Emp1003 biodiversity and classification

Biological Diversity

and Classification

Antoine Vella

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Scientific NamesAll organisms have different names in different languages. Besides these so-called ‘common’ names they also have one – in Latin - which is recognised all over the world. This is known as the scientific name.

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HISTORY OF TAXONOMY

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First StepsTaxonomy is that branch of biology dealing with the identification and naming of organisms.

Aristotle (384-322 BC) apparently began the discussion on taxonomy by attempting to put ‘order’ in the environment around him.

This is how Aristotle divided the objects around him and started taking the first steps in classification

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TaxonomyTaxonomy comes from the Greek taxis "arrangement" and nomia "method“. It is not simply the naming of organisms but refers to their classification – the names themselves are derived from this arrangement.


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Aristotle’sTaxonomy

Aristotle considered that nature is ordered from the lower to the higher, ranging from nonliving beings, to plants and animals, all the way to humans. These are the "steps of nature,“.


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Middle AgesHardly any progress was made in medieval times. In fact, there was a lot of confusion between real and mythical creatures.

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Renaissance

The Renaissance marked the beginning of a new era that would gradually bring about a disctinction between science and superstition.


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Modern Age

The discovery and gradual exploration of the New World produced large numbers of new plants and animals that needed naming, describing and classifying.


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The old systems made it difficult to study and locate all these new specimens within a collection and often the same plants or animals were given different names simply because there were too many species to keep track of.


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A system was needed that could group these specimens together so they could be found. In the late 16th – early 17th century, a systematic study of animals started being carried out.


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The system concerned familiar animals first and then was gradually extended until it developed enough to serve as basis for classification.


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John Ray (1627-1705) is credited with working on a concept of naming and describing organisms. He was an English naturalist and botanist who contributed significantly to the identification of different species and to making the "species" the ultimate unit of taxonomy.

First Steps


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Among Ray’s publications were Catalogus plantarum (1660), Ornithology (1676) (see plate right) and Historia insectorum (1710).


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Aquisition of New KnowledgeIn 1674, Antoine van Leeuwenhoek, sent a copy of his first observations of microscopic single-celled “animalcules” to the Royal Society of London.


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The First Microscope

His first microscope consisted of one very small spherical lens inserted in a tiny hole in a metal plate.

Antoine van Leeuwenhoek, is known as the "father of microscopy“.


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Micro-organisms

Until then the existence of such microscopic organisms was entirely unknown.

At first these organisms were divided into animals and plants and placed in the appropriate Kingdom.


MODERN TAXONOMY

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Carl Linne (1707-1778) , a Swedish doctor and naturalist, studied plants and other organisms and published several important books.

He was undoubtedly the most important scientist where classification is concerned and is considered the father of taxonomy.

Father of Taxonomy


In 1753 Linnaeus published his Systema Naturae describing plants and seeking to find out how they were related to each other.


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In the same year (1753) he published Species lantarum which reolutionised the way in which scientific names were applied to plants and fungi.


In this publication, Linneus stated that plants should be identified according to their flowers, not their leaves or other organs. This was a very intuitive observation and the method is still used today.


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Before Linneaus the Wild Briar Rose was known to botanists as Rosa sylvestris alba cum rubore, folio glabro (pinkish white woodland rose with hairless leaves), or Rosa sylvestris inodora seu canina (odourless woodland dog rose).


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How was one to know if these names referred to the same plant or two different ones?



By the Linnaean System the plant became simply Rosa canina

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Binomial Nomenclature


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A name of two wordsModern Classification systems use a two-word naming system called Binomial Nomenclature developed by Linnaeus to identify species.

Vicia sativa L.



Two words for a speciesIn this system, the FIRST WORD identifies the genus name of the organism. A genus (plural form = genera) consists of a group of similar species. The SECOND WORD, the descriptive word, often describing a characteristic of the organism, follows the genus name.

