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Diversity In Living Organisms

Our planet is gifted with numerous living organisms, which vary in their size, shape, habitat, nutrition, reproduction and a lot more. Based on their physical features and their habitat, these animals of Kingdom Animale are classified into different order and class.

Animals living in different environments, including the water, land, deserts, forests, grasslands, ice land and water and ice to deserts and forests and grasslands. All these organisms consist of something called cells.

Cells are the building blocks of life and one of the most important characteristics of living organisms. They are structural units of life carrying out specifically assigned functions. A group of such cells form a tissue.

Diversity in living organisms can be experienced everywhere on earth. The warm and humid regions of the earth are highly diverse and are called the region of mega biodiversity. 12 countries in the world have more than half of the biodiversity in the world. India is one of them.

Each individual has a unique DNA set up. We differ amongst human beings in the way we look and different attributes contributing to it such as our height, complexion etc. If we compare ourselves with a different species like a horse or a fish, we would definitely vary greatly in almost all aspects but if a horse is compared to a zebra, we would be able to draw a few differences only.

Classification

The arrangement of the organisms in groups on the basis of their similarities and differences is known as classification.

Basis Of Classification

Over millions of years, we have seen diversity in living beings. We have evolved from ape-like beings to homo sapiens. We look for similarities between organisms so that we can classify them into classes and hence study them as a whole, for this, fundamental characteristics need to be decided which would form the foundation for classifying.

Classification can be carried out based on many factors such as:

Presence of nucleus

Body design – make up of cells(Single-celled or Multicellular organisms)

Production of food

Level of the organization in bodies of organisms carrying out photosynthesis

In animals – an organization of one’s body parts, development of body, specialized organs for different functions

These features can differ in both plants and animals as they differ in their body design. Hence, these prominent designs and characteristic features can be used to make subgroups and not aa broad classification.

Classification System

The classification system is of two types:

Two-Kingdom Classification- This system was proposed by Carolus Linnaeus who classified organisms into two types- plants and animals.

Five-Kingdom Classification-  This kingdom was proposed by H.Whittaker who divided the organisms into five different classes:

Hierarchy of Classification

Carolus Linnaeus arranged the organisms into different taxonomic groups at different levels. The groups from top to bottom are:

Characteristics of Five Kingdoms

Kingdom monera.

These are unicellular prokaryotes.

They lack a true nucleus.

They may or may not contain a cell wall.

They may be heterotrophic or autotrophic.

For eg., Bacteria, Cyanobacteria

Kingdom Protista

These contain unicellular, eukaryotic organisms.

They exhibit an autotrophic or heterotrophic mode of nutrition .

They possess pseudopodia, cilia, flagella for locomotion.

For eg., amoeba, paramaecium

Kingdom Fungi

These are multicellular, eukaryotic organisms.

They exhibit a saprophytic mode of nutrition.

The cell wall is made up of chitin.

They live in a symbiotic relationship with blue-green algae.

For eg., Yeast, Aspergillus

Kingdom Plantae

The cell wall is made up of cellulose.

They prepare their own food by means of photosynthesis.

Kingdom Plantae is sub-divided into- Thallophyta, Bryophyta, Pteridophyta, Gymnosperms, Angiosperms.

For eg., Pines, ferns, Mango tree

Kingdom Animalia

These are multicellular, eukaryotic organisms without a cell wall.

They are heterotrophs.

The organisms in kingdom Animalia can be simple or complex.

They are genetically diverse.

They exhibit an organ-system level of organization.

It is sub-divided into different phyla such as Porifera, Coelenterata, Echinodermata, Chordata, etc.

For eg., Earthworms, Hydra, etc.

Also read : The Living World

Classification And Evolution

Classification of organisms is closely related to evolution. Evolution is the changes that have accumulated over the years in the body design of organisms for better survival. In 1859, Charles Darwin first described the idea of evolution in his book ‘The Origin Of Species’.

Listed below are inferences drawn when evolution is connected to classification:

‘Lower’ or ‘primitive’ organisms are the organisms having the ancient body type and seem to have not changed over the years.

‘Higher’ or ‘advanced’ organisms are those who are relatively recent and have acquired their particular body designs.

