Three-taxon analysis
BIO 123 Section 2, Spring 2017 Introduction
Phylogenetic analysis of dozens of species and hundreds of phenotypic features or thousands of DNA
base pairs is computationally intensive. Not only does it require computers, some problems can take
hours to run even on a fast computer. And when you’re done, you pretty much have to accept the
computer’s analysis—there’s no way to check it by hand.
But most complex problems can be broken down into simple pieces, and phylogenetic analysis is no
exception. The simplest piece is called a three-taxon analysis, and it involves looking at the three
possible three-taxon statements to see which is best-supported by the data. Here are those statements
depicted graphically:
A B C C A B B A C This will probably seem familiar as the basis of the example used in lecture, with the three species
Gymnogyps californianus, Equus caballus, and Myotis californicus.
When using three-taxon analysis to reconstruct phylogeny, you wouldn’t already know the relationships,
and you wouldn’t know which shared features were apomorphic, which were plesiomorphic, and which
were homoplastic. For this exercise, you’ll be approaching it from a different direction. For the three
species you’ve been assigned, the best-supported (“correct”) cladogram can be obtained from the
literature, either as an actual cladogram, or, more often, by their positions in a taxonomy formed from
monophyletic groups. Your job is to find the apomorphies that support the cladogram.
You will be haphazardly assigned your three species from a list, appended below. You will have a
“grade” in Blackboard called “3-taxon #”. Look for that number on the list, and those are your species. How to succeed
Here are some suggestions and safety tips to help you out:
•
• Read and follow the directions.
Make sure to transcribe information accurately. A misspelled or un-italicized scientific name is
wrong. BIO 123, Spring 2017, version 2017-04-07 1 • • • • • •
• Don’t be afraid to use Wikipedia. Its articles about individual species are generally accurate and
often well-written. Every species name in the list should take you to its own Wikipedia page; if it
doesn’t, let me know.
Don’t guess at the synapomorphy that unites two of your three species; you will almost always
be wrong. If you are having trouble finding a reference for the synapomorphy, check with me
early.
Synapomorphies are actual features, not types of features. For example, “lactation” is a
synapomorphy; “Method of feeding the young” isn’t. “Feathers” is a synapomorphy; “body
covering” isn’t. “Possession of a unique inverted repeat in the chloroplast genome” is a
synapomorphy; “DNA” isn’t (at least at that level). “Articulating premaxilla” is a synapomorphy;
“skull structure” isn’t. If you’re not sure, ask yourself whether your outgroup also feeds its
young, has body covering, DNA, and a skull. If it does, you’re not looking at a synapomorphy for
the two most related species.
Use the template. It ensures that you’ve put in all the necessary information, and it makes
grading easier for me. If you have some reason not to use the template, try to duplicate it as
closely as possible.
Do not submit the assignment in paragraph form. It obscures the information, making it
exponentially harder for me to grade, so I won’t grade it and will record a zero for the
assignment.
Do not include photographs. If a visual is absolutely necessary to make a point, put in a web link.
I will deduct 5% of the maximum possible grade for each photograph included.
Did I mention to follow directions? Required information
1. The scientific name for each species, as given in the list. Using the template, put the most
distant relative in the left column, the one of the close relatives that shares a homoplasy or
plesiomorphy with the distant relative in the middle column, and the other closest relative in
the right column.
2. A common name for each of your three species. Wikipedia is a good source for most. If there is
more than one common name (this is not uncommon), you only need to pick one. Many obscure
organisms have no common name. If that is the case with yours, enter “common name not
listed”. I will check the Wikipedia article if you do, so don’t just guess at it.
3. For each of your species, list its place in the taxonomic hierarchy. Minimally, it will include family
(remember that the genus name is already built into the binomial), order, class, and phylum.
There may be other levels, including unranked clades. You must include any of those other
levels that you use for determining the cladogram and synapomorphy. Levels that you don’t use
can be left out, but there’s no harm in including them. Wikipedia is again a good source—it is
generally up-to-date, and the editors work to make the “taxoboxes” consistent across related
groups. You can arrange from most inclusive to least inclusive, or least inclusive to most
inclusive, but you must be consistent across all three. BIO 123, Spring 2017, version 2017-04-07 2 4. Because the phylogenetic relationships were used to make the taxonomy, the taxonomy tells
you the phylogenetic relationships (this isn’t always true, but it is for all the sets of three species
that I chose for this assignment). Using this information, show which of the three statements is
the correct phylogeny (as currently interpreted). You may draw a tree, but you can also show
the same information with parentheses:
(Gymnogyps californianus (Equus caballus, Myotis californicus))
5. Okay, that was the easy part. Now you have to find and list at least one synapomorphy that
shows that two of your species are more closely related to each other than either is to the third.
