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Systematics Lab B:

Primate Phylogeny

AP Biology

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Bioinformatics

Bioinformatics is a field that combines statistics, mathematical modeling, and computer science to analyze biological data. Using bioinformatics resources, entire genomes can be quickly compared for similarities and differences. Furthermore, these tools will quantify how similar the sequences are, and can be used to construct a phylogeny from the results.

Universal Protein Resource

BLAST: Basic Local Alignment Search Tool

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Linnean taxonomy groups together in the order Primate those mammals with an opposable thumb and/or toe, allowing for a grasping action (among other features). This includes humans.

Consider the shared and distinct traits of each of the primates on the slides that follow. Discuss with your group what the relationship(s) between the species might be, based on morphology and geography.

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Chimpanzee

Pan troglodytes

Bonobo

Pan paniscus

Gorilla

Gorilla gorilla

Gibbon

Nomascus leucogenys

Human

Homo sapiens

Orangutan

Pongo abelii

Rhesus Monkey

Macaca mulatta

Primates

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Rhesus monkey

Bonobo

Skeleton

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Chimpanzee

Bonobo

Human

Orangutan

Gorilla

Gibbon

*not to scale

Rhesus monkey

Skull

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Rhesus Monkey

Distribution

Besides the Great Apes, who are the other apes?�There are a few other apes in addition to the great apes, called the "lesser apes". The family Hylobatidae consists of many species of gibbons. They are different physically, socially and mentally from the great apes (chimpanzees, gorillas, orangutans and humans). They are smaller in size, and unlike the great apes which live in complex social groups, gibbons live in pairs for life. They don't make nests like most of the great apes, and in some ways, they look more similar to monkeys than the great apes.

Lesser Apes - Gibbons�Though on the surface they may look like monkeys because of their smaller and more slender forms, gibbons are indeed apes. Like the great apes, they lack tails, and have the same dental formula. Their skulls are also similar to those of great apes, having enlarged braincases and huge eye orbits that face forward. Siamangs are the largest type of gibbon.

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Primate	Weight (kg) m f	brain mass (g)
Bonobo	43 37
Orangutan	87 37	400
Gorilla	181 85	500
Gibbon	5.6 5.8	100
Human	75 62	1300
Rhesus monkey	7 5	179
Chimpanzee	60 32	400

Body mass Brain mass

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Use the information on the previous slides to make a phylogeny/cladogram; this is your hypothesis regarding the relationships between the species. Note on the tree the characters used to separate groups or species at each branch point of the lineage.

Compare your tree - your hypothesis - to those of the other groups

Discuss the reasoning behind any differences
Make changes if you are convinced by another group’s argument

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TEST THE HYPOTHESIS

Test your hypothesis by searching online databases of protein sequence information using Uniprot.org.

link > Uniprot.org

choose > UniProtKB

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In the search bar, type in a protein name (ex: NADH Ubiquinone, chain 5), plus the abbreviated common name of one of the primates (ex: Homo sapiens is Homsa)

try a wikipedia search of human proteins for possibilities

Choose >‘show 250’ results

A list of protein sequences will result; check the box to the left for the sequence of interest. Click >‘Add to Basket’.

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FILL the ‘BASKET’

Search for the same protein and gene - by name - for each of the primate species. Add each to the basket.

In the basket, check the left box for any pair of species.

Click the > align button

After a few seconds

you’ll get the sequence

comparison data. (stars and

dots indicate differences)

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Scroll to the bottom to find the percent similarity under Identity. Record in the matrix.

Repeat for all pairs of organisms.

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Generate the Phylogenetic Tree

In the basket, select all the species, then click align.

Scroll down to see the tree. Print or record.

Analysis: does this additional data support your initial hypothesis?

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TEST THE HYPOTHESIS, v2

Test your hypothesis by searching online databases of gene sequence information via The National Center for Biotechnology Information

Link to https://www.ncbi.nlm.nih.gov/gene

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FIND A GENE SEQUENCE

Toggle to ‘gene’. Enter the name of a protein, prefaced by ‘human’, into the search bar

Suggestions: human insulin, myosin, kinase, cyclin, actin, growth factor, oxytocin, ubiquitin , hemoglobin, myoglobin – see the ‘list of proteins’ at Wikipedia

Choose a different gene than your lab partner(s)

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Scroll through the results list; choose one; click on the name abbreviation link

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Scroll a few pages down to “NCBI Reference sequence” > mRNA + Protein(s) > reference number (starts with NM or XP…)

Record the reference number on your data matrix next to H. sapiens. Click on the link.

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THE NUCLEOTIDE SEQUENCE

Lots of information on the sequence on this page

Click on the FASTA link for the full gene sequence of nucleotides
Copy and paste the entire sequence (starting at >) into a document

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FIND SIMILAR SEQUENCES

BLAST is a program that compares a selected sequence to other sequences in the database.

Choose ‘nucleotide BLAST’

>“Search set: Others”

> “Program Selection: highly similar sequences”

> click the BLAST button at the bottom

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IT’S A MATCH (OR CLOSE)

Scroll past the graphic to the ‘Sequences Producing Significant Alignments’ list; your search is the top listing.

human

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IT’S A MATCH (OR CLOSE)

Scroll down the list slowly, and stop at the first occurrence of each of the other primates in the matrix. Record their reference number (‘Accession’, far right).

Click on the first

one in the list that

is on the matrix

chimp

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IT’S A MATCH (OR CLOSE)

Click on the name link to see their sequence compared to the human sequence. Each vertical line between nt bases is a match; pairs lacking a line are differences. At the top, under ‘identities’, is the percent similarity between the human sequence and this one.

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Use the browser back button to return to your initial sequence.

The Ident column on the far right also lists the number of bases in the sequence in common. Record both Accession (reference number) and Ident for this species in the matrix

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COMPARE THE OTHERS

Use the browser back button to return to your initial sequence. Repeat to compare the primates proteins in the matrix with the human protein.

Once you have sequence data compared to humans, click on the Accession number of one of the other species in your matrix. Scroll this new list, and find the other species, making sure the reference number is the same as you’ve recorded.

Find the other primates sequences compared to this one. Repeat until the matrix is complete.

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ANALYSIS