotheses about evolutionary relationships.

• uses groups nested within more inclusive groups• constructed from series of dichotomies (2-way branch points)• each branch point represents a divergence of two

species from a common ancestor

cladogram – shows patterns of shared characteristics

clade – group of species that includes an ancestral species and all of its

descendants

cladistics – analysis of how species grouped into clades

• clades can be nested inside larger clades

– ex. cat family within a larger clade that includes dog family

monophyletic group – ancestral species and all of its descendants

paraphyletic group– when we lack information about some members of

the clade

polyphyletic group– several species that lack a common ancestor (need

more work to uncover species that tie them together into a monophyletic

clade)

Shared Characteristics – types of homologous similarities

Chordate characteristics

Shared primitive character – shared beyond the taxon.

Shared derived character – evolutionary novelty unique to that

clade.

Ex. hair only found in mammals

Why morphology alone does not show evolutionary relationship:

• Closely related organisms not always similar in appearance (rapid environmental change leads to rapid evolution; also, small changes in genes can lead to large morphological differences)

• Organisms that appear similar not always closely related (convergent evolution)

• Just because 2 groups share primitive characters does not mean they are closely related

outgroups – species or group of species closely related to the ingroup

• less closely related than members of the ingroup

• have a shared primitive character that predates both ingroup and outgroup members

phylogenetic trees – show estimated time since divergence

• chronology of a phylogenetic tree is relative; not absolute

phylograms – length of a branch reflects number of changes in a DNA sequence

ultrametric trees – length of branch reflects amounts

of time

maximum parsimony “Occam’s Razor”– first investigate the simplest explanation

that is consistent with the facts• Aim is to find the shortest tree that has the

smallest number of changes

The top tree has the most parsimony

maximum likelihood – given

certain rules of how DNA changes over time, a tree can be found that reflects the most likely sequence of

evolutionary events

Often the most parsimonious tree is also the most likely

phylogenic trees are hypotheses of how the organisms are related to each

other

• Best hypothesis is one that fits all the available data

• May be modified when new evidence introduced

• Sometimes there is compelling evidence that the best hypothesis is not the most parsimonious

Organisms’ genomes document their evolutionary history

• importance of studying rRNA and mitochondrial DNA (mtDNA)

rRNA changes very slowly; used to study divergences that happened a

very long time ago

mtDNA changes very rapidly; used to study divergences that happened

recently• – useful for studying relationships between

groups of humans

ex. how Native Americans

descend from Asian population that crossed the

Bering Land Bridge 13,000 years ago

• can lead to further evolutionary changes

Gene duplication one of most important types of mutation in

evolution because it increases # of genes in genome.

gene families – groups of related genes in an organism’s genome

• result of repeated duplications• have a common ancestor

orthologous genes – homologous genes passed in a straight line from

one generation to the next.• can diverge only after speciation• can be found in separate gene pools due to

speciation

paralogous genes – result of gene duplication. Found in more than one

copy of the same genome• can diverge in the same gene pool

Genome evolution

• Orthologous genes are widespread and can extend over huge evolutionary distances

• 99% of genes in humans and mice are orthologous; 50% of genes in humans and yeast are orthologous

– demonstrates that all living organisms share many biochemical and developmental pathways

Molecular clocks – way of measuring absolute time of evolutionary change

• based on some genes seem to evolve at a constant rate

• # of nucleotide substitutions in orthologous genes is proportional to time elapsed since the species branched from common ancestor

neutral theory – for genes that change regularly enough to use as a molecular clock, these changes are

probably a result of genetic drift and are mostly neutral (neither adaptive

nor detrimental)

• conclusion: much evolutionary change has no effect on fitness; therefore, not influenced by selection.

• most new mutations are harmful and therefore removed quickly

The universal tree of life

• Genetic code universal to all forms of life so all life must share a common ancestor

• Researchers trying to link all organisms in a “tree of life”

• use rRNA genes for this; as they evolve most slowly

The Tree of Life has three domains: bacteria, archae and eukarya

The early history of these domains is not yet clear

• due to horizontal gene transfer, substantial interchanges of genes between organisms of different domains

• horizontal gene transfer due to transposable elements and fusion of different organisms (first eukaryote fusion of ancient bacteria with ancient archae)