But these terms cannot used be used in classifying organisms, hence we use terms like ‘younger’ and ‘older’ organisms as there is a possibility of witnessing changes with passing time due to increase in the complexity of body designs. Hence, we can simply say, older organisms are simpler compared to younger organisms.

Also read : Cells

Diversity in Living Organisms is a fundamental topic introduced in the higher primary classes. We have reintroduced content revamped for better understanding and comprehension, leading to the creation of Diversity in Living Organisms Class 9.

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ENCYCLOPEDIC ENTRY

Biodiversity.

Biodiversity refers to the variety of living species on Earth, including plants, animals, bacteria, and fungi. While Earth’s biodiversity is so rich that many species have yet to be discovered, many species are being threatened with extinction due to human activities, putting the Earth’s magnificent biodiversity at risk.

Biology, Ecology

grasshoppers

Although all of these insects have a similar structure and may be genetic cousins, the beautiful variety of colors, shapes, camouflage, and sizes showcase the level of diversity possible even within a closely-related group of species.

Photograph by Frans Lanting

Biodiversity is a term used to describe the enormous variety of life on Earth. It can be used more specifically to refer to all of the species  in one region or ecosystem . Bio diversity refers to every living thing, including plants, bacteria, animals, and humans. Scientists have estimated that there are around 8.7 million species of plants and animals in existence. However, only around 1.2 million species have been identified and described so far, most of which are insects. This means that millions of other organisms remain a complete mystery.

Over generations , all of the species that are currently alive today have evolved unique traits that make them distinct from other species . These differences are what scientists use to tell one species from another. Organisms that have evolved to be so different from one another that they can no longer reproduce with each other are considered different species . All organisms that can reproduce with each other fall into one species .

Scientists are interested in how much biodiversity there is on a global scale, given that there is still so much biodiversity to discover. They also study how many species exist in single ecosystems, such as a forest, grassland, tundra, or lake. A single grassland can contain a wide range of species, from beetles to snakes to antelopes. Ecosystems that host the most biodiversity tend to have ideal environmental conditions for plant growth, like the warm and wet climate of tropical regions. Ecosystems can also contain species too small to see with the naked eye. Looking at samples of soil or water through a microscope reveals a whole world of bacteria and other tiny organisms.

Some areas in the world, such as areas of Mexico, South Africa, Brazil, the southwestern United States, and Madagascar, have more bio diversity than others. Areas with extremely high levels of bio diversity are called hotspots . Endemic species — species that are only found in one particular location—are also found in hotspots .

All of the Earth’s species work together to survive and maintain their ecosystems . For example, the grass in pastures feeds cattle. Cattle then produce manure that returns nutrients to the soil, which helps to grow more grass. This manure can also be used to fertilize cropland. Many species provide important benefits to humans, including food, clothing, and medicine.

Much of the Earth’s bio diversity , however, is in jeopardy due to human consumption and other activities that disturb and even destroy ecosystems . Pollution , climate change, and population growth are all threats to bio diversity . These threats have caused an unprecedented rise in the rate of species extinction . Some scientists estimate that half of all species on Earth will be wiped out within the next century. Conservation efforts are necessary to preserve bio diversity and protect endangered species and their habitats.

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Diversity in Living Organisms

What is diversity in living organisms.

Biodiversity is used to define the diversity of life forms worldwide. It is a word that is used more often to refer to the classification of living species found in a particular geographic region. The Diversity of living species of a geographic region in an area provides stability in the respective region.

There are numerous living organisms on earth with different sizes, shapes, habitats, nutrition, reproduction, and more.  That depends on their physical features and their habitat. Animals of any kingdom are classified into different orders and classes.

Animals live in different climates like water, land, grasslands, deserts, forests, ice, water, and ice to forests, deserts, and grasslands. All these organisms consist of cells.

Cells are one of the essential characteristics of living organisms.  Cells are structural units of life. It carries out specifically assigned functions in living species.  In this way, a group of cells from tissue in living species.

Diversity in living organisms can be seen everywhere on earth.  The region of the earth is highly diverse and is called the region of mega biodiversity. Twelve countries in the world have more than half of the biodiversity in the world. India is also one of them.