Vicia = common name in Latin for vetch sativa = cultivated

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Two words Names For A SpeciesThus, the scientific name of each species is made up of the generic name, followed by the descriptive specific name.

Vicia sativa Vicia faba


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Writing scientific namesThe genus name always begins with a capital letter, but the specific (second) name always begins with a lower case letter. Both names are always italicized or underlined.

Sometimes the genus may be written as an initial when it does not create confusion but the specific name is always written in full.

Vicia sativa or

V. sativa


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Groups within a speciesThe binomial name may be followed by another word which indicates the sub-species.

Vicia sativa nigraor

Vicia sativa ssp nigra


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ClassificationWhile he was naming organisms, Linneus also placed them in groups according to their characteristics

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CLASSIFICATION

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Groups within groups

Lineus placed organisms in groups known as taxa (singular taxon) according to their characteristicsThe broader the taxon the more general its characteristics & the more species it contains.Each taxon is a further broken-down level of classification found within each kingdom.


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Main Classification GroupsThe Kingdoms are divided into the following groups:

Phylum (aka Division or Type)ClassOrderFamilyGenusSpecies

Each group has also super-groups and sub-groups.

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Classification of a tick.




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Example of classificationOlive fly has the scientific name Dacus oleae.


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The genus Dacus

D. papayae D. punctatifrons D. newmanni

D. tryoni D. cucumis D. oleaeInstitute of Earth Systems

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Family Tephritidae

Genus Dacus Genus Ceratitis

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The Order DipteraFamily Tephritidae

Family Muscidae)

Family Culicidae

Family Phlebotomidae

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The Class Insecta

Order Diptera

Order LepidopteraOrder

Hymenoptera

Order Coleoptera



Phylum ArthropodaClassi Insecta

Class Arachnida

Class Crustacea


Kingdom Animalia

Phylum Arthropoda

Phylum Nematoda

Phylum Chordata

Phylum Mollusca

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Significance of ClassificationAs can be seen, therefore, classifying an organism does not consist only in naming it but, more importantly, placing it within a context of similar organisms.


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Taxonomic Relationships

Is the striped zebra related to the striped tiger or the grey rhino?


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The zebra is related to the rhino (same order) because, they have the same structure of the hooved odd-toed feet.


Such a character is what a taxonomist looks for when classifying an organism.

The bone structure of the foot is therefore a more significant character than the pattern of the coat.

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Taxonomic Relationships

The extinct Tasmanian wolf (thylacine) had the same dentition as the wolf. Are they related?


Taxonomic DifferencesThe two mammals are not related because the thylacine was a marsupial while the wolf is a placental animal.

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A newborn marsupial in its mother’s pouch.

A newborn wolf is relatively self-sufficient

The reproductive system is considered more important than dentition, to show relationship.

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Taxonomic DiagnosisThe characters which are relevant to classification are known as


diagnostic characters or taxonomic charactersOne of the most important skills of the taxonomist is recognising which particular characters are of taxonomic significance.

Example: Wings are taxonomic characters for insect orders.

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Phylogeny

This is the “history” of a group of organisms especially as regards their ancestry. In Greek, Phylon means ‘group’ or ‘tribe’ while Genesis means ‘creation’ or ‘birth’.


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PhylogenyWhen a group is descended from one ancestor it is said to be monophylitic.


When the group is descended from two or more ancestors it is said to be polyphylitic.

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PhylogenySometimes, a common ancestor may give rise to more than one group.


In this case each group, representing only a part of the descendents of that common ancestor, is said to be paraphylitic.

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Modern SystemAlthough the system devised by Linneus is still in use, time has obviously brought changes.One of them is that while Linneus divided all living creatures into two kingdoms* (Plant and Animal), these have now been divided into five.

*He was influenced by Aristotle according to whom the universe was made up of three Kingdoms: mineral, plant and animal.


THE KINGDOMS OF LIFE

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By the mid-19th century it had become clear that the existing boundary between plant and animal kigdoms as as created by Aristotle was becoming blurred and unsatisfactory.

