chapter 1: classification of -...

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CLASSIFICATION OF LIVING THINGS

MADAM HALIMAHTUN SAEDIAH BT ABU BAKAR KOLEJ TEKNOLOGI TIMUR

CHAPTER 1: CLASSIFICATION OF

LIVING THINGS

INTRODUCTION TAXANOMY

BINOMIAL SYSTEM OF

NOMENCLATURE

HIERARCHICAL CLASSIFICATION

CLASSIFICATION SYSTEM

FIVE KINGDOM SYSTEM

THREE DOMAIN SYSTEM

PHYLOGENY

PHYLOGENETIC TREES

CONSTRUCTING PHYLOGENETIC

TREES

SYTEMATICS

CLADISTICS SYSTEMATICS

PHENETIC & NUMERICAL TAXONOMY

EVOLUTIONARY SYTEMATICS

CHAPTER 1: CLASSIFICATION OF

LIVING THINGS

INTRODUCTION

Introduction

• Biological diversity or biodiversity is referred to the variety of living organisms and the variety of ecosystems they formed.

• It is also simply means the diversity, or variety, of plants and animals and other living things in particular area or region.

• Biodiversity also means the number, or abundance of different species living within particular region.

Introduction • Scientist sometimes refer to the biodiversity of an

ecosystem, a natural made of a community of plants, animals, and other living things in a particular physical and chemical environment.

• To study the diverse life forms in this planet and to effectively communicate their finding, biologists must organize their knowledge.

• The scientific study of the diversity of organisms and their evolutionary relationship is called systematics.

Introduction

• The goal of systematics is to have classification reflect the evolutionary relationships of species or phylogeny, based on shared characteristics.

• An important aspect of systematics is taxonomy.

• The term classification means organizing organisms into group based on their similarities, which reflect historical relationships among ancestry.

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Definition of taxonomy

• Taxonomy is the branch of biology dealing with the identification, naming and classifying the diverse form of life.

• Taxonomy is an ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences.


• Before the beginning of modern, genetically based evolutionary studies, European biology dealing with the taxonomy, or classification of organisms into different categories based on their physical characteristics.

• Even though classification by Linnaeus was not based on evolutionary relationship but just on resemblances, many features of his system stay useful in phylogenetic system.


• Two of these are binomial system of nomenclature or binomial designations for species and hierarchical classification.

The binomial system

• Linnaeus developed the binomial system of naming species or concept of binomial nomenclature, whereby scientists speaking and writing different languages could communicate clearly.

• The name is binomial because it has two parts. For example, Lilium buibiferum and Lilium canadese are two different species of lilies.

• The first word Lilium, is the genus (pl.,genera), a classification category that can include many species.

The binomial system

• The second word that is specific epithet, refers to one species within that genus.

• He also rationalized nomenclature, using the same name for both sexes and for adults and juveniles of a species.

• He used Latin in naming the organisms.

CHAPTER 1: CLASSIFICATION

OF LIVING THINGS

TAXANOMY

BINOMIAL SYSTEM OF

NOMENCLATURE

HIERARCHICAL CLASSIFICATION

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The binomial system

• The reason why organisms need to have a scientific name in Latin and why we do not use the common name for organisms because a common name will vary from country to country because different countries use different languages.

• Linnaeus used Latin because it is the universal language and the language that was well known by most scholars at that time.

The binomial system

• For example Man in English is Hombre in Spanish, Herr in German, Ren in Chinese, and Homo in Latin.

• If a scientist refers today to Homo, all scientists know what organism/taxon he or she means.

Hierarchical classification

• The hierarchical classification developed by Linnaeus was based on the idea that the species was the smallest unit, and that each species or taxon nested within a higher category.

• A taxon (pl. taxa) is a group of organisms that fill a particular category of classification.

• For example Rosa and Felis are taxa at genus level.


• Taxon (pl. taxa) refer to a group or category of related organisms.

• For example, at the lowest level, species is a taxonomic category as is genera and all the way on up to kingdom and domain.

• These groups become increasingly inclusive as they become larger, going from species to kingdom or domain.


• The taxa are dynamic, changing as our knowledge of organisms and evolutionary relationships change.

• Linnaeus hierarchy of taxa (singular: taxon) was kingdom, class, order, genus, and species, but later taxonomists added phylum, division, family, lots of sub- and supertaxa, and even such taxa as domain, cohort, tribe, and section.