Over millions of years, diversity has been going on in living beings.  Species have evolved from ape-like beings to homo sapiens.  People look for similarities between organisms to classify them, and hence they study them as a whole. Regarding this, fundamental characteristics need to be decided, which would form the foundation for classifying.

Introduction to Diversity in Living Organisms

Life exists in different forms on Earth. When it comes to the question of the number of living organisms found on the earth, the answer is unimaginable. This is so because of the large diversity of organisms continuously evolving into a different variety ever since the origin of life had taken place. Diversity is present at different levels like genetic diversity, species diversity, and ecological diversity. Mango alone has around 10,000 varieties in India. This alone example indicates how large and diverse are the living organisms. Gaining knowledge about this large diversity is impossible without classifying them. Thus classification becomes an important step towards the study of different organisms found on the earth.

Biological Classification

The process of putting all the organisms in certain groups on the basis of certain similarities and differences is known as Classification

Various characteristics are taken into account in order to classify an organism. Some of them are-

The type of cell present whether the organism is having a eukaryotic cell or a prokaryotic cell. 

The number of cells whether the organism is unicellular or multicellular.

Body organization whether the organization is cellular, tissue-level, or organ-level.

 The nutrition of organisms whether it's autotrophic or heterotrophic.

Morphological features of the organisms.

Anatomical features of the organism etc.

All these features including many others are taken into consideration during the classification

Classification System

Various scientists have proposed their own model of classifying organisms. Some of these are given below.

Two Kingdom Classification

Carolus Linnaeus gave the 2-kingdom system of classification and divided all the organisms into two groups as Plantae and Animalia. This kind of classification brought all the organisms which had a cell wall together within their cell in one group called the Plantae and the rest all were placed in the other group known as Animalia.

Plantae comprises bacteria, fungi with plants. All were very different from each other but still were kept together under two-kingdom classification. There was no distinction between the prokaryotes as well as eukaryotes. Thus this system of classification was not right but surely helped in evolving a better classification system.

Five Kingdom Classification

R.H Whittaker proposed a five-kingdom classification. This classification is accepted and corrected worldwide. A number of criteria were considered for making this model like the cell type, cell number, cell organization, nutrition, etc. 

It consists of 5 groups /kingdoms 

Animalia 

Characteristics of Five Kingdom

Kingdom Monera

This kingdom has organisms that are unicellular and have prokaryotic cell.

It includes bacteria, cyanobacteria, etc.

Their cell usually has a cell wall.

They can be autotrophic or heterotrophic.

(Image will be Uploaded Soon)

Kingdom Protista

This kingdom includes organisms that are also unicellular but have a eukaryotic cell.

They may be photosynthetic or heterotrophic.

They may possess structures like flagella and cilia.

Examples are amoeba, euglena, paramecium, etc.

Kingdom Fungi

This is the first kingdom with multicellular organisms.

They exhibit a heterotrophic mode of nutrition more specifically saprotrophic mode of nutrition.

They have a eukaryotic cell with a cell wall that is made up of chitin.

Example - yeast, mushroom

Kingdom Plantae

All organisms are eukaryotic and multicellular.

The body can be seen as differentiated into higher groups.

They are photosynthetic and exhibit an autotrophic mode of nutrition. Some members are partially heterotrophic.

Their cell has a cell wall made up of cellulose.

Examples- mango tree, red algae , etc.

Kingdom Animalia

All members are eukaryotic and multicellular.

Their cells lack a cell wall.

They are heterotrophs.

Examples- lion, dog, fish, etc.

Classification Hierarchy

The broadest group Kingdom is further divided into small groups to reach a point of maximum similarity in one group of organisms. Thus a hierarchy of classification is developed when the small groups are arranged from the lowest to the highest order. Each category in the hierarchy is known as Taxon.

Following is the Hierarchy of Classification:

Phylum / Division

 Genus

Species are the basic unit of classification.

Classification and Evolution

Classification of organisms is related to evolution. Evolution is the change that takes more over the years in the body design of organisms for better survival. Charles Darwin first described the concept of evolution in his book ‘The Origin Of Species’ in 1859.