Two Kingdoms



Three KingdomsIn 1866, a German biologist, Ernst Haeckel proposed a third kingdom of life to include the unicellular organisms.

Protista

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Four KingdomsBy mid 20th century the importance of having an enclosed nucleus became more evident and another kingdom (Monera) was proposed for organisms not having such a nucleus.


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Four Kingdoms

The organisms without a nucleus enclosed by a membrane were called the Monera and comprised the bacteria.



Five KingdomsThe next innovation involved the breaking up of the Plant Kingdom to take into account the differences between true plants and fungi.

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Five KingdomsThis system, proposed in 1969, has now become a popular standard and, with some refinement, is still used in many works. It forms the basis for modern multi-kingdom systems.


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Five Kingdoms


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Modern Trends

From around the mid-1970s onwards, there was an increasing emphasis on DNA to assess relationships between organisms. This is now considered more significant than outward appearance and physiology.


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Six KingdomsYet another new kingdom is sometimes being proposed today. The Protista (single-celled with enclosed nucleus) would be broken up to divide the algae from the rest of the unicellular organisms. This idea is not yet widely accepted.


THE FIVE KINGDOMS: AN OVERVIEW

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First Distinction: the Nucleus

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Kingdom Monera

Monera form the only kingdom composed of prokaryotic organisms.They have a cell wall but lack membrane-bound organelles, including a nucleus.


Monera - Bacteria

Monera can be rod-shaped, spiral-shaped or round and may have hairs (cilia) or tails (flagella) that let them move around. They reproduce by dividing and their populations can grow very quickly.

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Monera ClassificationThe kingdom is divided into two main groups:

Myxomonera – blue-green algaeMastigomonera - bacteria


Blue-green Algae

These photosynthesising organisms live in water and form groups of cells. They can survive in polluted waters and the remains of ancient organisms become petroleum.

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BacteriaBacteria are present in most habitats on Earth and are extremely abundant: their bimass exceeds that of all other organisms combined. They help to recycle nutrients, through processes such as the fixation of nitrogenfrom the atmosphereand putrefaction.


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ArchaebacteriaThe Archaebacteria, the most ancient members of this kingdom, are so different that they may belong to a separate kingdom.


Kingdom ProtistaThese are organisms that don’t seem to fit anywhere else. They include some of the earliest living things on Earth and gave rise to fungi, plants, and animals. The first eukaryotic cells are thought to have been protists.

Slim

e mould

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ProtistaThe most ancient eukaryotic kingdom, protists include a wide variety of organisms that can be heterotrophic or autotrophic. Perhaps they are best defined bywhat they are not: they are not fungi,animals, or plants.


ProtistaThe oldest fossils of eukaryotic cells are 1.5 billion years old although the earliest eukaryotic cells may have arisen 2.1 billion years ago. The oldest fossils of prokaryotes are 3.6 billion years old..

Protista Classification Th kingdom shows great diversity. It is made up by many groups of which the main ones are:Animal-like - all motile (protozoa)Plant-like - mostly non-motile; photosynthetic; often called algae or seaweedsFungus-like - grow in dark, shady habitats and are called slime moulds; most are colourful and can be found underneath rotting logs or leaves.

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Protista Classification


Protista - Protozoa

Protista - Algae

Protista – Fungus-like organisms

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Kingdom Fungi

FungiA fungus is a eukaryotic organism that digests its food externally and absorbs the nutrient molecules into its cells. Most are multicellular but some (the yeasts) are simple unicellular organisms probably evolved from multicellular ancestors.

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Vegetative StructuresThe fungus body is made of tiny filaments or tubes called hyphae, usually with cross-walls (septa) with a chitin cell wall.Each hyphae is one continuous cell that continually grows and branches.


