Biodiversity Lab
DOMAIN BACTERIA
Bacteria are incredibly diverse, but they’re usually really tiny and hard to see, even under a standard
microscope.
On an agar plate, bacteria have the nutrients to divide quickly, eventually leading to clusters of
rapidly dividing cells, or colonies, that are visible to the naked eye. Cyanobacteria, were the only lineage of
organisms to evolve the complicated process of photosynthesis from scratch and, in doing so, oxygenated
the Earth’s atmosphere paving the way for the evolution of Eukaryotes. Some Cyanobacteria, such as
Nostoc and Anabaena, adhere to one another as they divide and form colonies that look like multicellular
“algae” to the naked eye, thus leading to the common name “blue-green algae”. In low nitrogen
environments, some of the cells in the colony will even change function to become anatomically different cells
specialized for nitrogen fixation, which benefits the entire colony. Some other types of Cyanobacteria are
responsible for algal blooms that release toxins and gases that can be fatal to mammals such as dogs and
humans.
DOMAIN ARCHAEA
Archaea are mostly tiny and hard to see, like bacteria. Most are also extraordinarily difficult to cultivate due to
their extremophile lifestyles- thriving in extreme conditions that other organisms can’t tolerate. While we can’t
replicate an anoxic or deep sea environment in the lab, we can replicate an extremely salty environment that
halophilic Archaea such as Halobacterium prefer but which is toxic to nearly all other forms of life.
Many colors of life from left to right: 1. Anabaena, a photosynthetic blue-green alga (Domain Bacteria); 2. Halobacterium, a halophilic
Archaea; 3. Acrochaetium, a multicellular red alga (Archaeplastida); 4. Chlamydomonas, a single-celled, free swimming Chlorophyte
green alga (Archaeplastida); 5. Ectocarpus, a brown alga (Stramenopiles, S.A.R. clade)
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Eukaryotes
EUKARYOTE SUPERGROUPS
The best evidence from DNA sequences supports 4 major lineages within domain Eukarya; Excavata, S.A.R.
Clade, Archaeplastida, and Unikonta.
Excavata:
-Euglena is a flagellated, photosynthetic Excavata that acquired its chloroplasts by endosymbiosis of a
unicellular green alga (see Archaeplastida). They can move surprisingly fast, as you can see in this video:
Other lineages in Excavata cannot photosynthesize and must consume their food as existing organic matter.
Some even use humans as food, such as the brain-eating amoeba Naegleria fowleri and the organisms that
cause the diseases African Sleeping Sickness and Chagas.
S.A.R. Clade:
Stramenopiles:
– Diatoms produce cases made of silicon; they are photosynthetic and are important at the base of the food
chain in both freshwater and saltwater aquatic environments. Brown algae are also in this group, ranging
from single-celled to colonial to filamentous mulicellular organisms all the way to huge kelp almost 200 ft long.
Brown algae are large, multicellular Stramenopiles (S.A.R.)
Alveolates:
-Paramecium is a heterotrophic (=must feed on organic matter) ciliate that lacks chloroplasts and uses small
hair-like cilia to move around with amazing speed and agility for a single-celled organism as shown in this
video: https://youtu.be/mFSIUuT0EgM
-Dinoflagellates are photosynthetic flagellates that in high density cause toxic “red tides”. Some are also
bioluminescent when agitated, as you can see in this video: https://youtu.be/5MiUxopM5VM
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Node #4, Stramenopiles+Alveolates, is often referred to as the group Chromalveolata, the ancestor of which
likely picked up photosynthetic plastids by engulfing a unicellular Red Alga (see Archaeplastida).
Rhizaria:
-Foraminiferans most often make shells of Calcium Carbonate. Rhizaria extend long pseudopods out of
these shells to gather food. One lineage of Rhizaria is photosynthetic by way of chloroplasts acquired
through endosymbiosis of a unicellular green alga (Archaeplastida).
Archaeplastida:
Includes Red Algae, Green Algae, and plants; all red algae, green algae, and plants descended from a
common unicellular ancestor at node 5 that engulfed a photosynthetic Cyanobacterium which became the
earliest plastids in eukaryotes.
Embryophytes:
(nonvascular)
-Liverworts and Mosses spend the majority of their life cycle as haploid gametophyte plants that produce
sperm and egg, with a short-lived diploid sporophyte life stage that produces and disperses spores
The diploid sporophytes of mosses (left) often look like upside-down golf clubs, but the main body
of the plant is haploid. In hemisphaeric liverwort (center), the diploid sporophyte
generation only exists as short-lived, round yellow globes that produce spores (right)
(vascular spore plants)
-Lycophytes and Ferns still reproduce by spores like nonvascular plants and algae, but in vascular plants the
diploid sporophyte life stage grows large and the haploid, gametophyte stage of the life cycle is usually
small and short-lived
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Spikemosses (left) are diploid and produce spores. Ferns usually produce spores under their leaves (center). On the right, a dark green,
haploid fern gametophyte will soon be overgrown by the light green diploid sporophyte producing its first leaf.