• Recently, a higher taxonomic category, the domain has been added to this list.

• Two key characteristic of taxa are that

1. Members of lower level taxa (e.g., species) are more similar to each other than are members of higher level taxa (e.g., kingdoms or domain)

2. Members of specific taxa are more similar to each other than any are to members of different specific taxa found at the same hierarchical level (e.g., humans are more similar to apes, i.e., comparison between species, than either is similar to, for example, Escherichia coli)

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• The organisms that fill a specific classification category are distinguishable from other organisms by sharing a set of characteristics or characters.

• A character is any structural, chromosomal, or molecular feature that differentiates one group from another.

• Organisms in the same kingdom have general characters in common while those in the same species have most characters in common.


OF LIVING THINGS

CLASSIFICATION SYSTEM

FIVE KINGDOM SYSTEM

THREE DOMAIN SYSTEM

Classification Classification

Example: Blue Whale

• Kingdom: Animalia

• Whales belong to the kingdom Animalia because whales, have many cells, ingest food, and are formed from a "blastula" (from a fertilized egg).

Classification

Example: Blue Whale

• Phylum (Division for plants): Chordata

• An animal from the phylum Chordata has a spinal cord and gill pouches.

Classification

Example: Blue Whale

• Class: Mammalia

• Whales and other mammals are warm blooded, have glands to provide milk for their off-spring, and have a four-chambered heart.

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Classification

Example: Blue Whale

• Order: Cetacea

• Cetaceans are mammals live completely in the water.

Classification

Example: Blue Whale

• [Suborder]: Mysticeti

• Whales that belong to the suborder Mysticeti have baleen plates (big filters in their mouths) rather than teeth.

Classification

Example: Blue Whale

• Family: Balaenidae

• The family Balaenidae, also called rorqual whales. They have pleats around their throat that allow them to hold lots of water (which contains their food).

Classification

Example: Blue Whale

• Genus: Balaenoptera

• A genus is a group of species that are more closely related to one another than any group in the family. Balaenoptera refers to the genus.

Classification

Example: Blue Whale

• Species: musculus

• A species is a grouping of individuals that interbreed successfully. The blue whale species name is musculus.

Classification System

• During the 1700s, Swedish botanist Carolus Linneus classified all then-known organisms into two large groups: the kingdoms Plantae and Animalia.

• Robert Whittaker in 1969 proposed five kingdoms: Plantae, Animalia, Fungi, Protista, and Monera.

• Organisms were placed into these kingdoms based on type of cell (prokaryotic or eukaryotic), levels of organization (unicellular or multicellular), and type of nutrition.

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Five-kingdom system

• The five-kingdom system of classification distinguishes the fungi (yeast, mushroom, and molds) as separate kingdom.

• Whittaker indicate that plants, animals and fungi are all multicelular eukaryotes, but each has it’s own mode of nutrition, such as, plants are autotrophic by photosynthesis, animals are heterotrophic by ingestion and fungi are heterotrophic saprotrophs.

Five-kingdom system

• Kingdom Protista contain various group of organisms that are difficult to classify and identify.

• Monera are easily differentiated by their structure because they are prokaryotic whereas the organisms in other kingdom are eukaryotic.

• The only type of organism in the kingdom Monera is bacteria.

• Other schemes involving an even greater number of kingdoms have lately been proposed, however most biologists employ Whittaker's five kingdoms.

Five-kingdom system

• The only type of organism in the kingdom Monera is bacteria.

• Other schemes involving an even greater number of kingdoms have lately been proposed, however most biologists employ Whittaker's five kingdoms.

5 KINGDOM SYSTEM

Three-domain system

• Recent studies suggest that the three domains are Archaea, Bacteria, and Eukarya.

• This is known as three-domain system of classification. In this type of classification, bacteria diverged first in the tree of life, and the domain Eukarya diverged from Archaea after the archaeans and bacteria diverged.

• Domain Bacteria and domain Archaea include prokaryotic unicellular organisms that reproduce asexually.

Three-domain system

• Systematists are in the process of sorting out what kingdoms belong within the domains Bacteria versus Archaea.

• Domain Eukarya includes unicellular to multicellular organisms whose cells have a membrane-bounded nucleus.

• Most of them involve in sexual reproduction with various types of life cycles.

