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Taxonomy and Diversity

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Kelly Wessell

on 23 March 2015

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Transcript of Taxonomy and Diversity

Phylogenetics
Evolutionary history of a species or group of species
The process of classifying organisms according to their phylogeny
Molecular
fossil
Genetic
Systematics
&
Practice
Trees sometimes show timing of divergence.
Cladograms always show relatedness. (Of course!)
Monophyletic, Paraphyletic & Polyphyletic
This
can
be
confusing
Principle of Maximum Parsimony
Shared ancestral or primitive character
a character that originated in the ancestor of the taxon.
Shared derived character
a character that is unique to the taxon and distinguishs it from its ancestors
Construct a tree based on these data.
The tree that requires the fewest evolutionary events is the most likely.
You have to pick the right traits!
Clade
A group of organisms that includes an ancestral species and all of its descendants
Primitive vs. Derived Characters
Life as we know it.
What is taxonomy?
Kingdom Animalia
Phylum Arthropoda
Subphylum Hexapoda
Class Insecta
Order Coleoptera
Family Buprestidae
Genus Agrilus
Species planipennis
Ferns
Reptiles
Plants
Emerald Ash
Borer
Insects
Snakes
Beetles
Turtles
Maple Tree
Bryophytes
Conifers
Flies
Ants
Black
Flies
Mosquitoes
Bees
Wasps
Mammals
Rodents
Primates
Gorillas
Homo sapiens
Lizards
Why do we need to organize
LIFE?
Birds
Emerald Ash Borer
An Example
Heirarchical
Descriptive
Heirarchical
Heirarchical
Homo sapiens
T. rex
Homo sapiens
Is a chordate,
a mammal,
a primate,
an ape.
Taxonomy 101
Examples
The Basics
LIFE
History
How does it work?
Sounds like a good idea.
There's a lot we don't know...
Taxonomy and Diversity
Plant Diversity
Animal Diversity
Advantages and Challenges of Terrestrial Life?
Cuticle
For more than the first 3 billion years of Earth’s history, the terrestrial surface was lifeless
Since colonizing land, plants have diversified into roughly 290,000 living species
Plants supply oxygen and are the ultimate source of most food eaten by land animals
Greening of the Earth
Many characteristics of land plants also appear in a variety of algal clades, mainly green algae

Comparisons of both nuclear and chloroplast genes point to charophytes as the closest living relatives of land plants

Sporopollenin (tough outer walls of spores and pollen)
Cell wall formation is similar.

Note that land plants are not descended from modern charophytes, but most recently share a common ancestor with modern charophytes
Evidence
Systematists are currently debating the boundaries of the plant kingdom
Some biologists think the plant kingdom should be expanded to include some or all green algae
Until this debate is resolved, we will retain the embryophyte definition of Kingdom Plantae
Some key traits appear in nearly all land plants but are absent in the charophytes:

Alternation of generations (with multicellular, dependent embryos)
Walled spores (with sporopollenin) produced in sporangia
Apical meristems
Bryophyta
Pterophyta
Gymnosperms
Angiosperms
Seeds & Pollen
Flowers
Vascular Tissue
The gametophyte is haploid and produces haploid gametes by mitosis
Fusion of the gametes gives rise to the diploid sporophyte, which produces haploid spores by meiosis
The diploid embryo is retained within the tissue of the female gametophyte
Nutrients are transferred from parent to embryo through placental transfer cells
Land plants are called embryophytes because of the dependency of the embryo on the parent
Alternation of Generations with Dependent Embryos
In all three bryophyte phyla, gametophytes are larger and longer-living than sporophytes.
Sporophytes are typically present only part of the time.
What is the advantage of vascular tissue?
Living vascular plants are characterized by:
Life cycles with dominant sporophytes

Vascular tissues called xylem and phloem

Well-developed roots and leaves
Xylem and Phloem
Xylem conducts most of the water and minerals and includes dead cells called tracheids
Phloem consists of living cells and distributes sugars, amino acids, and other organic products
Water-conducting cells are strengthened by lignin and provide structural support
Increased height was an evolutionary advantage
Sporophyte Dominant
In contrast with bryophytes, sporophytes of vascular plants are the larger generation, as in the familiar leafy fern.

