Chapter 2 - Classification

CHAPTER 2

CLASSIFICATION OF LIVING THINGS

INTRODUCTION

• To trace phylogeny or the evolutionary history of life, biologists use evidence from paleontology, molecular data, comparative anatomy and other approaches.

Tracing phylogeny is one of the main goals of systematics, the study of biological diversity in an evolutionary context.

Systematics includes taxanomy, which is the naming and classification of species and groups of species.

Taxanomy employs a hierarchical system of classification• Taxonomy is the branch of biology dealing with the

identification, naming and classifying the diverse form of life.

• Taxonomy is the science of the classification of living things, and phylogeny is evolutionary history.

• The Linnean system, first formally proposed by Carolus Linnaeus in Systema naturae in the 18th century, it has two main characteristics.i) each species has a two-part name.ii) species are organized hierarchically into broader and broader groups of organisms.

Binomial System of Nomenclature

• The Linnaean system of naming species is referred to as the binomial system of nomenclature because each species is assigned to a two-part name.

• The first part of the name is a genus, and the second part, the species epithet, designates a particular species belonging to that genus.

• The generic name is always capitalized; the species epithet is not capitalized.

• Both names are always italicized or underlined.

• Under the binomial system, each species is assigned a two-part latinized name, a binomial.The first part, the genus, is the closest group to

which a species belongs.The second part, the specific epithet, refers to one

species within each genus.The first letter of the genus is capitalized and both

names are italicized and latinized.e.g Homo sapiens, Panthera tigris, Mimosa pudica

etc.

• A hierarchical classification will group species into broader taxonomic categories.

• Species that appear to be closely related are grouped into the same genus.

e.g. The leopard, Panthera pardus, belongs to a genus that includes the African lion (Panthera leo) and the tiger (Panthera tigris)

Biology’s taxonomic scheme formalizes our tendency to group related objects.

Phylogenetic trees reflect the hierarchical classification of taxonomic groups nested within more inclusive group.

SYSTEMATICS AND PHYLOGENETIC BIOLOGY

• 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.

Modern phylogenetic systematics is based on cladistic analysis

• A phylogeny is determined by a variety of evidence including fossils, molecular data, anatomy and other features.

• Most systematists use cladistic analysis, developed by a German entomologist Willi Hennig to analyze the data.

• A phylogenetic diagram or cladogram is constructed from a series of dichotomies.

cladogram

• Genera are grouped into progressively broader categories : family, order, class, phylum, kingdom and domain.

• Each taxonomic level is more comprehensive than the previous one.

as an example, all species of cats are mammals, but not all mammals are cats.

• The named taxonomic unit at the genus level, the generic name for various species of pine trees.

e.g: Pinus is a taxon at the genus level, the generic name for various species of pine trees.

Mammalia, a taxon at the class level, includes all the many orders of mammals.

• Determining which similarities between species are relevant to group the species in a clade is a challenge.

• It is important to distinguish similarities that are based on shared ancestry or homology from those that are based on convergent evolution or analogy.

• As a general rule, the more homologous parts that two species share, the more closely related they are.- Adaptation can obscure homology and convergence can create misleading analogies.

• Also, the more complex two structures are, the less likely that they evolved independently.– e.g. the skulls of a human and chimpanzee are

composed not of a single bone, but a fusion of multiple bones that match almost perfectly.

Constructing 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, structure and behavior, 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.

Homology• Homologies are anatomical features of different

organisms that have a similar appearance or function because they were inherited from a common ancestor.

• 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

• Homology indicates similarity in different species that results from their derivation from a common ancestor. The features that exhibit such similarity are called homologous features.

Nonhomology• Nonhomologous structural similarities

between species. • In these cases, the common ancestor did not

have the same anatomical structures as its descendants.

• Misleading similarities are called homoplasies. • Homoplastic structures can be the result of

parallelism, convergence, analogies, or mere chance.

Homoplasies• Parallelism, or parallel evolution, is a similar evolutionary

development in different species lines after divergence from a common ancestor that had the initial anatomical feature that led to it.

• Convergent evolution, distantly related groups may come to resemble one another in structure and function as they become adapted to similar modes of life.

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

Homoplasy

• Homoplasy indicates similarity in the characters in different species that is due to convergent evolution, not common descent.

• The features that exhibit such similarity are called homoplastic features.

Both parallelism and convergence are thought to be due primarily to separate species lines experiencing the same kinds of natural selection pressures over long periods of time.

• These dichotomous branching diagrams can include more taxa.

• The sequence of branching symbolizes historical chronology.

• Each branch or clade can be nested within larger clades.

• A clade consists of an ancestral species and all its descendants, a monophyletic group.

• Groups that do not fit this definition are unacceptable in cladistics.

Polyphyletic groups

Phylogenetic taxa

Monophyletic taxon

A group of organisms made up of a common ancestor and all of its descendants.

Example : Birds – sole descendants of a group of arboreal Triassic reptile.

