BIS 2C Lab Practical

Basic anatomy of a phylogeny and data matrix: nodes

the most recent common ancestor of specified descendant organisms and/or species

Basic anatomy of a phylogeny and data matrix: roots

most recent common ancestry (MRCA)

Basic anatomy of a phylogeny and data matrix: taxa

any organism, or species, or group of species that we designate or name

Basic anatomy of a phylogeny and data matrix: sister taxa

two clades or species that are each other's closest relatives (the two descendant taxa of a single node)

Basic anatomy of a phylogeny and data matrix: characters

an observable feature/trait of an organism, either acquired or inherited

Basic anatomy of a phylogeny and data matrix: character states

versions of a characters- ex. Character = horns, character states = straight, curly, ...

Basic anatomy of a phylogeny and data matrix: polytomies

a section of a phylogeny in which the relationships cannot be fully resolved to dichotomies, thus presenting an unlikely picture of many apparently simultaneous temporally based branches.

Monophyletic

a group of organisms consisting of their most recent common ancestor (MRCA) and all its descendants

We try to make sure that when we name groups of species there are monophyletic...why?

1. Non-monophyletic groups are artificial groups

2. Non-monophyletic groups cannot be delimited by features that arose in a unique common ancestor

Paraphyletic

a group of organisms consisting of their MRCA but excluding some of its descendants

Homology

traits that are inherited from a common ancestor

Homoplasy

traits that are a result of convergent evolution

Phylogeny

a hypothesis of relationships among a set of taxa

How can relationships be tested in a phylogeny?

phylogenetic relationships= inferred from the similarities that are observed among species or populations (terminal taxa)

1. Apply codes to character states

2. Record character states for each terminal taxa with data matrix

3. Evaluate similarity between taxa and create a tree

4. Apply principle of parsimony for least amount of character changes

How to construct a simple data matrix?

1. Choose the taxa. You decide to study the major clades of vertebrates shown in the leftmost column of the table.

2. Determine the characters. After studying the vertebrates, you select a set of traits, which seem to be homologies, and build a data table to record your observations.

How to generate trees?

Build your tree following these rules:

1. All taxa go on the endpoints of the tree, never at nodes.

2. All nodes must have a list of synapomorphies, which are common to all taxa above the node (unless the character is later modified).

3. All synapomorphies appear on the tree only once unless the character state was derived separately by evolutionary parallelism.

How to decide among trees using parsimony?

Basic procedure for finding the most parsimonious trees:

1. Ignore parsimony-uninformative characters (for the moment).

2. Consider possible trees.

3. For each informative character count the minimum number of steps required on each tree.

4. Sum over all characters to get the "score" (number of steps) for each tree. Add the count for the parsimony-uninformative characters (which is the same for all trees).

5. The most parsimonious tree(s) is/are the one(s) with lowest score.

How to read, interpret, and root unrooted trees?

Unrooted tree: a tree in which the root has been removed and relationships among taxa are more ambiguous ; remove root & straighten branch; shows branch splitting events but says nothing about the temporal sequence of these events ; no direction

How to evaluate character conflict and congruence on a phylogeny?

Congruence - synapomorphy coupled with weight of evidence from other character data. --true synamorphies

Conflict - similarities which are not true synapomorphies may be due homoplasy (convergence, parallel evolution, or reversal) or symplesiomorphy (shared, ancestral similarity).

What are the causes of homoplasy? Provide examples from lab.

traits inherited from convergent evolution

Cladogram

only relative branching order shown, no meaning to branch lengths

Phylogram

branch length proportional to amount of character change; units of character divergence

Chronogram

branch length proportional to time; units of time

Unrooted Tree

does not show temporal sequence or direction

How does rooting a tree affect our interpretations?

Unrooted trees do not imply a known ancestral root- shows relationships among taxa due to character traits

Distinguish among the three domains of life; what is LUCA? What are the major characteristics of each of the domains?

last universal common ancestor

major characteristics of each of the domains?

Archaea:

Unicellular-Consists of only one cell. Prokaryotic-Cells which contain no nulcleus and lack internal complexity. (Hint: this domain is closest to bacteria)

Bacteria:

Unicellular-Consists of only one cell. Prokaryotic-Cells which have no nucleus and lack internal complexity.

Eukarya:

Unicellular and Multicellular-May consist of one or more cells. Eukaryotic-Cells which contain a nucleus and internal complexity.