The gametophytes are tiny plants that grow on or below the soil surface.
Patterns
Seedless vascular plants.
Sporophyte-dominant.
Ferns are the most diverse seedless vascular plants, with more than 12,000 species
They are most diverse in the tropics but also thrive in temperate forests
Horsetails were diverse during the Carboniferous period, but are now restricted to the genus Equisetum
Whisk ferns resemble ancestral vascular plants but are closely related to modern ferns
In addition to seeds, the following are common to all seed plants
Reduced gametophytes
Heterospory
Ovules
Pollen
What are the evolutionary advantages of having seeds?
What is a seed?
A seed develops from the whole ovule
A seed is a sporophyte embryo, along with its food supply, packaged in a protective coat
What is a seed?
An ovule consists of a megasporangium, megaspore, and one or more protective integuments
Gymnosperm megaspores have one integument
Angiosperm megaspores usually have two integuments
Ovules and Egg Production
Microspores develop into pollen grains, which contain the male gametophytes
Pollination is the transfer of pollen to the part of a seed plant containing the ovules
Advantages?
If a pollen grain germinates, it gives rise to a pollen tube that discharges two sperm into the female gametophyte within the ovule
Pollen and Sperm Production
The gymnosperms have “naked” seeds not enclosed by ovaries and consist of four phyla:
Cycadophyta (cycads)
Gingkophyta (one living species: Ginkgo biloba)
Gnetophyta (three genera: Gnetum, Ephedra, Welwitschia)
Coniferophyta (conifers, such as pine, fir, and redwood)
Phylum Cycadophyta
Phylum Ginkophyta
Phylum Gnetophyta
Phylum Conferophyta
This phylum is by far the largest of the gymnosperm phyla.

Most conifers are evergreens and can carry out photosynthesis year round.
Angiosperms are seed plants with reproductive structures called flowers and fruits.
They are the most widespread and diverse of all plants.
All angiosperms are classified in a single phylum, Anthophyta.
Fruit
The flower of the sporophyte is (usually) composed of both male and female structures
Male gametophytes are contained within pollen grains produced by the microsporangia of anthers
The female gametophyte, or embryo sac, develops within an ovule contained within an ovary at the base of a stigma
Most flowers have mechanisms to ensure cross-pollination between flowers from different plants of the same species
A pollen grain that has landed on a stigma germinates and the pollen tube of the male gametophyte grows down to the ovary
The ovule is entered by a pore called the micropyle
Double fertilization occurs when the pollen tube discharges two sperm into the female gametophyte within an ovule
One sperm fertilizes the egg, while the other combines with two nuclei in the central cell of the female gametophyte and initiates development of food-storing endosperm
The endosperm nourishes the developing embryo
Within a seed, the embryo consists of a root and two seed leaves called cotyledons
Angiosperm Life Cycle
Pollination of flowers and transport of seeds by animals are two important relationships in terrestrial ecosystems
Clades with bilaterally symmetrical flowers have more species than those with radially symmetrical flowers
This is likely because bilateral symmetry affects the movement of pollinators and reduces gene flow in diverging populations
Flower Shape and Speciation
Coevolution
How are animals classified?
Animals are heterotrophs that ingest their food.
Animals are multicellular eukaryotes
Their cells lack cell walls.
Their bodies are held together by structural proteins such as collagen.
Nervous tissue and muscle tissue are unique to animals.
What is an Animal?
Symmetry
Number of tissue layers and formation of coelom (this has recently fallen out of favor)
Fate of blastopore
Larval type
Other derived traits…
Classification is based on:
Reproduction and Development
Hox Genes
All animals, and only animals, have Hox genes that regulate the development of body form
Although the Hox family of genes has been highly conserved, it can produce a wide diversity of animal morphology
Hox genes are a group of related genes that specify the anterior-posterior axis and segment identity of metazoan organisms during early embryonic development
Symmetry
Animals can be categorized according to the symmetry of their bodies, or lack of it.
Some animals have radial symmetry