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Vegetative StructuresTangled mats of hyphae are known as mycelium.Hyphae grow rapidly from the tips by cell division


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Reproductive StructuresMost fungi reproduce asexually and sexually by means of spores. Asexual reproduction produces identical organisms and is the most common method used. Sexual reproduction occurs when nutrients or water are scarce. Wind, animals and water spread spores.


Sexual sporulation is the main character used to identify and classify fungi.

LifestyleThe majority of fungi are decomposers, breaking dead organisms down and returning inorganic nutrients to the ecosystem. Many other forms are parasitic, especially on plants but sometimes also on animals or other fungi.

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Still other forms are predatory on animals such as nematodes.


Pathogens

Some fungi also cause disease (yeast infections, rusts and blights), while others are useful in baking, brewing, as foods, drugs and sources for antibiotics.

Claviceps purpurea, causing ergot disease of rye

The cell walls are similar in structure to plants’ but differ in chemical composition - fungal cell walls are composed mostly of chitin rather than cellulose. This is one of the taxonomic characters that distinguish fungi from true plants

Food StorageMost fungi store glucose as glycogen (like animals) while plants store food as starch.

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Classification of FungiFungi may be grouped in four Classes:Oomycetes – Mycelium without septa. Reproduce by conjugation of large and small cell (oogonium and antheridium). Ascomycetese - Sexual reproduction via spores produced in asci (sac-like cases)Basidiomycetes - Sexual reproduction via club-shaped reproductive structures: basidia.


Deuteromycetes - Diverse group of unclassified species. Sexual structures unknown, hence also called Imperfect fungi.

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Kingdom Plantae


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Plants are immobile, multicellular eukaryotes that produce their food by photosynthesis and have cells encased in cellulose cell walls.


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They are important sources of oxygen, food, textiles, construction materials and other products.


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They are important sources of oxygen, food, and clothing/construction materials, as well as pigments, spices, dyes, and drugs.


The kingdom Plantae includes all land plants: mosses, ferns, conifers and flowering plants.

With more than 300,000 species, they are second in size only to the Phylum Arthropoda.

Taxonomic CharactersAmong the characters which distinguish plants from other organisms are the following:

Multicellular Cellulose cell walls Autotrophic Growth occurs in specific regions Reproduction vegetative or sexual

Plants have adapted to life on land and have adaptations to reduce water loss, such as:• Leaves and stems are covered by an impermeable

waxy cuticle. • Leaf openings

(stomata) that open and close to regulate gas and water exchange.

Classification of PlantsPlants are divided into two main groups:

Green Algae - Bryophytes - Non-vascular plants Tracheophytes - Vascular plants

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Plant DiversityAll plants are thought to have evolved from ancestral green algae.Within the plant kingdom, there are many different types

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Main DivisionsThe Plantae may be divided first of all in two main groups:

Green algaeEmbryophytes (terrestrial plants)


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Green AlgaeThese are a large group from which the embryophytes (higher plants) emerged. There are about 6000 species. Many are single cells, while other species form colonies or long filaments.


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The advantages of being a water plant include: More access to waterMore support (from the surrounding water) Water helps disperse gametes


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Land Plants

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The advantages of being a land plant include

• High concentrations of CO2 in air (compared to water)

• More access to sunlight• Initially: less competition for

resources, fewer predators


BryophytesThis group includes:

Hornworts – Liverworts – Mosses

BryophytesThese small plants lack specialized tissues for transporting water, minerals, and organic nutrients and have no roots, leaves or stems. Because of this they dry out very quickly, so they are usually found in moist habitats.

Hornworts

Liverworts

Mosses

Division of Vascular Plants

The main character used to divide Tracheophytes is whether they produce seeds or not.

Tracheophyte ClassificationThis group is divided in 2 sections:Seedless Plants – including horsetails and fernsSeed Plants – Plants which produce flowers and seeds

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Seedless PlantsSeedless tracheophytes are further divided into two groups:

Lycophytes – club moss and horsetails Pterophytes - Ferns


Typical lycophytes – club mosses

Horsetails

Ferns

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Ferns grow in moist, shady habitats because their water-saving adaptations are not as efficient as those of other plants. Their leaves are called fronds.