Paraphyletic taxon

• A group of organisms made up of a common ancestor and some, but not all of its descendants are included in the grouping.

• Example : Modern reptiles because their amphibian ancestor also give rise to the birds and mammals.

Polyphyletic taxon

• A group made up of organisms that evolved from two or more different ancestors.

• Example : The group including all insectivorous animals.

Shared derived characters

• originate in a recent common ancestor and are present in its descendants.

• Species that share derived characters form a clade.• Systematists use shared derived characters to identify

points where groups diverged from one another.• More recent common ancestor is indicated by

classification into less inclusive taxonomic groups with more specific shared derived characters.

Example :

• If we compare dogs, goats and dolphins (all of which are mammals), only dogs and goats have hair whereas dolphins do not have hair. Hair is an ancestral trait in mammals and cannot be used as evidence that dogs and goats share a more recent common ancestor. In contrast, the virtual absence of hair in mature dolphins is a derived character within mammals.

• For example, the presence of hair is a good character to distinguish the clade of mammals from other tetrapods.- It is a shared derived character that uniquely identifies mammals.

• However, the presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals.- Among vertebrates, the backbone is a shared primitive character

because if evolved in the ancestor common to all vertebrates.

• Shared derived characters are useful in establishing a phylogeny, but shared primitive characters are not.

• The status of a character as analogous versus homologous or shared versus primitive may depend on the level at which the analysis is being performed.

All similar character

homologies analogies

Primitive derived(ancestral) (unique to a clade)

• For example, the forelimbs of bats and birds are analogous adaptations for flight because the fossil record shows that both evolved independently from the walking forelimbs of different ancestors.- Their common specializations for flight are convergent, not

indications of recent common ancestry.

• The presence of forelimbs in both birds and bats is homologous, through, at a higher level of the cladogram, at the level of tetrapods.

• The question of homology versus analogy often depends on the level of the clade that is being examined.

• Systematists must sort through homologous features of characters to separate shared derived characters from shared primitive characters.

• A shared derived character is uniquely to a particular clade.

• A shared primitive character is found not only in the clade being analyzed, but older clades too.

• Shared derived characters are useful in establishing a phylogeny, but shared primitive characters are not.

• In an outgroup analysis, the assumption is that any homologies shared by the ingroup and outgroup must be primitive characters already present in the ancestor common to both groups.

• Homologies present in some or all of the ingroup taxa must have evolved after the divergence of the ingroup and outgroup taxa.

- In our example, a notochord, present in lancets and in the embryos of the ingroup, would be a shared primitive character and not useful.

- The presence of a vertebral column, shared by all members of the ingroup but not the outgroup, is a useful character for the whole ingroup.

- Similarly, the presence of jaws, absent in lampreys and present in the other ingroup taxa, helps to identify the earliest branch in the vertebrate cladogram.

• A key step in cladistic analysis is outgroup comparison which is used to differentiate shared primitive characters from shared derived ones.

• To do this we need to identify an outgroup:- a species or group of species that is closely related to the species

that we are studying, - but known to be less closely related than any study-group

members are to each other.

• To study the relationships among five vertebrates ( the ingroup): a leopard, a turtle, a salamander, a tuna, and a lamprey, on a cladogram, then an animal called the lancet would be a good choice.- The lancet is closely related to the most primitive vertebrates

based on other evidence and other lines of analysis.- These other analyses also show that the lancet is not more closely

related to any of the ingroup taxa.

• Systematists can use cladograms to place species in the taxonomic hierarchy.- For example, using turtles as the outgroup, we can assign

increasing exclusive clades to finer levels of the hierarchy of taxa.

• However, some systematists argue that the hierarchical system is antiquated because such a classification must be rearranged when a cladogram is revised based on new evidence.- These systematists propose replacing the Linneaen system with a

strictly cladistic classification called phylocode that drops the hierarchical tags, such as class, order, and family.

- So far, biologists still prefer a hierarchical system of taxonomic levels as a more useful way of organizing the diversity of life.

• Analyzing the taxonomic distribution of homologies enables us to identify the sequence in which derived characters evolved during vertebrate phylogeny.

• A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms.- However, this chronology does not indicate the time of origin of the

species that we are comparing, only the groups to which they belong.

- For example, a particular species in an old group may have evolved more recently than a second species that belongs to a newer group.

• Most molecular systematics is based on a comparison of nucleotide sequences in DNA, or RNA.- Each nucleotide position along a stretch of DNA represents an

inherited character as one of the four DNA bases: A (adenine), G (guanine), C (cytosine), and T (thymine).

- Systematists may compare hundreds or thousands of adjacent nucleotide positions and among several DNA regions to assess the relationship between two species.

- This DNA sequence analysis provides a quantitative tool for constructing cladograms with branch points defined by mutations in DNA sequence.

• The rates of change in DNA sequences varies from one part of the genome to another.- Some regions (e.g., rRNA) that change relatively slowly are useful

in investigating relationships between taxa that diverged hundreds of millions of years ago.