(seed plants- Gymnosperms)
-Cycads are often called Sago Palms, although real palm trees are angiosperms that flower and fruit.
-Ginkgo is represented by a single modern species; 270 million year-old fossils look identical (stasis).
-Conifers are the largest group of living gymnosperms; most are needle-bearing evergreens.
-Gnetophytes: Welwitschia mirabilis is a Namib Desert plant that only makes two continuously-growing
leaves throughout its life
Representatives of the 4 extant Gymnosperm lineages
(seed plants-Angiosperms)
-Amborella trichopoda: All other 250,000+ species of flowering plant are more closely related to each other
than they are to this woody shrub from the south pacific island of New Caledonia.
-Monocots usually produce flower parts in 3’s or multiples thereof and parallel-veined leaves. Orchids are the
largest family of monocots with over 25,000 species, and grasses are another huge family that provides most
calories consumed by the human population (sugarcane, corn, wheat, oats, barley, rice, etc.)
-Eudicots: Usually flower parts in 4s and 5s, net-veined leaves. The Sunflower family is the largest family of
eudicots (and flowering plants overall) with more than 30,000 species. The “flowers” of members of the
sunflower family are actually aggregations of up to hundreds of flowers.
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Amborella (left); representative eudicot and monocot flowers and fruits (right)
Unikonta:
The first major division in Unikonta (node 6) separates Amoebozoans from Opisthokonts.
-Amoebozoans: Chaos carolinensis is a large amoeba that changes cell shape to extend pseudopods and
engulf potential food particles for internal digestion as seen in this video: https://youtu.be/zgtWbJ2wSeg
Fungi: Fungi range from unicellular (yeasts) to huge multicellular organisms, most of which grow as long,
filamentous strands of cells known as hyphae. Masses of hyphae that are visible macroscopically are known
as a mycelium.
-Lichens: Lichens are actually a symbiotic relationship between two different supergroups: fungal hyphae
(Unikonta) and a unicellular photosynthetic organism, usually a green alga (Archaeplastida). The hyphae
farm the green alga as a carbon source while providing inorganic nutrients to the alga by slowly breaking
down rock, bark, mineral soil, and other substrates.
(left) Lichens can be found growing on bark, rocks, or bare ground; even though they are given scientific names, they are really an
ecosystem of multiple organisms living together closely. (right) Giant puffball mushroom growing in lawn grass.
-Mushrooms: Most mushrooms form from a dikaryotic mycelium; the hyphae forming the mycelium originate
from fusion of hyphae from two haploid individuals. After these fuse, each cell of the dikaryotic mycelium
contain two separate haploid nuclei and grow into a fruiting body. In surfaces that generate spores, individual
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cells will fuse the haploid nuclei into a zygote where recombination can occur. The zygote then undergoes
meiosis to generate haploid spores that can disperse to grow haploid hyphae with new genetic combinations
of both parents.
-Molds are mycelia with filamentous hyphae that invade their substrate and secrete digestive enzymes to
break down the substrate before absorbing small molecules.
Animals: Animal phylogeny and diversity is mapped on its own tree. Keep in mind that the closest relative of
animals in Unikonta are single-celled Choanoflagellates, and the closest relatives of fungi are single-celled
Nucleariids. Thus, animals and fungi evolved multicellularity independently from one another.
Animal lineages represented in the tree are listed below:
Phylum Porifera: Sponges
Phylum Cnidaria: Jellyfish, Hydra, Corals, etc.
Deuterostomes:
Phylum Hemichordata: Acorn Worms
Phylum Echinodermata: Sea Stars, Sea Cucumbers, Sea Urchins
Phylum Chordata:
Cephalochordata: Lancelets/Amphioxus
Tunicata: Tunicates, Sea Squirts
Cyclostomes: Jawless Fish (Hagfish, Lamprey)
Chondrichthyes: Cartillaginous Fish (Sharks, Rays)
Actinopterygii: Ray-finned Fish, the most diverse lineage of vertebrates
Dipnoi: Lungfish
Amphibia: Caecilians, Salamanders, Frog & Toads
Reptilia: Turtles, Lizards, Snakes, Crocodilians, Birds
Mammalia: Mammals
Lophotrochozoa:
Phylum Platyhelminthes: Flatworms
Phylum Mollusca: Clams, Oysters (bivalves), Snails, Slugs (gastropods), Octopus, Squid (Cephalopods)
Phylum Annelida: Segmented Worms
Ecdysozoa:
Phylum Nematoda: Roundworms
Phylum Arthropoda:
Subphylum Chelicerata: Horseshoe Crabs, Ticks, Mites, Spiders, Scorpions
Subphylum Myriapoda: Centipedes, Millipedes
Subphylum Crustacea: Crabs, Shrimp, Pillbugs, Barnacles, etc.
