Bio 94 Midterm 3

Deep homology

homologies shared from a. very late ancestor

Q: How many animals exist on our planet today? How many have been described?

3 million to 10 million, 1.4 million species

Q: What type of eukaryotes did we originate from?

we originated from single cell eukaryotes

Q: What lineage are animals from? What does the linkage include?

Animals are from the Opisthokonta lineage that includes fungi, choanoflagellates, and animals

Q: What group are animals most closely related to?

Choanoflagellates are closest living relatives to animals, share common ancestor 900 million years ago

Q: What key traits do all animals have?

1) multicellular 2) cells lack cell walls but have extracellular matrix (ECM- proteins specialized for cell-cell adhesion and communication) 3) heterotrophs (obtain carbon compounds from other organisms) 4) all move under their own power 5) All animals other than sponges have neurons and muscle cells

What type of groups are animals? What is one synapomorphy that is in their common ancestor?

monophyletic group, multicellular

Q: What types of data is used to understand animal evolutionary relationships?

1) fossils - show direct evidence of what ancient animals looked like, when they existed, and where they lived 2) comparative morphology - provides information of morphological characteristics that can define the fundamental architecture or body plan of each animal lineage (can show which characteristics arose first and which animal groups are more closely related) 3) Comparative development - provides info on patterns of gene expression and morphological change during development 4) Comparative genomics - information about the similarity of genes or whole genomes

Q: What is the sponge-first hypothesis? What is the evidence that supports this hypothesis?

A: the hypothesis that sponges are the most ancient lineages of animalsA: Fossil Evidence: They were the earliest animals to appear in the fossil record (700 mya), multicellular sponges existed in fossil record before other multicellular organisms

A: Morphological Evidence: sponges share several key characteristics with choanoflagellates

● Both are benthic - live at the bottom of aquatic environments and sessile - adults like

permanently attached than moving freely

● Both feed in a similar way using nearly identical morphology (both have flagella..

Specialized cells to digest food particles..) feeding occurs at cellular level

● Choanoflagelltes form colonies (groups of attached individuals), sponges were once

colonies of single-cell protist

○ Now: sponges contain many specialized cell types that are dependent on each

other and are surrounded by ECM

A: Molecular Evidence: sponges contain a complex set of developmental tool-kit genes necessary for basic molecular processes required by multicellular animals:

● Specialization of cell types

● Regulation of cell cycling and growth

● Adhesion among cells

● Adhesion between cells and the ECM

● Recognition of self/nonself = innate immunity

● Developmental signaling and gene regulation

● Some have true epithelium = layer of cells that cover interior and exterior surface of

animal, which is necessary for animal form and function

Q: What do sponges lack that makes them differ from most multicellular animals?

A: complex tissues - groups of similar cells that are organized into tightly integrated structural and functional units

Diploblasts

animals whose embryos have two types of tissues, or germ layers (ectoderm and endoderm)

Triploblasts

animals whose embryos have three germ layers (ectoderm, mesoderm, endoderm)

Ectoderm

skin and nervous system

Endoderm

lining of digestive tract and organs, respiratory system

Mesoderm

rise to circulatory system, muscles, and internal structures (bones and most organs)

Q: What is deep homology?

A: when growth and differentiation processes are governed by the same genes and processes amongst almost all species

Q: What processes/genes do diplo and triploblastic share amongst themselves (deep homology)?

A: mesoderm-like cells in mesoglea, genes coding for structural components of mesodermal cells, some can change the shape of their bodies, actin and myosin

Q: What processes/genes do diplo and triploblastic differ in (convergent evolution)?

mesodermal specification genes, well defined mesoderm, true muscles

how is functional symmetry achieved

convergent evolution with deep homology

what is body symmetry

A: a key morphological aspect of an animal's body plan. A body is symmetrical if it can be divided by a plane so the resulting pieces are identical

Q: What is radial symmetry? What are some examples of organisms that have radial symmetry?

Having at least two planes of symmetryA: Cnidarians, Ctenophores, some spongesA: however, internal morphology of some species can actually be bilaterally symmetric (EX: sea anemone)

Q: What is bilateral symmetry? What group are bilaterally symmetric? Where does the symmetry in bilaterians result from?