- Other regions (e.g., mtDNA) evolve relatively rapidly and can be employed to assess the phylogeny of species that are closely related or even populations of the same species.

3. Systematists can infer phylogeny from molecular evidence

• The application of molecular methods and data for comparing species and tracing phylogenies has accelerated revision of taxonomic trees.- If homology reflects common ancestry, then comparing genes and

proteins among organisms should provide insights into their evolutionary relationships.

- The more recently two species have branced from a common ancestor, the more similar their DNA and amino acid sequences should be.

• These data for many species are available via the internet.

• Molecular systematics makes it possible to assess phylogenetic relationships that cannot be measured by comparative anatomy and other non-molecular methods.- This includes groups that are too closely related to have

accumulated much morphological divergence.- At the other extreme, some groups (e.g., fungi, animals, and

plants) have diverged so much that little morphological homolgy remains.

• In 1969, R.H Whittaker argued for a five-kingdom system: Monera, Protista, Plantae, Fungi, and Animalia.

• The five-kingdom system recognizes that there are two fundamentally different types of cells: prokaryotic (the kingdom Monera) and eukaryotic (the other four kingdoms).

• Three kingdoms of multicellular eukaryotes were distinguished by nutrition, in part.- Plant are autotrophic, making organic food by photosynthesis.- Most fungi are decomposers with extracellular digestion.- Most animals digest food within specialized cavities.

• The first step in DNA comparisons is to align homologous DNA sequences for the species we are comparing.- Two closely related species may differ only in which base is

present at a few sites.- Less closely related species may not only differ in bases at many

sites, but there may be insertions and deletions that alter the length

of genes.- This creates problems for establishing homology.

4. The five-kingdom system reflected increased knowledge of life’s diversity

• Traditionally, systematists have considered kingdom as the highest taxonomic category.

• As a product of a long tradition, beginning with Linnaeus organisms were divided into only two kingdoms of life-animal or plant.- Bacteria, with rigid cell walls, were placed with plants.- Even fungi, not photosynthetic and sharing little with green plants,

were considered in the plant kingdom.- Photosynthetic, mobile microbes were claimed by both botanists

and zoologists.

• Many microbiologists have divided the two prokaryotic domains into multiple kingdoms based on cladistic analysis of molecular data.

• A second challenge to the five kingdom system comes from systematists who are sorting out the phylogeny of the former members of the kingdom Protista.- Molecular systematics and cladistics have shown that the Protista

is not monophyletic.- Some of these organisms have been split among five or more new

kingdoms.- Others have been assigned to the Plantae, Fungi, or Animalia.

• In Whittaker’s system, the Protista consisted of all eukaryotes that did not fit the definition of plants, fungi, or animals.- Most protists are unicellular.- However, some multicellular organisms, such as seaweeds, were

included in the Protista because of their relationships to specific unicellular protists.

- The five-kingdom system prevailed in biology for over 20 years.

5. Arranging the diversity of life into the highest taxa is a work in progress

• During the last three decades, systematists applying cladistic analysis, including the construction of cladograms based on molecular data, have been identifying problems with the five-kingdom system.- One challenge has been evidence that there are two distinct

lineages of prokaryotes.- These data led to the three-domain system: Bacteria, Archaea, and

Eukarya, as superkingdoms.

Different approach in classifying organism

• How data are analyzed and interpreted depends on the systematist’s approach

1. Phenetic2. Cladistic3. Classical evolutionary taxonomy

Phenetics

• Phenetics is based on measurable phenotypic similarities and differences.

• A comparison is made of as many characters (atonomical characteristics) as possible without attempting to sort homology from analogy.

• The phenetic approach is also called numerical taxonomy.

• Pheneticists do not attempt to distinguish between homoplastic and homologus characteristics.

• The inclusion of homoplastic characteristics may lead to inaccurate taxonomic classifications.

• Clearly, taxonomy at the highest level is a work in progress.- It may seem ironic that systematists are generally more confident

in their groupings of species into lower tax than they are about evolutionary relationships among the major groups of organisms.

- Tracing phylogeny at the kingdom level takes us back to the evolutionary branching that occurred in Precambrian seas a billion or more years ago.

• There will be much more research before there is anything close to a new consensus for how the three domains of life are related and how many kingdoms there are.- New data will undoubtedly lead to further taxonomic modeling.- Keep in mind that phylogenetic trees and taxonomic groupings are

hypotheses that fit the best available data.

Cladistics

• Phylogenetic systematics (cladistics) emphasizes phylogeny.

• Cladists use shared derived characters to reconstruct phylogenies by outgroup analysis.

• Cladograms illustrate branching between taxa.

• Ancestral and derived characters are used to construct cladograms

Classical evolutionary taxonomy

• Allows paraphyletics group which attempts to balance the extent of divergence and the branching sequence.

• Predates both phenetics and cladistics, but now incorporates some ideas from both.

• In cases of systematic conflict, a subjective judgement is made about which type of information receives the highest priority.

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