What is LGT and why is it problematic for phylogeny reconstruction?

the transmission of genes between individual cells.

These mechanisms not only generate new gene assortments, they also help move genes throughout populations and from species to species.

There is no obvious line of descent and it interferes with the task of identifying earlier ancestors based on existing traits.

What are symbioses? Use examples from lab.

interaction between two different organisms living in close physical association, typically to the advantage of both--mutualism!

Rhizobium

Rhizobia and legume symbiosis - bacteria take N2 from the atmosphere and convert it into Nitrate/Nitrite, which the plant can take up into its proteins sugar from plant

Anabaena

Water fern Azolla and bacteria anabena - Anabena is a cyanobacteria meaning that it's metabolism is photosynthetic (green!) so doesn't need sugars from plant, plants gives shelter and bacteria gives N2

termite hindgut

Termite gut—Has (digestion of cellulose) bacteria, archaea, and (microbial) eukaryotes. Bacteria lives in the gut that can break down cellulose, allowing the termites to digest different food sources! Bacteria gets shelter and food supply

What is bioremediation? How are Arachaea and Bacteria used in the process?

the use of either naturally occurring or deliberately introduced microorganisms or other forms of life (like prokaryotes!!(bacteria and archaea)) to consume and break down environmental pollutants, in order to clean up a polluted site.

**To clean up oil spills, bacteria are introduced to the area of the spill where they break down the hydrocarbons of the oil into carbon dioxide; this is an example of bioremediation.

Why is metabolic diversity among microbes important in the context of bioremediation?

Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.

What are the basics of compound microscopy: microscope anatomy, function, slide preparation, and size estimation?

Microscopy: Estimating size?

Total magnification: multiply magnification of the eyepieces (10X) and the object (4X, 10X, 40X) so either 40X, 100X, or 400X

Look at organism and, considering field of view, estimate how many of them would fit across the field of vision?

How many fit across the field, find the field diameter, divide the size by the field diameter.

Explain the endosymbiotic theory.

explains how eukaryotic cells may have evolved from prokaryotic cells. Symbiosis is a close relationship between two different organisms. ... Later, a host cell engulfed a prokaryotic cell capable of photosynthesis.

What are the levels of symbiosis?

Mutualism: both partners benefit.

Commensalism: only one species benefits while the other is neither helped nor harmed.

Parasitism: One organism (the parasite) gains, while the other (the host) suffers.

Euglena

Teeny-tiny dots, closer up we see there is 1 flagella connected

Photosynthetic

Locomotion: zig-zag

Blepharisma

Medium sized pink ovals with cilia, not photosynthetic

Locomotion: quick, cilia

Paramecium

Medium sized ovals with lots of cilia not photosynthetic

Locomotion: slowed with slow solution but QUICK otherwise

Naeglaria

(Amoeba)

multi-nuclide

lots of little nuclei insides squiggle shape

green so it's photosynthetic

Locomotion: slow/stable, cytoplasmic streaming

Chlamydomonas

Teeny-tiny dots with two flagella attached, photosynthetic

Locomotion: cilia, strumming, jiggle

Stentor

Large cone shaped with lots of little hairs, photosynthetic

Locomotion: cilia, strumming

What are the microbes involved in termite gut endosymbiosis? To what domain do they belong?

The termite gut contains organisms from all three domains of life, Bacteria, Eukarya, and Archaea.

(1) There is a great diversity of microbes in the termite gut, many of which are unidentified because of the tiny size of termites and also due to the challenge of growing them outside of the termite gut. Additionally many of the bacterial species are exclusively found in termite guts.

(2) Termite digestion of lignocellulose is assisted by the microbes in their gut, and allows them to greatly contribute to the carbon cycle.

Coevolution

2 or more species having a close ecological relationship evolve together such that one species adapt to the changes of the other

Host Switching

organism cont to exploit the same resources, but in new hosts/environments. ecological fitting

Biologically explain the results of the Naegleria experiment.

can transition shape depending on environment

Alternation of generations life cycle

Bryophytes (mosses and liverworts): dominant generation is haploid so gametophyte comprises what we think of as the main plant.