In the case above, the two mammals are, well, mammals, and they share all the apomorphies
that distinguish mammals. Easy-peasy. But what if, instead of Myotis californicus, you were
given Tapirus terrestris. It and Equus caballus are both members of the order Perissodactyla, so
you might think that you would need the synapomorphies of that order. And if your third
species were Mus musculus (another mammal), you would. But Gymnogyps californianus isn’t a
mammal, so you could still use the mammal synapomorphies in this example. You can use
whichever taxonomic level provides the easiest-to-find synapomorphies, as long as two of the
species share it, and the third doesn’t.
Because a lot of phylogenetic analysis these days is based on DNA, and the analysis of DNA
sequences doesn’t really generate lists of synapomorphies, in some cases you may find only a
single synapomorphy to unite two of your three species. But you should always try to find more.
If I can think of several off the top of my head, one won’t be enough.
6. The next part is actually easier, but it may require some creativity. List a single feature that one
of your two closest-related species shares with the most distant species. In the case of our
example, it would be wings, shared by Gymnogyps californianus and Myotis californicus. In our
example, wings is homoplastic, but in other cases you might choose a plesiomorphy. For
example, Carnegiea gigantea and Yucca brevifolia are both flowering plants, more closely
related than either is to Ephedra nevadensis, but Carnegiea gigantea and Ephedra nevadensis
share the feature of two cotyledons (Yucca brevifolia has one), which is the ancestral state in the
seed plants.
You may have to stretch to find this feature. Some other possibilities are habitat (salt water
vs. fresh water), structure (aseptate filaments vs. septate), or even color (red lophophore vs.
colorless lophophore).
7. And last, for each of your species, write down what you think is the most interesting or
unexpected thing about it. This is your personal opinion, so as long as the information is correct,
whatever you choose is right.
8. Don’t forget references:
a. For every Wikipedia article you use, list the title (I should be able to copy it, paste it into
the Wikipedia search box, and go directly to your article), and the date you accessed it
(so that if it changed, I can go to the page history and see the page you saw). You don’t
need to include the three species names; I assume you will have looked at them, and I
BIO 123, Spring 2017, version 2017-04-07 3 looked at every one of them when I developed the assignment. You shouldn’t include
any articles that were dead ends, or otherwise not helpful.
b. For any reference not in Wikipedia, provide a URL that I can use to access it on the web.
If you use the textbook, just copy and paste the citation from the course syllabus. Submitting your assignment
Go to this course in Blackboard and open the Assignments page. Find “Three-taxon analysis” and click
“View/Complete”. Make sure “Submit:” at the top says “Single File Upload”. Enter the requested
information (use Three-taxon analysis as the title), and select your file. Click on the Upload button at the
bottom of the form. BIO 123, Spring 2017, version 2017-04-07 4 An Example
Be sure to put the two closest relatives in the two columns on the right. Note that if we switched Myotis
californicus and Equus caballus, it would appear that horses have wings.
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8a
8b Gymnogyps californianus
Myotis californicus
Equus caballus
California condor
California myotis
horse
Kingdom: Animalia
Kingdom: Animalia
Kingdom: Animalia
Phylum: Chordata
Phylum: Chordata
Phylum: Chordata
Class: Aves
Class: Mammalia
Class: Mammalia
Order: Cathartiformes
Order: Chiroptera
Order: Perissodactyla
Family: Cathartidae
Family: Vespertilionidae
Family: Equidae
(Gymnogyps californianus (Myotis californicus, Equus caballus))
Hair, lactation, three bones in the middle ear, cheekbones
Wings (homoplasy)
State Bird of California
Tiny feet
Domestic animal
Mammal
Bird
Freeman, S., et al. 2014. Biological Science, 5th Edition. Pearson. This table, not filled out, is also in the template, with instructions on the second page. BIO 123, Spring 2017, version 2017-04-07 5 List of taxa
Choose the number that corresponds to the number assigned to you in Blackboard.