A: Only one plane of symmetry and tend to have a long, narrow bodyA: triploblasts

A: Hox genes - regulate development of anterior-posterior axis, decapentaplegic (dpp) genes - regulate development of the dorsal-ventral axis

Q: What is a coelom? What is its function?

a fluid-filled cavity associated with mesodermally derived tissues in bilateriansA: Provides space for the circulation of oxygen and nutrients + enables internal organs to move independently of inner and outer tubes

Q: What are coelomates, acoelomates, and pseudocoelomates? Draw picture?

A: Bilaterians whose coelom is completely lined with mesoderm derived tissue (aka true coelom)

B: Bilaterians that have no coelom (EX: flatworms)Bilaterians whose coelom is only partially lined with mesoderm derived tissues (EX: roundworms)

Q: What are phylogenetic data that support the evolution of coelomates?

A: morphological data - predicted gradual evolution from simple acoelomates to pseudo to coelomatesA: molecular data - coelom arose in ancestral bilaterian and was modified, reduced, or lost in many lineages. Evolutionary flexibility of coelom only used as a diagnostic synapomorphy for bilaterian animals (don't have purpose)

Q: What major groups occur within the bilaterian acoelomates?

A: protostomes (first mouth) - embryonic development of mouth before anusA: deuterostomes (second mouth) - embryonic development of anus before mouth

Q: Describe the process of gastrulation.

A: gastrulation - embryonic germ cells form

A: 1) cells move from surface into interior of embryo 2) creates pore that opens to outside (blastopore)in deuterostomes, blastopore become anus and mouth forms later

Q: What are the differing views about the blastopore in protostomes?

Traditional view - protostomes - blastopore becomes mouth and anus forms later

Recent view - development is highly variable in protostomes

Q: What is segmentation? What are examples of segmentation?

A: Division of body or part of body into series of similar structures EX: segmented backbone in vertebrates, segmented bodies in annelids (worms) and arthropods (insects and spiders)

A: Segmentation enables specialization - small changes in expression of toolkit genes can lead to novel body segments, shapes, etc

- Natural selection favor these variations which leads to diversification

Q: Did segmentation arise by convergent evolution or is it homologous?

A: evidence support homology - some tool-kit genes for segmentation arose early in animal evolution and they are homologous in different phyla

A: evidence supporting convergent evolution - some toolkit genes were lost in some lineages and used in different ways, which led to convergent evolution of morphological segmentation in distantly related phyla

Q: How do biologists study the feeding of individuals?

A: distinguish what individuals eat and how they eat

A: animals within same lineage might have different food sources/feeding strategies if niche differs

A: animals from different lineages with similar niches may pursue same food source/feeding

Q: How do ecological roles affect what animals eat?

A: Detritivores - feed on dead organic matter

B: Carnivores - feed on animals

C: Herbivores - feed on plants or algae

D: Omnivores - feed on a combination of plants, animals, fungi, protists, archaea, bacteria

Q: What is Parasitism? What are two forms of parasites?

A: harvesting nutrients from parts of their host

A: endoparasites - live inside hosts and have simple wormlike bodies

A: ectoparasites - live outside hots and have limbs or mouthparts that allow them to grasp onto host

Q: How do animals eat?

A: Suspension feeders - capture food by filtering out particles floating in water or drifting through air

B: fluid feeders - suck or mop up liquids like nectar, plant sap, blood or fruit juice

C: Deposit feeders - ingest organic material that have been deposited within a substrate or on its surface

D: mass feeders - take chunks of food into their mouths

Q: What is cephalization?

-concentration of sensory organs in head region, great deal of diversity of sensory abilities + structures among animals

-sight hearing taste smell touch temperature

What characteristics are shared between diploblastic and triploblastic?

A: both have mesoderm like cells in mesoglea, gene coding for structural components of mesoderm, some can change the shape of their bodies, both have actin and myosin

What characteristics of the mesoderm are missing in the diploblast?

A: mesodermal specification genes, well-defined mesoderm, true muscles

What is body symmetry?

A: key morphological aspects of animal's body plan

What is radial symmetry?

Radial symmetry - multiple rotations will give you the same shape (starfish)

What is bilateral symmetry? What blasts are bilaterally symmetric?