Lower organisms are the organisms that seem to have not changed over the years.

Higher organisms are relatively recent and have their particular body designs.

Diversity in Living Organisms is a fundamental topic introduced in students in higher and junior classes.  It is a primary and essential topic of Study, for this one can easily follow Vedantu and know about interesting facts about Diversity.

Yeast is the only unicellular fungus.

Lichens are organisms in which algae and fungi live together and exhibit symbiotic relationships.

FAQs on Diversity in Living Organisms

1. Why is there diversity among organisms? 

Calculation of biology is never perfect, and one can not achieve the exact copy. There are numerous steps in molecular biology that do not give the exact copy from replication to a functional protein. This incident leads to mutation, changes, and Diversity. This Diversity is then screened by natural selection. Whoever survives the present environmental condition will reproduce if naturally selected as per evolution.

2. Why is biodiversity so important?

Biodiversity refers to the number of different species living in the regions.  It represents the wealth of biological wealth in nature. It globally varies with the regions. Many natural factors affect biodiversities like temperature, soils, and other natural things. It maintains the balance of climate and nature in a recycled way. Biodiversity also affects social life like recreation, education, research, human health, industry, and culture. Thus one can say that biodiversity is crucial for the well-being of life on earth.

3. Why does evolution result in so much biodiversity?

The earth is much bigger than we can think. There are lots of species that are still not discovered. They also survive in various possible ways by fighting with nature. There are many attainable ways for organisms to survive.  A planet has its way to protect the lives in it.  There are several chemicals set up to make them survive. And this is also getting evolved day by day in their need.

4. Describe the significance of the study of living organisms for students?

Most people believe that everyone must study living organisms as humans are also part of evolution. By studying, one can know detailed information about nature, from recycling every natural thing and the life of every living species. There are many things about what a person may know. It is also an essential part for students as they should know about the Living species in nature. Diversity is now included in the study syllabus of the students.

5. How can a student get to know detailed information about living organisms?

The biodiversity of living organisms is a critical topic for students. If any student wants to know about that from the internet, they can find many research materials, and there are thousands of results and online learning websites where one can get help in any subject or topic. But choosing the best is the priority.

6. Comment on the relationship between classification and evolution.

As we take a closer look at the classification of organisms and how the kingdoms and phyla are arranged one after the other, depicting a change from simple to complex forms,  it actually indicates the pattern of evolution that has taken place on the earth in the past years. Classification and its hierarchy is the direct evidence of evolution. Higher groups are evolved from the lower groups from gradual evolution and these groups are placed accordingly in the hierarchy. Thus Classification is interrelated to evolution though were developed and studied independently.

7. Define the artificial system of classification.

Organisms were also classified on the basis of habitat and feeding habits are known as an artificial system of classification.

Some groups on the basis of habitats are mentioned below :

Aquatic- Organisms that live in water are considered aquatic organisms. It has many other subgroups like Benthos (bottom-dwelling), sedentary (fixed in water), etc.

Terrestrial- Organisms that live on land are known as terrestrial. They can be scansorial (wall climbers), arboreal (tree climbers), cursorial (fast-moving ), etc. Example- ants, monkeys, etc.

Amphibious- These types of organisms can live both on land and water. Example- Frog and Crocodile.

Biology • Class 9

Module 1: Introduction to Biology

The diversity of life, learning outcomes.

• Explain the “diversity of life”

Figure 1. Life on earth is incredibly diverse.

Biological diversity is the variety of life on earth. This includes all the different plants, animals, and microorganisms; the genes they contain; and the ecosystems they form on land and in water. Biological diversity is constantly changing. It is increased by new genetic variation and reduced by extinction and habitat degradation.

What Is Biodiversity?

Biodiversity refers to the variety of life and its processes, including the variety of living organisms, the genetic differences among them, and the communities and ecosystems in which they occur. Scientists have identified about 1.9 million species alive today. They are divided into the six kingdoms of life shown in Figure 2. Scientists are still discovering new species. Thus, they do not know for sure how many species really exist today. Most estimates range from 5 to 30 million species.