Ferns

Spermatophyta – Seed PlantsClassification of this group varies but we’re considering here a simplified version which contains two Classes. :

Gymnosperms – conifersAngiosperms – broad-leaved plants

The two groups of seed-plants are divided by whether or not they have enclosed seeds -protected inside a fruit - or if the seeds are exposed to the environment.

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Tracheophytes

Seedless Seeded

Gymnosperms Angiosperms “naked” or

exposed seeds Flowers produce fruit

w/ enclosed seeds

Spermatophyta - Seed plantsCharacters of Gymnosperms (Conifers)

– Seed is not protected by fruit

– Has conesCharacters of Angiosperms (Flowering Plants)

– Seed is further protected by a fruit

– Has flowers

Gymnosperm means “naked seed”.

They are more advanced than ferns and do not have spores but seeds.

Their seeds lack a protective enclosure (unlike flowering plants which have flowers and fruit).Examples of gymnosperms:

Conifers (pine trees),cycads,Ginkgo biloba

Gymnosperms

Gymnosperms

Pinophyta-The ConifersConifers, which bear seeds in cones, are most important group of gymnosperms.

Staminate cones – male conesOvulate cones – female cones

Conifer FamiliesCupressaceae, Pinaceae, Taxaceae, Taxodiaceae

They do not produce any flowers or fruit. The seeds are carried on an open ‘scale’.

Conifers are adapted to temperate to cold regions. They have narrow leaves (needles) to help conserve water and protect them from the cold. The plants are covered by resins for protection from predators, fire, etc

Angiosperms

Angiosperm means “covered seed”. They have flowers, fruits with seeds. Live everywhere – dominant plants in the world260,000 species (88% of Plant Kingdom)

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Angiosperm ClassificationThe phylogenetic classification of Angiosperms is complex and in continuous evolution. We will here use a simplified version that is sufficient for our purposes Angiosperms may be divided in two sub-classes:

Monocotyledonae – one cotyledonDicotyledonae – two cotyledons.

The Dicotyledonae may be further subdivided into several groups.


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Angiosperm ClassificationAlthough the names of the two sub-groups are derived from the number of cotyledons, there are several other taxonomic characters which distinguish them.


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Although the names of the two sub-groups are derived from the number of cotyledons, there are several other taxonomic characters which distinguish them.


Monocot and Dicot

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Kingdom Animalia


Kingdom ANIMALIAAnimals are organisms with the following characteristics:

Multicellular Have cell membranesHeterotrophic Growth occurs all over body Motile Sexual ReproductionIrritability Food stored as glycogen

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AnimaliaAnimals are multicellular, heterotrophic eukaryotes that are capable of motility at some stage during their lives, and that have cells lacking cell walls. Animals provide food, clothing, fats, scents, companionship and work.


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Traditional Classification

The Protozoa are now placed in the Kingdom Protista and no loner considered animals so that the grouping matazoa has become irrelevant.


AnimalsTraditionally (going back to Aristotle) multicellular animals were split into two major groups:

The grouping vertebrates has now been replaced by Chordates as there are animals which have a spinal chord but no vertebrae.

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InvertebratesThis is an informal and not a monophyletic grouping as it comprises practically all animals except Chordates.


Invertebrate ClassificationInvertebrates are animals that do not have backbones.They constitute 97 % of the Animal Kingdom and can be found in aquatic and damp encironments. Several types have have exoskeletons.

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Phylum Porifera


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Porifera


Phylum: Porifera

Characters include: Bodies made of loosely joined cells

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Phylum Cnidaria


Cnidarian CharactersCharacters include: Thin sack-like bodies Tentacles with stinging cells

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The Cnidaria include the jellyfish and sea anemones.