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Three-domain system CHAPTER 1: CLASSIFICATION

OF LIVING THINGS

PHYLOGENY

PHYLOGENETIC TREES

CONSTRUCTING PHYLOGENETIC

TREES

PHYLOGENY LEADS TO CLASSIFICATION

Phylogenetic trees • Taxonomy is part of a larger division of biology known as

systematic, which is the study of the diversity of organisms at all levels of organization.

• In Greek, systematics comes from work systema, an orderly arrangement. Determination of phylogeny is a goal of systematics. This is done by the construction of phylogenetic tree.

• Phylogenetic tree is a branching diagram that shows a hypothesis about evolutionary relationships among organisms. To build these phylogenetic trees, we must have data that comes from the characteristics used in classification.

The relationship of classification and phylogeny for some carnivores

Phylogenetic tree showing relationship between human and apes

• In order to classify organisms and to construct phylogenetic trees, it is required to determine the characters of various taxa.

• Characters have a morphocline, or direction of evolutionary transformation, that runs from primitive to derive.

• Primitive characters are structural, physiological or behavioral trait or feature that is present in the ancestor and all members of a lineage.

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• Derived characters are structural, physiological or behavioral trait or features that are found in members of a lineage or descent but not found in the ancestors of the lineage.

• Different lineages diverging from common ancestor may have different derived characters.

• For example, the animals in the family Cervidae have antlers, but the antlers are palmate or having the shape of hand in reindeer and highly branch in red deer.

SYSTEMATICS IN RECONSTRUCTING PHYLOGENIES

• Systematists collect various data so as to discover the evolutionary relationship between species.

• They depend on a combination of data from many sources such as fossil record, homology, and molecular data in order to determine the right sequence of common ancestors in any particular group of organisms.


• Biologists are interested in the phylogenetic relationships among organisms for many reasons.

• To understand the evolution of structures they need to know which traits are ancestral and which are derived.


• They need a good phylogeny in order to determine how fast various traits have evolved in different lineages.

• Phylogenetic information is essential for the study of nearly all aspects of adaptation.

• Phylogeny is the complete evolutionary history of a kind or a group of organisms.

DEVELOPING PHYLOGENETIC CLASSIFICATION

Fossil record • Traits shared due to descent from a common

ancestor are called ancestral traits.

• The ancestral traits can be recognized by studying the traces of organisms that lived in the past.

• A fossil is any recognizable structure from an organism, or any impression from such a structure, that has been preserved.


Fossil record • A good fossil record helps reveal ancestral traits.

• For example, the excellent fossil records of horses’ show those modern horses, which have one toe on each foot, evolved from ancestors that had multiple toes.

• A trait, such as the modern horse's single toe, that differs from the ancestral trait in the lineage is called a derived trait.

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Homology • Homologies are anatomical features of different organisms

that have a similar appearance or function because they were inherited from a common ancestor that also had them.

• For example, the forelimb of a bear, the wing of a bird, and human arm have the same functional types of bones as did our shared reptilian ancestor where these bones are homologous structures.

• Homologous structures are structures that are similar in different species of common ancestry.

• The more homologies two organisms possess, the more likely it is that they have a close genetic relationship.


Homology • There can also be nonhomologous structural

similarities between species.

• In these cases, the common ancestor did not have the same anatomical structures as its descendants.

• Instead, the similarities are due to independent development in the now separate evolutionary lines.

• A characteristic that superficially looks to be homologous, but is actually independently acquired, is known to show homoplasy.


Homology • For example, shark and dolphin have similar,

but independently derived, body form because they have become adapted to similar aquatic environment and predatory lifestyles.

• Analogies are anatomical features that have the same form or function in different species that have no known common ancestor.


Homology • For instance, the wings of a bird and a butterfly

are analogous structures because they seem similar in appearance and function.

• However, their wings are quite different on the inside.

• Bird wings have an internal framework consisting of bones, while butterfly wings do not have any bones at all and are kept rigid mostly through fluid pressure.

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Shared derived characters • The shared ancestral characters, or

plesiomorphic characters, are traits that were present in an ancestral species and remain present in the entire group that descended from that ancestor.

• For example, the vertebral column, present in all vertebrates, is an ancestral character found in classes within subphylum Vertebrata.


Shared derived characters • Shared derives characters, or synapomorphic

characters, are traits found in two or more taxa that first appeared in their most recent common ancestor.

• For example, birds and reptiles, have a common ancestor, and both share the ancestral or plesiomorphic characters of laying eggs.