Figure 2. Click for a larger image. Known life on earth

Cogs and Wheels

To save every cog and wheel is the first precaution of intelligent tinkering. —Aldo Leopold, Round River: from the Journals of Aldo Leopold , 1953

Leopold—often considered the father of modern ecology—would have likely found the term biodiversity  an appropriate description of his “cogs and wheels,” even though idea did not become a vital component of biology until nearly 40 years after his death in 1948.

Literally, the word biodiversity  means the many different kinds ( diversity ) of life ( bio -), or the number of species in a particular area.

• The most precise and specific measure of biodiversity is genetic diversity or genetic variation within a species. This measure of diversity looks at differences among individuals within a population, or at difference across different populations of the same species.
• The level just broader is  species diversity , which best fits the literal translation of biodiversity : the number of different species in a particular ecosystem or on Earth. This type of diversity simply looks at an area and reports what can be found there.
• At the broadest most encompassing level, we have ecosystem diversity . As Leopold clearly understood, the “cogs and wheels” include not only life but also the land, sea, and air that support life. In ecosystem diversity, biologists look at the many types of functional units formed by living communities interacting with their environments.

Although all three levels of diversity are important, the term biodiversity usually refers to species diversity!

Video Review

Watch this discussion about biodiversity:

You can view the transcript for “Biodiversity from ‘the Wild Classroom'” here (link opens in new window).

Biodiversity provides us with all of our food. It also provides for many medicines and industrial products, and it has great potential for developing new and improved products for the future. Perhaps most importantly, biological diversity provides and maintains a wide array of ecological “services.” These include provision of clean air and water, soil, food and shelter. The quality—and the continuation— of our life and our economy is dependent on these “services.”

Australia’s Biological Diversity

Figure 2. The short-beaked echidna is endemic to Australia. This animal—along with the platypus and three other species of  echidnas—is one of the five surviving species of egg-laying mammals.

The long isolation of Australia over much of the last 50 million years and its northward movement have led to the evolution of a distinct biota. Significant features of Australia’s biological diversity include:

• over 80% of flowering plants
• over 80% of land mammals
• 88% of reptiles
• 45% of birds
• 92% of frogs
• Wildlife groups of great richness. Australia has an exceptional diversity of lizards in the arid zone, many ground orchids, and a total invertebrate fauna estimated at 200,000 species with more than 4,000 different species of ants alone. Marsupials and monotremes collectively account for about 56% of native terrestrial mammals in Australia.
• Wildlife of major evolutionary importance. For example, Australia has 12 of the 19 known families of primitive flowering plants, two of which occur nowhere else. Some species, such as the Queensland lungfish and peripatus, have remained relatively unchanged for hundreds of millions of years.
• Revision and adaptation. Authored by : Shelli Carter and Lumen Learning. Provided by : Lumen Learning. License : CC BY-NC: Attribution-NonCommercial
• Biodiversity. Provided by : CK-12. Located at : http://www.ck12.org/biology/Biodiversity/lesson/Biodiversity-BIO/?referrer=featured_content . License : CC BY-NC: Attribution-NonCommercial
• Conserving Australia's biological diversity. Provided by : Australian Government, Department of the Environment and Energy. Located at : https://www.environment.gov.au/sustainability/education/publications/conserving-australias-biological-diversity-teachers-notes . License : CC BY: Attribution
• Long-beaked Echidna. Authored by : Jaganath. Located at : https://commons.wikimedia.org/wiki/File:Long-beakedEchidna.jpg . License : CC BY-SA: Attribution-ShareAlike
• Biodiversity - from The Wild Classroom. Authored by : Rob & Jonas Filmmaking Tips. Located at : https://youtu.be/vGxJArebKoc . License : All Rights Reserved . License Terms : Standard YouTube License

The Diversity of Life

The fact that biology, as a science, has such a broad scope has to do with the tremendous diversity of life on earth. The source of this diversity is evolution, the process of gradual change during which new species arise from older species. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems.

The evolution of various life forms on Earth can be summarized in a phylogenetic tree (Figure 1). A phylogenetic tree is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of branches (the lines) and nodes (places where two lines diverge). The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch is proportional to the time elapsed since the split.