Two-sided symmetry is called bilateral symmetry
Bilaterally symmetrical animals have:
A dorsal (top) side and a ventral (bottom) side
A right and left side
Anterior (head) and posterior (tail) ends
What is the advantage of bilateral symmetry?
Tissues and Body Cavity
Animal body plans also vary according to the organization of the animals tissues.
Tissues are collections of specialized cells isolated from other tissues by membranous layers.
During development, three germ layers give rise to the tissues and organs of the animal embryo.
Ectoderm is the germ layer covering the embryo’s surface.
Endoderm is the innermost germ layer and lines the developing digestive tube, called the archenteron.
Diploblastic animals have ectoderm and endoderm.
Triploblastic animals also have an intervening mesoderm layer; these include all bilaterians.
Most triploblasts have a body cavity.
Fate of the Blastopore
All animals share a common ancestor.
Sponges are basal animals.
Eumetazoa is a clade of animals (eumetazoans) with true tissues.
Most animal phyla belong to the clade Bilateria, and are called bilaterians.
Chordates and some other phyla belong to the clade Deuterostomia.
Points of Agreement
The morphology-based tree divides bilaterians into two clades: deuterostomes and protostomes.
In contrast, recent molecular studies indicate three bilaterian clades: Deuterostomia, Ecdysozoa, and Lophotrochozoa.
Ecdysozoans shed their exoskeletons through a process called ecdysis.
Some lophotrochozoans have a feeding structure called a lophophore.
Other phyla go through a distinct developmental stage called the trochophore larva.
Resolving Differences
What is the advantage of having a coelom?
The Evolution of Eukaryotic Cells
The oldest fossils of eukaryotic cells date back 2.1 billion years.
The hypothesis of endosymbiosis proposes that mitochondria and plastids (chloroplasts and related organelles) were formerly small prokaryotes living within larger host cells.
An endosymbiont is a cell that lives within a host cell.
The prokaryotic ancestors of mitochondria and plastids probably gained entry to the host cell as undigested prey or internal parasites
In the process of becoming more interdependent, the host and endosymbionts would have become a single organism
Serial endosymbiosis supposes that mitochondria evolved before plastids through a sequence of endosymbiotic events
Similarities in inner membrane structures and functions.

Division is similar in these organelles and some prokaryotes.

These organelles transcribe and translate their own DNA.