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Phylum Echinodermata


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Echinodermata


Phylum: Echinodermata

Characters include: Bodies divided into five partsSpiny outer covering


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Phylum Platyhelminthes


Phylum: Platyhelminthes

Characters include:Small sizeFlat worm-like bodies

Phylum Nematoda

Phylum: Nematoda

Have long thin round non-segmented bodies covered by a cuticle.Mouthparts consist of a set of stylets and a pharynx.Nematodes may be parasitic on plants or animals or free-living, predatory or living on decaying matter.

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Annelids


Phylum: Annelida

Characters include: Round worm-like bodies divided into segments. They live mostly on decaying matter but some are parasitic (leeches)

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Phylum Arthropoda


Phylum: ArthropodaHave lots of legs and segmented bodies. There are several Classes of arthropods including:

– Arachnids– Centipedes – Millipedes– Crustaceans– Insects

Class ArachnidaCharacters include:• Four pairs of legs.• Bodies may be

divided into two sections

Classes Chilopoda Diplopoda

Long thin segmented bodies. One (Chilopoda) or two (Diplopoda) pairs of legs on each body segment.

Class CrustaceaCharacters include: Five-seven pairs of legs First pair often used as pincers

Class InsectaCharacters include: Three pairs of legs.Bodies divided into three sections.Two pairs of wings

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Phylum Mollusca


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Phylum: Mollusca

Characters include:Fleshy pad for locomotion.Shell external or internal

Vertebrates

These are animals with a backbone.There are five groups of vertebrates:

–Mammals–Birds–Reptiles–Amphibians–Fish

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Fish


World’s Tiniest fish

Paedocypris progenetica, the world's tiniest fish, which lives in swamps in South-East Asia.

Fish

Have wet scalesLay eggs in waterLive in water

Fish CharacteristicsThis is the largest group of vertebrates. They live only in water, breathe through gills and are usually covered in scales.

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Fish ClassificationThe old class pisces is no longer used. Instead fish are divided into three classes:a) Agnatha - jawless fishb) Chondrichthyes - cartilaginous fishc) Osteichthyes - bony fish


a

b

c

Amphibians

World’s tiniest frog

Amphibians

Loss of habitat makes this the most endangered group of all animals.

Amphibian CharacteristicsAmphibians are cold-blooded and hatch fromjelly-coated eggs. As juveniles they have gillsand live in water. Their skin is smoothand moist.

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Amphibian ClassificationThe 6000+ species are divided in three orders:Anura - frogsCaudata or Urodela - newts, salamandersGymnophiona or Apoda - caecilian


Reptiles

One of the world tiniest reptiles

Reptiles

Reptile Characteristics

Reptiles are covered in scales andlay leathery-shelled eggs on land. Their body temperature varies with theirenvironment and they are always free-living.

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Reptile ClassificationThe old Class Reptilia has around 8000 species in four orders:Crocodilia — crocodiles Sphenodontia — tuataras Squamata — lizards and snakes Testudines — turtles and tortoises


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Class Aves


Class Aves

Bird CharacteristicsBirds are warm-blooded, have true wings and feathers and lay hard-shelled eggs. The usually have hollow bones. They are always free-living, never parasitic.

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Bird taxonomyThere are about 10 thousand species divided into 20 orders. The main taxonomic differences regard the bills and feet.


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Bird Bills


Pygmy shrew

Class Mammalia

Mammals

Characters include:Milk productionPresence of hairPresence of diaphragm

Characters of mammalsProduce milk to feed their young. Females possess a modified sweat gland – a mammary gland – activated by hormonal changes that occur with pregnancy. In fact, this trait is what inspired the term “mammal,” a derivation of “mammary.”

Characters of mammalsSkin covered with fur or hair. A characteristic that's seen only in mammals.

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Classification of MammalsMammals are divided into 14 ordersMonotremata and Marsupials are two of them


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Classification of MammalsMammals are divided into 14 orders.


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Emp1003 biodiversity and classification