While this is the most common way that is used to group organisms, other divisions have been proposed.

• Some scientists believe that organisms should be divided into two groups: Prokaryota (or Monera) and Eukaryota. In this method, Archae is typically included in Prokaryota. This view has become less popular due to scientific advancements, specifically genetic analysis of various organisms.
• Another two-group division groups Archae with Eukaryotes. This is often called the “Eocyte hypothesis”. This hypothesis has become more popular as the genomes of more Archaeic organisms are sequenced.

None of the three systems currently include non-cellular life. As of 2011 there is talk about Nucleocytoplasmic large DNA viruses possibly being a fourth branch domain of life, a view supported by researchers in 2012.

Stefan Luketa in 2012 proposed a five-domain system, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains.

Evolution Connection

Carl woese and the phylogenetic tree.

In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The organizational scheme was based mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which are used by modern systematics. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. The first two are prokaryotic cells with microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms together with the four original kingdoms (excluding bacteria). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (Figure 1). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape).

Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese’s approach was revolutionary because comparisons of physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (Figure 3). The comparison of homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified the separation of the prokaryotes into two domains: bacteria and archaea.

Unless otherwise noted, images on this page are licensed under CC-BY 4.0  by  OpenStax .

Text adapted from:

OpenStax , Concepts of Biology. OpenStax CNX. May 25, 2017 https://cnx.org/contents/[email protected]:gNLp76vu@13/Themes-and-Concepts-of-Biology

Eocyte Hypothesis, Wikipedia.  May 25, 2017. https://en.wikipedia.org/wiki/Eocyte_hypothesis

Domain (biology), Wikipedia. May 25, 2017. https://en.wikipedia.org/wiki/Domain_(biology)

Principles of Biology Copyright © 2017 by Lisa Bartee, Walter Shriner, and Catherine Creech is licensed under a Creative Commons Attribution 4.0 International License , except where otherwise noted.

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1.6: The Origins, Evolution, Speciation, Diversity and Unity of Life

• Last updated
• Save as PDF
• Page ID 16413

• Gerald Bergtrom
• University of Wisconsin-Milwaukee

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The question of how life began has been with us since the beginnings or recorded history. It is now accepted that there was a time, however brief or long, when the earth was a lifeless (prebiotic) planet. Life’s origins on earth date to some 3.7-4.1 billion years ago under conditions that favored the formation of the first cell, the first entity with all of the properties of life. But couldn’t those same conditions have spawned multiple cells independently, each with all of the properties of life? If so, from which of these did life, as we know it today, descend? Whether there were one or more different “first cells”, evolution (a property of life) only began with those cells.

115 Properties of Life

The fact that there is no evidence of cells of independent origin may reflect that they never existed. Alternatively, the cell we call our ancestor was evolutionarily successful at the expense of other life forms, which thus became extinct. In any event, whatever this successful ancestor may have looked like, its descendants would have evolved quite different appearances, chemistries and physiologies. These descendant cells would have found different genetic and biochemical solutions to achieving and maintaining life’s properties. One of these descendants evolved the solutions we see in force in all cells and organisms alive today, including a common ( universal ) genetic code to store life’s information, as well as a common mechanism for retrieving the encoded information. Francis Crick called is commonality the “Central Dogma” of biology. That ancestral cell is called our Last Universal Common Ancestor , or LUCA .

116 The Universal Genetic Code 117 Origins of Life 118 Life Origins vs Evolution

Elsewhere we consider in more detail how we think about the origins of life. For now, our focus is on evolution, the property of life that is the basis of speciation and life’s diversity.

Natural selection was Charles Darwin’s theory for how evolution led to the structural diversity of species. New species arise when beneficial traits are naturally selected from genetically different individuals in a population, with the concomitant culling of less fit individuals from populations over time. If natural selection acts on individuals, evolution results from the persistence and spread of selected, heritable changes through successive generations in a population. Evolution is reflected as an increase in diversity and complexity at all levels of biological organization, from species to individual organisms to molecules. For an easy read about the evolution of eyes (whose very existence according to creationists could only have formed by intelligent design by a creator), see the article in National Geographic by E. Yong (Feb., 2016, with beautiful photography by D. Littschwager).