• The feathers and beaks of birds are not shared by reptiles.

• They are derived characters that evolved in birds.


Molecular biology • The molecules of organisms constitute their

micromorphology just as shapes of body parts constitute their gross morphology.

• Among the most important biochemical traits of organisms are their nucleic acids-DNA and RNA-and the proteins whose synthesis are directed by the nucleic acids.


Molecular biology A. Protein Comparisons

• More precise information about phylogenies can be obtained by comparing the amino acid sequence of proteins.

• For example, the differences in amino acid sequence of the blood protein hemoglobin and cytochrome c, an ancient protein common to all aerobic organisms, were shown to be greater the more phylogenetically distant the species.


Molecular biology B. DNA sequence

• The structure of the genes themselves where their base sequences provides the most direct evidence of evolutionary relationships among organisms.

• It is possible to determine DNA similarities by nucleic acid hybridization or DNA-DNA hybridization.

• In this process, DNAs can be compared; even if the precise sequences of their bases are not known, by a process called nucleic acid hybridization.



• Nucleic acid hybridization measures the extent of hydrogen bonding between single-stranded DNA that came from two sources.

• The tightness of the DNA of one species bind to the DNA of the other depending on the degree of similarity as base pairing between complementary sequence holds the two strands together.


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• Nucleic acid hybridization has already yielded some surprising results.

• For instance, the DNAs of humans and chimpanzees are much more similar than would be expected in relation the considerable morphological differences between the two species .

• This indicates that humans and chimps diverged from a common ancestor more recently than thought before.



Molecular biology C. RNA sequence analysis

• Ribosomes are present in all cells because they are important in protein synthesis.

• Moreover, the genes that code for ribosomal RNA (rRNA) have changed very slowly during evolution as compared to other genes.

• Thus, it is believed that comparative sequence of rRNA give a reliable indicator of the similarity between organisms.


Molecular biology D. Molecular clock analysis

• A comparison of the DNA nucleotide sequences of related organisms in order to estimate when they diverged from one another during the course of evolution.

• Molecular clocks are calibrated in actual time by graphing the number of amino acid or nucleotide differences against the times for a series evolutionary branch point obtained from fossil record.

• The graph then can be used to estimate the time of divergence for species and higher taxa, such as kingdom and phyla.


Taxa reflect evolutionary relationships

• Based on molecular data and other taxonomic criteria, systematists identify three kinds of taxonomic grouping: monophyletic, paraphyletic, and polyphyletic.

• Monophylectic related to a taxon derived from a single ancestral species that gave rise to no species in any other taxa.


TAXA REFLECT EVOLUTIONARY RELATIONSHIPS

• In monophylectic taxon, the taxon contains all the descendent species that come from a single common ancestor and no descendent species can be in any other taxon.

• The taxon is based on shared derived characters. • Paraphyletic taxa may have a common ancestor,

but do not include all descendents of the stem species

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Taxa reflect evolutionary relationships • Polyphyletic taxa consist of several

evolutionary lines and not including the most recent common ancestor of the included lineage.

• The organisms in polyphyletic group evolved from different ancestors.


OF LIVING THINGS

SYTEMATICS

CLADISTICS SYSTEMATICS

PHENETIC & NUMERICAL TAXONOMY

Systematics • The three main schools of systematics are

phenetics or numerical systematics, evolutionary systematics, and phylogenetic systematics, also known as cladistics..

Cladistics Systematics • Cladistics or phylogenetic classification is a

type of systematics developed by Willi Hennig, who attempted to develop a more objective method of classifying organisms.

• Cladistics is an approach to classification based on recency of common ancestry, rather than degree of structural similarity.

• Cladistics analysis involves the identification of clades.

Cladistics Systematics • Clades are evolutionary branches that consist of an

ancestral species and all its descendents. Such a group of organisms, whether it is a genus, family, or some higher taxon, is said to be monophylectic.

• Cladistics organizes closely related taxa into “sister taxa” and classifies them according to their phylogenetic relationships and its goal is to create monophylectic (not paraphyletic) taxa.

• The objective of cladistic systematics is to determine the evolutionary histories of organisms and then to express those relationships in phylogenetic trees and this is called a cladogram.

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Cladistics Systematics • Cladogram is a branching diagrams and each

branch on a cladogram represents the divergence or splitting of two new groups from a common ancestors.