1 Saccharomyces cerevisiae Agaricus bisporus 2
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Ailuropoda melanoleuca
Pseudacris hypochondriaca
Salmo salar
Caulophacus elegans
Gloeocapsa magma
Bertholletia excelsa
Scutigera coleoptrata
Telopea speciosissima
Archilochus colubris
Daphnia pulex
Artemia salina
Solanum tuberosum
Cyperus papyrus
Elgaria multicarinata
Latrodectus geometricus
Vaucheria litorea
Clostridium perfringens
Periphylla periphylla
Sylvicapra grimmia
Helicobacter pylori
Cassytha filiformis
Cerastoderma edule
Papilio rutulus
Calypte anna
Aquilegia caerulea
Oryctolagus cuniculus
Coenagrion puella
Orcinus orca
Closterium setaceum
Micropterus salmoides
Pinus monophylla
Orycteropus afer
Stachys affinis
Procyon lotor
Mus musculus
Acrasis rosea Agkistrodon piscivorus
Ailurus fulgens
Ambystoma mexicanum
Amia calva
Amoeba proteus
Anabaena circinalis
Anacardium occidentale
Anadenobolus monilicornis
Anigozanthos manglesii
Apus apus
Armadillidium vulgare
Armadillidium vulgare
Artemisia dracunculus
Arundo donax
Atractosteus spatula
Atrax robustus
Bacillaria paxillifer
Bacillus anthracis
Bergtrollus dzimbowski
Bison bison
Borrelia burgdorferi
Botrychium lunaria
Busycon carica
Caenorhabditis elegans
Caiman crocodilus
Calochortus nuttallii
Cavia porcellus
Ceratitis capitata
Choeropsis liberiensis
Corallina officinalis
Corvus corax
Cycas revoluta
Cyclopes didactylus
Cynara cardunculus
Dasypus novemcinctus
Dasypus novemcinctus
Dictyostelium discoideum BIO 123, Spring 2017, version 2017-04-07 Batrachochytrium
dendrobatidis
Python regius
Ursus arctos
Xenopus laevis
Huso huso
Allomyces macrogynus
Frankia alni
Mangifera indica
Scolopendra heros
Swainsona formosa
Apteryx haastii
Artemia salina
Callinectes sapidus
Raphanus sativus
Pennisetum glaucum
Macrochelys temminckii
Pycnogonum stearnsi
Bigelowiella natans
Escherichia coli
Branchiostoma floridae
Antilocapra americana
Treponema pallidum
Pseudotsuga macrocarpa
Lobatus gigas
Octopus bimaculatus
Iguana iguana
Cypripedium reginae
Mesocricetus auratus
Aedes aegypti
Hippopotamus amphibius
Trentepohlia aurea
Turdus merula
Sequoia sempervirens
Myrmecophaga tridactyla
Helianthus tuberosus
Canis latrans
Sarcophilus harrisii
Lycogala epidendrum
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79 Protonotaria citrea
Vaucheria litorea
Sequoia sempervirens
Viola cucullata
Equisetum arvense
Equus hemionus
Ictalurus punctatus
Amoeba proteus
Aphelocoma californica
Fulica americana
Macrocystis pyrifera
Testudo graeca
Struthio camelus
Metroxylon sagu
Pusa sibirica
Lumbricus terrestris
Cuscuta pentagona
Equisetum hyemale
Glomus aggregatum
Kallstroemia grandiflora
Psilocybe
angustipleurocystidiata
Pholcus phalangioides
Funaria hygrometrica
Suricata suricatta
Ziphius cavirostris
Rhincodon typus
Cryptochiton stelleri
Alopecurus aequalis
Entamoeba gingivalis
Eschscholzia californica
Hydnora triceps
Vulpes macrotis
Ara ararauna
Sylvilagus audubonii
Pleurobrachia bachei
Oxycomanthus bennetti
Coriandrum sativum
Phataginus tricuspis
Ginkgo biloba
Atrax robustus
Vorticella campanula BIO 123, Spring 2017, version 2017-04-07 Dipodomys ingens
Elysia chlorotica
Ephedra sinica
Epigea repens
Equus caballus
Equus zebra
Felis catus
Fuligo septica
Gavia immer
Gavialis gangeticus
Gelidium sesquipedale
Gopherus agassizii
Haliaeetus leucocephalus
Hatiora salicornioides
Helarctos malayanus
Hirudo medicinalis
Hydnora africana
Juncus effusus
Laccaria bicolor
Larrea tridentata
Lophophora williamsii Rana muscosa
Ectocarpus siliculosus
Selaginella lepidophylla
Cypripedium acaule
Trachurus trachurus
Diceros bicornis
Nepeta cataria
Nosema apis
Passer domesticus
Gavia immer
Thalassiosira pseudonana
Chelus fimbriata
Catherpes mexicanus