-single plane of symmetry and long, narrow bodies

-all triploblasts are bilaterally symmetric

What are bilaterians?

-triploblastic, bilaterally symmetric animals

How is the body symmetry associated with the nervous system?

-function of neurons

-nerve net (radially symmetric)

-central nervous system (bilaterians)

What is cephalization?

-cephalization - evolution of head where structures for feeding, sensing environment, and processing information are concentration

What is a tube-within-a-tube body plan?

A body shape of bilaterian which

-outer tube = forms nervous system and skin

-inner tube - gut with a mouth on one end and an anus at the other

-mesoderm - muscles and organs

Describe the origin of the coelom

Coelom is a enclosed, fluid filled body cavity between the tubes (IN mesoderm)

- Space for oxygen and nutrients to circulate

- Enables internal organs to move independently from each other

True coelomates - coelom is completely lined with mesoderm (with cavity)

Acoelomates - no cavity in the mesoderm (EX: flatworms)

Pseudocoelomates - coelom is only partially lined with mesoderm tissue

What are 2 major subgroups of early embryonic development?

Protostomes, deuterostomes

What are synapomorphies of the two major subgroups?

Bilateral symmetry, triploblasty, cephalization, coelom = all synapomorphies of bilateral protostomes (mouth first) and deuterostomes (anus first)

What is segmentation?

The division of body or part of body into series of similar structures

-alot of the genes for segmentation is shared amongst organisms

-segmentation allows organs to have a common set of instructions and later gives more specific information for development of specific organs

Fungi are

decomposes and symbionts, which are types of heterotrophs, frequently mutualistic symbiosis

There are

110,000 species of fungi that have been described and named - hundreds more are discovered each year

As many as

6 million species of fungi may be found worldwide. in one study, over 650 fungal species were found in guts of 27 species. 200 of these species had never been described.

Fungal mutualisms are very important for plants to

obtain nutrients and protect plants from herbivores

Animals also participate in

fungal mutualisms. guts and gardens. fungi is important in nutrient cycling too

Why do people care about fungi?

disease, essential for crop growth, important in crop spoilage, food source, antibiotics, bread, bear, cheese, soy sauce, wine, chocolate, and industrial enzymes

Fungi are more closely related to animals than to land plants

fungal infections in humans are more difficult to treat than bacterial infections ——- recent shared ancestry results in similar cellular and molecular structures and drugs that disrupt fungal physiology are likely to damage humans

Key traits linking animals and fungi:

DNA sequence data, both animals and fungi synthesize chitin, flagella in chytrid spores and gametes are similar to animal flagella, and animals and fungi store glucose as the polysaccharide glycogen

Single-called, parasitic eukaryotes called microsporidians are fungi

not a distantly related sister group to fungi. hypothesis: fungicides (substances that can kill fungi or slow their growth) can cure microsporidian infections in bee colonies, silkworm colonies, and AIDS patients

Chytrid spores and zygomycetes are poorly resolved

polytomy on phylogenetic tree, swimming gametes and zygosporangium evolved more than once, both were present in a common ancestor but lost in certain lineages

Glomeromycota is monophyletic

Adaptations that allow these species to live with plant roots as mycorrhizae evolved once

Basidiomycetes are monophyletic (Basidiomycota, or club fungi):

The basidium evolved once

Ascomycetes are monophyletic (Ascomycota, or sac fungi):

The ascus evolved once

Basidiomycota and Ascomycota form a monophyletic group:

Both form septate hyphae and large "fruiting" structures; this growth habit evolved once

Sister group to fungi comprises animals plus choanoflagellates:

Hypothesis: Earliest fungi were aquatic, and the switch to terrestrial life

occurred early in evolution of fungi

Fungi have very simple bodies. Two growth forms exist

single called forms (yeast) and multicellular, filamentous forms (mycelia) ——— some species adopt both forms

Because mycelia are made of branching networks of very thin hyphae:

fungi have the highest surface-area-to-volume ratio of all multicellular organisms —- nutrient absorption is extremely efficient

Fungi are

prone to drying out - thus most abundant in moist environments, reproductive spores are resistant to drying out, and spores can endure dry periods and then germinate

The Nature of the Fungal Mycelium

All mycelia are dynamic:

- They constantly grow in the direction of food sources and die back in areas where food is running out

The body shape of a fungus can change almost continuously throughout its life

Panel 1) Both the reproductive structure and mycelium are composed of hyphae.