• Cladogram also suggesting a classification of organisms based on the time sequence in which evolutionary branches arise.

• A cladogram traces the evolutionary history of the group being studied. Clade is evolutionary branch of a cladogram or a monophylectic taxon

BIRD AND LIZARD CLADE

CLADISTICS TAXONOMY • Cladists group organisms based on shared derived

characters, not on original traits or primitive characters.

• Groups of organisms that share a new or derived trait are more closely linked to one another than groups which have only the original set of traits or primitive characters.

• On the diagram below, shared derived characters are indicated as hauchers across the lines.

• The mammal clade is united by fur, the lizard, pigeon, mouse-chimp clade is united by claws or nails, etc.

CLADOGRAM OF THE VERTEBRATE CHORDATES CLADOGRAM

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• The closeness of organisms on a cladogram indicates the presumed time since they diverged from their most recent common ancestor.

• Since the goal is to show phylogenies, taxa in a cladistic classification are clades and are monophyletic; that is each taxon is a single lineage that includes all-and only-the descendants of a single ancestor.

• Important parts of cladistic analysis are a comparison between ingroup and outgroup.

• Ingroup refers to the group taxa that are actually being analyzed.

• The outgroup refers to the taxa that is known to have relationship to the ingroup but it is not the member of ingroup.

• For example, the turtle which is a reptiles is outgroup and the mammal is collectively ingroup are all linked to each other because they are vertebrates.

• Thus, vertebral column or backbone is a shared primitive character while hair and mammary glands are derived characters that differentiate reptiles from mammals.

• Traits those evolved relatively recently and so are not present in the ancestral species being considered is called a derived trait or derived characters.

• Another important aspect of cladistic analysis is known as parsimony.

• Parsimony refers to the search for the least complex explanation for an observed phenomenon.

• Parsimony results in the simplest cladogram possible and by referring to the minimum number of assumptions is the most logical.

• Parsimony in systematics means that the principle based on the experience that the simplest explanation is most probably the correct ones.

• Systematists use the principle of parsimony to build the phylogenetic trees which correspond to the smallest number of evolutionary changes.

• For example, parsimony leads to the hypothesis that a beaver is more closely linked to the kangaroo than the platypus because both the beaver and kangaroo have gestation.

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PHENETICS OR NUMERICAL TAXONOMY

• This method, invented in the 1750's by Michel Adanson, only became practical in recent decades as a result of the development of computers.

• The phenetic or phenotypic system is a numerical taxonomy based on similarities of many characters.

• Organisms are classified according to the number of characters or anatomical characteristics they share without trying to determine whether their similarities are homologus or analogous.

• Phenetic taxonomy is done by counting up differences in features between organisms and working out a classification from those counts, with the species having the fewest differences being the closest.

• Systematists of this school measure as many traits as possible and use the measurements to estimate the degree of relatedness.

• They argue that because no information on evolutionary history is available for most organisms, it is a mistake to attempt to reflect that history in classifications.

CHAPTER 1: CLASSIFICATION OF LIVING THINGS

EVOLUTIONARY SYTEMATICS

Evolutionary Systematics

• Evolutionary systematists or classical evolutionary systematists consider both evolutionary branching and the extent of divergence.

• It is based on shared ancestral characters as well as shared derived characters.

• These systematists mostly utilize anatomical data to classify organisms and build phylogenetic trees based on evolutionary principles.

CLASSICAL EVOLUTIONARY CLASSIFICATION OF REPTILES, BIRDS, AND

MAMMALS. • Data used in evolutionary systematics stresses

both common ancestry (monophyletic group) and the amount of divergence among groups.

• The evolutionary systematists, according to Linnaeus view, are that birds have feathers, reptiles have scales, and mammals have hair.

• Using this as a major character, a classification like that above has been constructed.

EVOLUTIONARY SYSTEMATICS

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• Fossils, evidence of past life, are not included in this classification.

• Since all of these groups have the amniotic egg, or a modification of it, they would be united in a larger taxon.

• Linnaeus placed each of these groups in a separate class within the Phylum Chordata.


• A primitive character is one present in the common ancestor and all members of the group, such as the amniotic egg.

• A derived character is one found only in a particular lineage within the larger group.

• In the example above, hair and feathers may be viewed as derived characters. A classical view of the example group is that birds and mammals evolved from reptiles due to their unique derived characters.


THE END BIO320: CHAPTER 1

chapter 1: classification of -...

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