Their ribosomes are more similar to prokaryotic than eukaryotic ribosomes.
Evidence supporting endosymbiotic theory
Sponges are sedentary animals from the phyla Calcarea and Silicea.
They live in both fresh and marine waters.
Sponges lack true tissues and organs.
Formerly classified as “Parazoa” (Beside the Animals)
Phylum Cnidaria
All animals except sponges and a few other groups belong to the clade Eumetazoa, animals with true tissues.
Cnidarians have diversified into a wide range of both sessile and motile forms including jellies, corals, and hydras.
They exhibit a relatively simple diploblastic, radial body plan.
The basic body plan of a cnidarian is a sac with a central digestive compartment, the gastrovascular cavity.
A single opening functions as mouth and anus.
There are two variations on the body plan: the sessile polyp and motile medusa.
Phylum "Porifera"
Phylum Cnidaria
Phylum Platyhelminthes
Phylum Nematoda
Phylum Annelida
Phylum Arthropoda
Phylum Mollusca
Phylum Echinodermata
Phylum Chordata
Eumetazoa
Bilateria
Deuterostomes
Protostomes
Lophotrochozoa
Ecdysozoa
The clade Lophotrochozoa was identified by molecular data.
Some develop a lophophore for feeding, others pass through a trochophore larval stage, and a few have neither feature.
Lophotrochozoa includes the flatworms, rotifers, ectoprocts, brachiopods, molluscs, and annelids.
Members of phylum Platyhelminthes live in marine, freshwater, and damp terrestrial habitats.
Although flatworms undergo triploblastic development, they are acoelomates.
They are flattened dorsoventrally and have a gastrovascular cavity.
Monogeneans and trematodes live as parasites in or on other animals.
They parasitize a wide range of hosts, and most have complex life cycles with alternating sexual and asexual stages.
Trematodes that parasitize humans spend part of their lives in snail hosts.
Most monogeneans are parasites of fish.
Blood Fluke
Schistosoma mansoni
Class Turbelleria
Class Cestoda
Tapeworms are parasites of vertebrates and lack a digestive system
Tapeworms absorb nutrients from the host’s intestine
Fertilized eggs, produced by sexual reproduction, leave the host’s body in feces
There are four major classes of molluscs:
Polyplacophora (chitons)
Gastropoda (snails and slugs)
Bivalvia (clams, oysters, and other bivalves)
Cephalopoda (squids, octopuses, cuttlefish, and chambered nautiluses)
Class Gastropoda
About three-quarters of all living species of molluscs are gastropods.
Most gastropods are marine, but many are freshwater and terrestrial species.
Most have a single, spiraled shell.
Slugs lack a shell or have a reduced shell.
The most distinctive characteristic of gastropods is torsion, which causes the animal’s anus and mantle to end up above its head.
Class Bivalvia
Molluscs of class Bivalvia include many species of clams, oysters, mussels, and scallops.
They have a shell divided into two halves.
Class Cephalopoda
Class Cephalopoda includes squids and octopuses, carnivores with beak-like jaws surrounded by tentacles of their modified foot.
Most octopuses creep along the sea floor in search of prey.
The phylum Annelida is divided into three classes:
Oligochaeta (earthworms and their relatives)
Polychaeta (polychaetes)
Hirudinea (leeches)
Annelids, unlike Nematodes, are segmented.
Class Oligochaeta: Earthworms
Class Hirudinea: Leeches
Class Polychaeta
Nematodes, or roundworms, are found in most aquatic habitats, in the soil, in moist tissues of plants, and in body fluids and tissues of animals.
They have an alimentary canal (complete), but lack a circulatory system.
Some nematodes are important parasites of plants and animals.
Warning
The next few pictures are rated G for Gross. If you're eating, I'd stop now.
Hemimetabolous
vs.
Holometabolis
Subphylum Myriopoda
Millipedes and centipedes
Myriapods are terrestrial, and have jaw-like mandibles
Millipedes, class Diplopoda, are mostly herbivores
Centipedes, class Chilopoda, are carnivores
Subphylum Hexapoda
Class Insecta
Two out of every three known species of animals are arthropods.
Members of the phylum Arthropoda are found in nearly all habitats of the biosphere.
The arthropod body plan consists of a segmented body, hard exoskeleton, and jointed appendages, and dates to the Cambrian explosion (535–525 million years ago).
Early arthropods show little variation from segment to segment.
Arthropod evolution is characterized by a decrease in the number of segments and an increase in appendage specialization.
These changes may have been caused by changes in Hox gene sequence or regulation.
Regier et al. 2010. Nature 463:1079-1083
Most insects have separate males and females and reproduce sexually
Individuals find and recognize members of their own species by bright colors, sound, or odors
Some insects are beneficial as pollinators, while others are harmful as carriers of diseases, or pests of crops
Insects are classified into more than 30 orders
Subphylum Cheliceriformes
Named for clawlike feeding appendages called chelicerae.
Most marine cheliceriforms are extinct, but some species survive today, including horseshoe crabs.
Most modern cheliceriforms are arachnids, which include spiders, scorpions, ticks, and mites.
While arachnids and insects thrive on land, crustaceans, for the most part, have remained in marine and freshwater environments.
Crustaceans, subphylum Crustacea, typically have branched appendages that are extensively specialized for feeding and locomotion.
Most crustaceans have separate males and females.
Ernst Haeckel's Kunstformen Natur (1904)
http://en.wikipedia.org/wiki/Artforms_of_Nature
Subphylum Crustacea
Why are there relatively few marine insects?
Sea stars and most other echinoderms are slow-moving or sessile marine animals.
A thin epidermis covers an endoskeleton of hard calcareous plates.
Echinoderms have a unique water vascular system, a network of hydraulic canals branching into tube feet that function in locomotion, feeding, and gas exchange.
Males and females are usually separate, and sexual reproduction is external.
Which group is
Paraphyletic?
Monophyletic?
Polyphyletic?

1. Blue
2. Yellow
3. Red
Concept Check
Concept Check
Which one is different? In a sentence or two, describe how.
Concept Check
Relative to other chordates which of these is a derived character of mammals?
1. Cellular respiration
2. Lactation
3. Dorsal nerve cord
4. All of the above
For all mammals, which of these is a primitive character??
1. Cellular respiration
2. Lactation
3. Dorsal nerve cord
4. All of the above
Diploid Organisms
Have one chromosome
Have two chromosomes
Have two copies of each gene per chromosoms
Have two copies of each gene on homologous chromosomes
Meiosis
Produces haploid cells from haploid cells
Produces diploid cells from diploid cells
Produces haploid cells from diploid cells
Produces diploid cells from haploid cells
What Makes a Plant a Plant?
The gametophyte
produces the gametes by mitosis.
is sometimes a growth stage.
is haploid.
All of the above.
If you carve your name into the trunk of a tree at eye level
it will be at the same height 20y from now.
you will have to look up to see it in 20y.
Concept Check
Sperm nucleus (n)
(Produces sperm)
(Produces pollen tube)
Gymnosperm Seed Formation
Sperm + 2 polar nuclei
A way to organize
According to this tree, what can you say about timing of divergence?
(WP1)
(WP2)
(WP3)
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