Cycas revoluta
Zalophus californianus
Riftia pachyptila
Phoradendron macrophyllum
Schoenoplectus californicus
Pleurotus ostreatus
Eschscholzia californica
Turbina corymbosa Loxosceles reclusa
Lycopodium clavatum
Lynx rufus
Madoqua kirkii
Manta birostris
Megascolides australis
Myosurus apetalus
Naegleria fowleri
Nandina domestica
Nuytsia floribunda
Nyctereutes procyonoides
Nymphicus hollandicus
Ochotona princeps
Orbicella annularis
Orchesella cincta
Origanum vulgare
Orycteropus afer
Oryza sativa
Panulirus interruptus
Paramecium caudatum Odontodactylus scyllarus
Silene acaulis
Panthera onca
Trichechus manatus
Chiloscyllium indicum
Chelidonura varians
Equisetum arvense
Balamuthia mandrillaris
Phyllostachys bambusoides
Monotropa uniflora
Procyon lotor
Melopsittacus undulatus
Lepus californicus
Nematostella vectensis
Gluvia dorsalis
Stachys affinis
Manis pentadactyla
Tetrapanax papyrifer
Paralithodes camtschaticus
Cryptosporidium hominis
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86 Pygoscelis papua
Stentor coeruleus
Dactylis glomerata
Procambarus clarkii
Illicium verum
Crassostrea gigas
Podosphaera fuliginea 87
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99 Ginkgo biloba
Helarctos malayanus
Nitella flexilis
Vicugna vicugna
Photocorynus spiniceps
Ustilago maydis
Stemonitis fusca
Nautilus pompilius
Acer rubrum
Ipomoea batatas
Taricha torosa
Zerene eurydice
Dendraster excentricus 100
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Thomomys bottae
Erinaceus europaeus
Nosema apis
Strongylocentrotus purpuratus
Noctiluca scintillans
Alexandrium tamarense
Loxodonta cyclotis
Upupa epops
Pelvetia canaliculata
Pyropia tenera
Trentepohlia aurea
Gynaephora groenlandica
Lepisma saccharina
Pteropus vampyrus
Dawsonia superba
Asparagus setaceus
Balaenoptera musculus
Orcinus orca BIO 123, Spring 2017, version 2017-04-07 Pelecanus erythrorhynchos
Pfiesteria piscicida
Phleum pratense
Photinus pyralis
Pimpinella anisum
Placopecten magellanicus
Pseudoperonospora
cubensis
Pteridium aquilinum
Pusa sibirica
Rafflesia arnoldii
Rangifer tarandus
Regalecus glesne
Rhizopus stolonifer
Rhizopus stolonifer
Sepia officinalis
Sequoia sempervirens
Solanum tuberosum
Sphenodon punctatus
Squalus acanthias
Strongylocentrotus
purpuratus
Struthio camelus
Sylvilagus audubonii
Tachyglossus aculeatus
Taphrina pruni
Tonicella lineata
Toxoplasma gondii
Toxoplasma gondii
Trichechus senegalensis
Trichoplax adhaerens
Ulva lactuca
Ulva lactuca
Ulva lactuca
Ursus arctos
Vespula pensylvanica
Vulpes zerda
Welwitschia mirabilis
Woodwardia areolata
Physeter macrocephalus
Phocoena phocaena Branta canadensis
Phytophthora ramorum
Medicago sativa
Stagmomantis carolina
Glycyrrhiza glabra
Helix aspersa
Cladosporium
cladosporioides
Cycas circinalis
Tremarctos ornatus
Scenedesmus dimorphus
Camelus ferus
Lepisosteus oculatus
Pilobolus crystallinus
Chinchilla chinchilla
Argonauta argo
Canis rufus
Dioscorea esculenta
Neoceratodus forsteri
Canis familiaris
Antedon mediterranea
Mellisuga helenae
Castor canadensis
Geogale aurita
Puccinia graminis
Cestum veneris
Euglena gracilis
Plasmodium falciparum
Odobenus rosmarus
Solenodon cubanus
Pyropia tenera
Palmaria palmata
Gelidium sesquipedale
Hypsibius dujardini
Callinectes sapidus
Bassariscus astutus
Tmesipteris elongata
Agave tequilana
Eschrichtius robustus
Eubalaena glacialis 8 119 Dioscorea mexicana 120
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122 Phyllostachys bambusoides
Brassica oleracea
Piper nigrum BIO 123, Spring 2017, version 2017-04-07 Grammatophyllum
speciosum
Juncus effusus
Helianthus annuus
Schinus molle Vanilla planifolia
Lamarckia aurea
Lactuca sativa
Capsicum chinense 9

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