Repeated speciation occurs with the continual divergence of life forms from an ancestral cell through natural selection and evolution. Our shared cellular structures, nucleic acid, protein and metabolic chemistries (the ‘unity’ of life) supports our common ancestry with all life. These shared features date back to our LUCA! Most living things even share some early behaviors . Take our biological clock , an adaptation to our planet’s 24 hour daily cycles of light and dark that have been around since the origins of life; all organisms studied so far seem to have one!. The discovery of the genetic and molecular underpinnings of circadian rhythms (those daily cycles) earned Jeffrey C. Hall, Michael Rosbash and Michael W. Young the 2017 Nobel Prize in Medicine or Physiology (click Molecular Studies of Circadian Rhythms wins Nobel Prize to learn more)!

The molecular relationships common to all living things largely confirm what we have learned from the species represented in the fossil record. Morphological, biochemical and genetic traits that are shared across species are defined as homologous , and can be used to reconstruct evolutionary histories. The biodiversity that scientists (in particular, environmentalists) try to protect is the result of millions of years of speciation and extinction. Biodiversity needs protection from the unwanted acceleration of evolution arising from human activity, including blatant extinctions (think passenger pigeon), and near extinctions (think American bison by the late 1800s). Think also of the consequences the introduction of invasive aquatic and terrestrial species and the effects of climate change.

Let’s look at the biochemical and genetic unity among livings things. We’ve already considered what happens when cells get larger in evolution when we tried to explain how larger cells divided their labors among smaller intracellular structures and organelles. When eukaryotic cells evolved into multicellular organisms, it became necessary for the different cells to communicate with each other and to respond to environmental cues.

Some cells evolved mechanisms to “talk” directly to adjacent cells and others evolved to transmit electrical (neural) signals to other cells and tissues. Still other cells produced hormones to communicate with cells to which they had no physical attachment. As species diversified to live in very different habitats, they also evolved very different nutritional requirements, along with more extensive and elaborate biochemical pathways to digest their nutrients and capture their chemical energy. Nevertheless, despite billions of years of obvious evolution and astonishing diversification, the underlying genetics and biochemistry of living things on this planet is remarkably unchanged. Early in the 20th century, Albert Kluyver first recognized that cells and organisms vary in form appearance in spite of the essential biochemical unity of all organisms (see Albert Kluyver in Wikipedia ). This unity amidst the diversity of life is a paradox of life that we will probe further in this course.

A. Genetic Variation, the Basis of Natural Selection

DNA contains the genetic instructions for the structure and function of cells and organisms. When and where a cell or organism’s genetic instructions are used (i.e., to make RNA and proteins) are regulated. Genetic variation results from random mutations. Genetic diversity arising from mutations is in turn, the basis of natural selection during evolution.

119 The Random Basis of Evolution

B. The Genome: An Organism’s Complete Genetic Instructions

We’ve seen that every cell of an organism carries the DNA including gene sequences and other kinds of DNA. The genome of an organism is the entirety of its genetic material (DNA, or for some viruses, RNA). The genome of a common experimental strain of E. coli was sequenced by 1997 (Blattner FR et al. 1997 The complete genome sequence of Escherichia coli K-12. Science 277:1452-1474). Sequencing of the human genome was completed by 2001, well ahead of the predicted schedule (Venter JC 2001 The sequence of the human genome . Science 291:1304-1351). As we have seen in the re-classification of life from five kingdoms into three domains, nucleic acid sequence comparisons can tell us a great deal about evolution. We now know that evolution depends not only on gene sequences, but also, on a much grander scale, on the structure of genomes. Genome sequencing has confirmed not only genetic variation between species, but also considerable variation between individuals of the same species. Genetic variation within species is in fact the raw material of evolution. It is clear from genomic studies that genomes have been shaped and modeled (or remodeled) in evolution. We’ll consider genome remodeling in more detail elsewhere.