Tracheophytes(vascular plants): diploid generation is dominant and the sporophyte comprises the main plant

2 life cycles or generations either being the sporophyte(meiosis) or the gametophyte(mitosis)

nonvascular plants (liverworts, mosses, hornworts)

-cuticles

-low growing

-rhizoids

-gametophytes

-specialized tissues for internal transport of water

-air dispersed spores

-antheridia & archegonia

seedless vascular plants

-branched sporophyte

-vascular tissue

-typical tracheids

-overtopping roots

-multiflagellate sperm

-chloroplast DNA inversion

gymnosperms

-cycads, gingko, gnetophytes, conifers

-secondary growth

-xylem & phloem

-pollen bifacial vascular cambium

-heterspory

angiosperms

-double fertilization, carpels, flowering

-monocots 3s, parallel veins

-dicots 4s and 5s, netted veins

Seven major land plant groups

1. liverworts

2. mosses

3. horwarts

4. lycophytes

5. monilophytes

6. gymnosperms-cycads, ginkgo, gnetophytes, conifers

7. angiosperms-flowering plants

Algal relatives of land plants, aspects of their growth and life cycles

contains rings of cellulose-synthesizing complexes. do not exhibit alteration of generation. no multi cellular sporophyte

phragmoplast(plant cell structure that forms during cytokinesis to form cell wall) method of cell division

Types of growth and trends of growth of plant phylogeny

3 Types of Apical Growth:

1. meristems-primary(tip) growth(height)

protoderm-outside of stem and develops into epidermis

2. procambium-inside protoderm and develops into primary xylem and poem, makes vascular and cork cambium. gives rise to pericycle-produces lateral roots in eudicots

3. ground meristem-develops into cortex and pith

Identify two basic types of leaves

megaphyll and microphyll

Origin of leaves

earliest vascular plants-simple, branched photosynthetic stems, allowed them to inc in size and area, cylindrical stem is not the most efficient shape for capturing the light needed for photosynthesis. branching systems reduced and flattened, asymmetric growth(overtopping). webbing of photosynthetic tissue developed between branches(megaphylls)

Leaves in different environments

hot-spikey, thick, short

moist/humid-thin, taller

lycopodium-microphylls, small

leafier-megaphylls, shorter, denser middle to obtain leftover sunlight

Monocots

flowering plants belonging to the class Liliopsida of angiosperms, one cotyledon in seed, endogenous growth

scattered vascular bundles

adventitous roots

leaves have parallel veins

Dicot

flowering plants

2 photosynthetic cotyledons in seed

taproot growth

x4 or x5

circular vascular bundles

secondary growth

taproot system

net like veins

What is the structure and function of the bifacial cambium?

produces secondary xylem and phloem

phloem grows outward

xylem grows inwards and allows plant to grow thicker to support tall heights

Gymnosperm life cycle

"naked" bare seeds, no flowers, haploid tissue, cones, wind dispersal for reproduction

Angiosperm life cycle

seeds normally enclosed in fruit, triploid tissue, flowers, animals for reproduction

Pollination syndromes of flowers

flower traits due to natural selection bc of diff. pollen vectors (wind, water, animal)

flower size, shape, color, nectar, flowering timing

Example: red flowers with lots of nectar attract birds, foul smelling flowers attract flies

Simple Fruit

1 fruit, 1 ovary, 1 flower (apple)

Aggregate Fruit

lots of ovaries, 1 flower (raspberries)

Multiple Fruit

lots of flowers formed together (pineapple)

Role of secondary metabolites in plants

chemical synthesized by plants are secondary to plant survival --- behind carbs, proteins, lipids, and nucleic acids

include toxic, bad smelling/tasting chemicals for plant survival

Interaction between plants and humans

Specific traits humans select for in plants:

cabbage - terminal buds

broccoli - stems/flowers

brussel sprouts - lateral buds

cauliflower - flower clusters

kale - leaves

epiphytes

grows harmlessly upon another plant, grows on another plant for support and does not negatively affect the host

Example: moss, liverwort, lichens, algae, seaweeds

biogeography

species more spread out around the world= older lineage, species located in an area= younger, due to continental drift isolation

stem modifications

stem has nodes

Example: rhizomes, bulbs, stolons, tubers

leaf modifications

Example: tendrils, spines, storage leaves, reproductive leaves, bracts

pollination syndromes

Example: red flowers with copious nectar often attract birds, foul smelling ones attract carrion flies or beetles

Roots

below ground, indeterminate growth can grow forever, no nodes but can produce new branches,

Stems

indeterminate growth, nodes!! = regions of meristematic tissue like joints where they can grow out more

Leaves

determinate growth (set size and stop), leaves are the same size for the same plants, no nodes

Ascomycetes vs. Basidiomycetes

hyphae typically haploid, fusion of haploid hyphae & nuclei at same time = diploid cell, 8 ascospores

Basidiomycetes

4 basidiospores

Lichens and their associated symbionts

made up of a fungus and a photosynthetic partner

7 Phyla of Metazoa

porferia

cnidaria

echinodermata

arthropoda

annelida

mollusca

chordata

Key characters of: porferia

monoblastic

irregular cleavage

assymetrical

no gut

filter feeder

choanocytes & spicules

sponges!!