Reproductive Structures of Fungi

• Mycelia are an adaptation that supports external digestion and the absorptive lifestyle of fungi

• Fungi also produce dense, fleshy reproductive structures

• Many species do not reproduce sexually:

- In those lineages, important morphological differences are seen

Panel 2) Most hyphae are divided into compartments by septa.

The Nature of Hyphae

Hyphae are the long, narrow filaments of mycelium

Filaments are divided into cells by septa (cross-walls):

- Pores allow materials to flow between compartments

Coenocytic hyphae consist of multinucleate cells

Some fungi are coenocytic, meaning they lack septa:

- Many nuclei are scattered throughout the mycelium

- Nutrients can move rapidly through septa pores or through coenocytic fungi from uptake to growth areas

Key stages of the chytrid life cycle

1. Haploid adults form gametangia:

- Mitosis produces male and female swimming gametes

2. Gametes fuse to form a diploid zygote

3. The zygote grows into a diploid sporophyte

4. Haploid spores, which disperse by swimming, are produced by meiosis inside the sporophyte's sporangium

- Sexually produced gametes and asexually produced spores of chytrids have flagella. The only known motile fungal cells

Zygomycetes

• Sexual reproduction starts when hyphae from different mating types fuse

• Plasmogamy forms a spore-forming zygosporangium that develops a tough, resistant coat

• Inside the zygosporangium, nuclei from the mating partners fuse—meaning that karyogamy occurs

• Mycelia can also reproduce asexually by making sporangia, which produce haploid spores by mitosis:

• The spores are then dispersed by the wind

Zygosporangia

• Distinctive spore-producing structures of zygomycetes

• Formed from fusion of cells from joined-together haploid hyphae from two individuals

Basidiomycetes

• Mushrooms are sexual reproductive structures produced by basidiomycetes

• All basidiomycete reproductive structures originate from the dikaryotic hyphae of mated individuals:

- The club-like, spore-producing cells, called basidia, form at the ends of dikaryotic hyphae

- Karyogamy occurs within the basidia

Basidia

• Basidiomycetes or "club fungi" form basidia, specialized club-like cells at the ends of hyphae

• Each basidium produces four spores

Ascomycetes

• Hyphae or specialized structures from different mating types fuse:

- Forms a heterokaryotic cell with many nuclei

• Short dikaryotic hypha with cells containing two nuclei emerges:

- Grows into reproductive structure with asci at tips

• After karyogamy, meiosis and one round of mitosis result in production of eight haploid spores

• When the ascus matures, the spores inside are forcibly ejected

Asci

• Ascomycetes, or "sac fungi," form asci, reproductive sac-like cells at the ends of hyphae

• Each ascus produces eight spores

All fungi

absorb food from their surroundings. evolution of novel methods for absorbing nutrients from a wide array of food sources drove the diversification of fungi

The first plants in the fossil record are closely associated with fungal fossils:

- The ability to absorb nutrients from fungi may have been crucial in the early evolution of land plants

Fungi and land plants

often have a symbiotic relationship ("together-living")

Mutualistic symbiosis

relationships benefit both species

Parasitic relationships

one species benefits at the expense of the other

Commensalism relationships

benefit one species while the other is unaffected

Ectomycorrhizal Fungi (EMF)

• Found on many tree species in temperate regions

• Form a dense network of hyphae that cover plant roots and extend into the soil but do not enter the root cells

• Ectomycorrhizal Fungi (EMF)

• EMF hyphae penetrate decaying material and release peptidases:

- Peptidases cleave proteins, releasing amino acids that the hyphae

transport to spaces between the plant root cells:

▪ The plant can now absorb the amino acids

- EMF also provide phosphate ions to the host plant:

▪ In return, the EMF receive sugars

Arbuscular Mycorrhizal Fungi (AMF)

• Hyphae grow into the cells of root tissue:

- Also called endomycorrhizal fungi because they grow inside root cell walls

• Hyphae inside the plant cell wall are an adaptation that increases surface area for exchange of molecules between fungus and host

• Hyphae form a pipeline extending from inside plant roots into the soil well beyond the root

Endophytes

• Endophytes ("inside-plants")—organisms that live between and within plant cells

• Live in close association with roots or aboveground tissues of land plants

• Unknown before the 1940s but extremely common and highly diverse:

- Some increase drought tolerance of their host plants

- Some produce compounds that benefit plants by deterring or killing herbivores

- Receive benefits by absorbing sugars from plants

What Adaptations Make Fungi Such Effective Decomposers?