Subphylum Hexapoda, Class Insecta: Insects (well over half of all described animal species)
(left) Insects like this Pipevine Swallowtail make up more than half of all named animal species. Ray-finned fish, like the Etowah Darter
(center) are the most diverse lineage of vertebrates. Birds, including Burrowing Owls (right), are the most diverse land vertebrate lineage.
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QUESTIONS
Use the phylogenetic trees at the end of this pdf to answer the following questions. Clicking on the lineages
on the phylogenetic trees will take you to the Wikipedia entry for that group.
1. Which node in the 3-domain supertree (the first tree) represents the common ancestor of eukaryotes and
Archaea? Which node in the 3-domain tree represents the common ancestor of all Eukaryotes? What are
some characteristics that would have been present in the common ancestor of all eukaryotes? Think about
characteristics that are shared between your cells and the cells of all these other groups (2 pts).
2. List all of the acquisitions of photosynthetic found in eukaryotes below (give either the numbered node
where it evolved or the name of the lineage in which it occurred) (2 pts).
3. Unikonta don’t have any true chloroplasts or photosynthetic lineages, but describe the similarities and
differences between Lichens and chloroplast-containing eukaryote lineages. (1 pt)
4. Identify the node in the Archaeplastida phylogeny where the diploid sporophyte generation became the
dominant stage in the life cycle (1 pt).
5. Identify the node in the Archaeplastida phylogeny where land plants evolved. (1 pt)
6. Which node represents the most recent common ancestor of Seed Plants? (1 pt)
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7. Which node represents the most recent common ancestor of Gymnosperms. Conifers are, by far, the
most species-rich lineage of modern Gymnosperms; do you think the most recent common ancestor of seed
plants would have had needles like a pine tree or broad leaves more like most angiosperms? (2 pts)
8. Which node is the most recent common ancestor of Angiosperms (flowering plants)? These are now the
most species-rich lineage of embryophytes by far with approximately 350,000 species. Most of these species
(including all monocots) are herbaceous, meaning they don’t form a woody trunk with internal vascular rings
or bark Amborella trichopoda is a shrub from New Caledonia that represents the basal branch of
Angiosperms (i.e. all other flowering plants are more closely related to each other than they are to
Amborella). Do you think the ancestor of angiosperms was woody or herbaceous? What about the ancestor
of all seed plants? (hint: Amborella, Ginkgo, all conifers, Gnetophytes, and Cycads have woody “trunks”)? (2
pts)
9. Sponges have specialized individual cells but lack true tissue (masses of coordinated cells, like muscle,
nerve, etc.). At what node in the animal phylogeny did true tissues evolve? (1 pt)
10. At what node in the animal phylogeny did bilateral symmetry evolve (hint: sponges and cnidarians aren’t
bilaterally symmetric, but every other organism on the animal tree technically is)? Bilaterally symmetric
animals have a left and right side, as well as a dorsal and ventral side. Based on the organisms on this tree,
what do you think this bilateral common ancestor may have looked like? (2 pts)
11. You have two forelimbs (arms) and two hindlimbs (legs). At which node in the phylogeny did these paired
appendages evolve? Are there any instances of convergent evolution of paired appendages? Are there any
instances of losses of paired appendages? Give the examples, if they exist (2 pts).
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12. Identify the node in the phylogeny where your ancestor first colonized land (hint: this is also the common
ancestor of organisms with fingers and toes). Give an example of a descendant from that ancestor that has
gone back to living a fully aquatic lifestyle. List any other examples of animal lineages that appear to have
colonized land independently of your ancestor (2 pts).
13. Are fish (i.e. jawless fish, cartilaginous fish, ray-finned fish, and lungfish) monophyletic? i.e. Do they trace
back to a single common ancestor, and are all descendants of that most recent ancestor considered fish? (1
pt).
14. Chambered Nautilus is the first-branching lineage of Cephalopods. Do you think Octopuses/Octopi
evolved from a shelled ancestor? Explain why or why not (1 pt).
15. List all of your ancestors (list of node numbers) from both the animal tree and the 3-domain tree. (2 pts).
16. Go outside and take photographs of 4 different organisms, each representing a different terminal group
on the tree. Identify where they belong on the tree and submit photographs. A maximum of 2 animals or 2
plants are allowed, and at least one of your selections must be something other than an animal or plant. (2
pts)
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