Key characters of: cnidaria

diploblastic

irregular cleavage

radial symmetry

incomplete gut

suspension & predator

Key characters of: echinodermata

triploblastic

radial regulative

mosaic cleavage

pentaradial

complete, one-way gut

predator, scavenger, grazer

suspension, deposit

no head/brain

water vascular system!

tube feet & spines

Key characters of: annelida

Annalids = segmented, looks like a worm

Annalids = worm with a tunic outside, segmented

triploblastic

spiral mosaic

bilateral

complete, 1 way gut

deposit

spaghetti worm, rag worm, feather duster

segemented body!!, paired setea, filter feeding

Key characters of: mollusca

triploblastic

spiral mosaic

bilateral

complete, 1 way gut

suspension feeder, grazer, predator

specialized muscular foot for locomotion radula w/ shell

sea hair

Key characters of: chordata

triploblastic

radial regulative

bilateral

complete, 1 way gut

suspension feeder

notochord(rod that runs along embryo, adds support)

Key characters of: anthropoda

ECHDYSIS

barnacles

triploblastic

spiral mosaic

complete, 1 way gut

scavenger, grazer

suspension predator

segmented body!!

jointed appendages!!

exoskeleton made of chitin

fluorescence under uv light

Developmental sequence of metazoan

zygote

2c

4c

radial

spiral cleavage--> blastula

Main features of earthworm anatomy

Pharynx - muscular thing to suck in soil w/ food

Prostomium/Crop - upper lip pushes food into mouth

Seminal receptacles - stores sperms from another worm

Hearts - pumps blood, segmented (5)

Seminal vesicles- store sperms

Gizzard - muscular organ where food goes/grinds up

Clittellum - swollen vessicle to hold eggs

Transitions from water to lands

dessication issues

loss of H2O

change from permeable membranes to less so

land animals add wax coatings to reduce water loss

modified behavior: surface to breathe, coming up to the surface

modified morphology: blowholes, bradycardia, breathing thru skin

Symbiosis

dinoflagellate algae living in Anemones & corals provide carbon based products of photosynthesis --> receive protection & N2 in return

gut protists living inside guts of termites break down the cellulose consumed by termites & produce acetate used as energy & carbon source by host termite

Pollination

bees - pollinate brightly covered plants but cannot see the color red

hummingbirds - like to pollinate unscented flowers

moths -- white plants/smelly plants at night

Pollination shift

plant evolves to pollinator --> leads to irreversible speciation

example: hummingbirds and flowers

Coevolution

plants and flowers evolve with each other, may be reversible, leads to specialization

Morphological adaptations

spines evolved as an antipredator defence through convergent evolution

Limb loss

not homologous trait in lizards

in tree lab, showed leglessness evolved 9 times & according to habitat

easier motion in H2O

ability to burrow

Advantages:

1. locomotion

2. utilize crevices

3. burrow

4. reproduction

ancestor snakes are fully 4 limbed but evolution reduced to stubs

Homoplasy and convergence

external morphology may not indicate the best evolutionary relationship due to convergent evolution/homoplasy

Morphology stasis

unchanging environments cause evolutionary stasis in diff. species

Horseshoe crabs being living fossils and what would that look like? Ancestral looks similar to modern, over time there was super strong stabilizing selection!

example: sharks, ray, chimeras

Body modification and character polarity

evolution in body form in sessile organisms depends on availability of food sources in environment

trades offs = food gathering, competition, predation

barnacles ancestral form is stalk squat form to hold tight to surfaces, thin stalk form allows for farther reach for food

Diversity within mollusca

Gastropoda: snails, slugs

Chitons: marine grazers

Bivalves: clames and muscles

Cephalopods: squid shells for protection

All molluscs have some sort of shell & muscle!