• Given enough time, fungi can turn even the hardest, most massive trees into soft soils

• Large surface area of a mycelium makes nutrient absorption exceptionally efficient

• Saprophytic fungi can grow toward the dead tissues that supply their food

Extracellular Digestion

• Fungi must digest their food before they can absorb it

• Fungi thus perform extracellular digestion:

- Digestion that takes place outside the organism

- Simple compounds resulting from enzymatic action are absorbed by hyphae

- The two most abundant organic molecules on Earth

are digested by fungi:

▪ Lignin—in plant secondary cell walls

▪ Cellulose—in plant primary and secondary cell walls

Saprophytes

• Fungi that digest dead plant material

• Saprophytes help cycle carbons through terrestrial systems

• The carbon cycle on land has two basic components:

• Fixation of carbon by land plants

• Release of CO2 from cellular respiration

• For many carbon atoms, saprophytic fungi connect the two components

• Fungi Speed Up the Carbon Cycle as They Break Down Dead Trees in Terrestrial Ecosystem

Fungi Speed Up the Carbon Cycle as They Break Down Dead Trees inTerrestrial Ecosystems

Lignin and cellulose are hard for most organisms to use. Without fungi, a lot of carbon would be locked away in dead plant matter.

Lignin Degradation

• Saprophytic fungi use lignin peroxidase to break down lignin and expose cellulose that can fuel growth and reproduction

• Fungi can't live on lignin alone

Cellulose Degradation

• Fungi secrete cellulases into the extracellular environment

• Cellulases convert cellulose into glucose that the fungus can absorb and use as a source of food

Fungi Speed Up the Carbon Cycle as They Break Down Dead Trees inTerrestrial Ecosystems: Cellulose Degradation

• Fungi break down cellulose with enzymes called cellulases

• Fungi secrete these enzymes into the extracellular environment

• These cellulases together convert cellulose into glucose that the fungus can absorb and use as a source of food

Animals

• Between 3 million and 10 million animals exist on our planet today:

- Some similar to you, others quite different

- Only 1.4 million species have been described to date

- Scientists are in a race to discover and describe more animal species before more of them go extinct

Animals originated from single-called eukaryotes

- Occur in lineage called Opisthokonta

- Choanoflagellates are closest living relatives to animals:

▪ Share common ancestor 900 million years ago

Animals form monophyletic clades with key traits

- Multicellular eukaryotes, with no cell walls but with an extensive

extracellular matrix (ECM):

▪ Includes proteins specialized for cell-cell adhesion and communication

- Heterotrophs

- Move under own power at some point in life cycle

- All animals other than sponges have (1) neurons that transmit electrical signals to other cells and (2) muscle cells that change shape of body by contracting

Animals are a monophyletic group

- All animals have a single common ancestor that was multicellular

- Single origin of animals based on data from:

▪ Fossils

▪ Comparative morphology

▪ Comparative development

▪ Comparative genomics

• Prevailing hypothesis is that sponges are most ancient lineage of animals

Data to understand animal evolutionary relationships

fossils, comparative morphology, comparative development, comparative genomics

Porifera (Sponges)

• Sponges may be a paraphyletic group—containing some, but not all, descendants of common ancestor

• Sponges have the basic genetic tool kit needed for multicellularity:

- Cell-cell adhesion

- Cell-ECM adhesion

- Few even have epithelium

• Sponges do not have complex tissue:

- Groups of similar cells that are organized into tightly integrated structural and functional units

• Some sponges have true epithelium:

- Layer of tightly joined cells that covers interior and exterior surface of animal

- Epithelium is essential to animal form and function

• Ctenophores first? Possible, but we won't consider that.