C. Genomic ‘Fossils’ Can Confirm Evolutionary relationships.

It had been known for some time that gene and protein sequencing could reveal evolutionary relationships and even familial relationships. Read about an early demonstration of such relationships based on amino acid sequence comparisons across evolutionary time in Zuckerkandl E and Pauling L. (1965) Molecules as documents of evolutionary theory. J. Theor. Biol. 8:357-366. It is now possible to extract DNA from fossil bones and teeth, allowing comparisons of extant and extinct species. DNA has been extracted from the fossil remains of humans, other hominids, and many animals. DNA sequencing reveals our relationship to each other, to our hominid ancestors and to animals from bugs to frogs to mice to chimps to Neanderthals to… Unfortunately, DNA from organisms much older than 10,000 years is typically so damaged or simply absent, that relationship building beyond that time is impossible. Now in a clever twist, using what we know from gene sequences of species alive today, investigators recently ‘constructed’ a genetic phylogeny suggesting the sequences of genes of some of our long-gone progenitors, including bacteria (click here to learn more: Deciphering Genomic Fossils ). The comparison of these ‘reconstructed’ ancestral DNA sequences suggests when photosynthetic organisms diversified and when our oxygenic planet became a reality.

120 Genomic Fossils- Molecular Evolution

Why is biodiversity important?

Biodiversity is essential for the processes that support all life on Earth, including humans. Without a wide range of animals, plants and microorganisms, we cannot have the healthy ecosystems that we rely on to provide us with the air we breathe and the food we eat. And people also value nature of itself.

Some aspects of biodiversity are instinctively widely valued by people but the more we study biodiversity the more we see that all of it is important – even bugs and bacteria that we can’t see or may not like the look of. There are lots of ways that humans depend upon biodiversity and it is vital for us to conserve it. Pollinators such as birds, bees and other insects are estimated to be responsible for a third of the world’s crop production. Without pollinators we would not have apples, cherries, blueberries, almonds and many other foods we eat. Agriculture is also reliant upon invertebrates – they help to maintain the health of the soil crops grow in.  Soil is teeming with microbes that are vital for liberating nutrients that plants need to grow, which are then also passed to us when we eat them. Life from the oceans provides the main source of animal protein for many people.

Trees, bushes and wetlands and wild grasslands naturally slow down water and help soil to absorb rainfall. When they are removed it can increase flooding. Trees and other plants clean the air we breathe and help us tackle the global challenge of climate change by absorbing carbon dioxide. Coral reefs and mangrove forests act as natural defences protecting coastlines from waves and storms. 

Many of our medicines, along with other complex chemicals that we use in our daily lives such as latex and rubber, also originate from plants. Spending time in nature is increasingly understood to lead to improvements in people’s physical and mental health. Simply having green spaces and trees in cities has been shown to decrease hospital admissions, reduce stress and lower blood pressure.

Further reading

Plural valuation of nature matters for environmental sustainability and justice by Berta Martin-Lopez, Social-Ecological Systems Institute, Faculty of Sustainability, Leuphana University of Lüneburg, Germany

Climate change and biodiversity

Human activities are changing the climate. Science can help us understand what we are doing to habitats and the climate, but also find solutions.

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Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002.

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Molecular Biology of the Cell. 4th edition.

The diversity of genomes and the tree of life.

The success of living organisms based on DNA , RNA , and protein , out of the infinitude of other chemical forms that one might conceive of, has been spectacular. They have populated the oceans, covered the land, infiltrated the Earth's crust, and molded the surface of our planet. Our oxygen-rich atmosphere, the deposits of coal and oil, the layers of iron ores, the cliffs of chalk and limestone and marble—all these are products, directly or indirectly, of past biological activity on Earth.

Living things are not confined to the familiar temperate realm of land, water, and sunlight inhabited by plants and plant-eating animals. They can be found in the darkest depths of the ocean, in hot volcanic mud, in pools beneath the frozen surface of the Antarctic, and buried kilometers deep in the Earth's crust. The creatures that live in these extreme environments are unfamiliar, not only because they are inaccessible, but also because they are mostly microscopic. In more homely habitats, too, most organisms are too small for us to see without special equipment: they tend to go unnoticed, unless they cause a disease or rot the timbers of our houses. Yet microorganisms make up most of the total mass of living matter on our planet. Only recently, through new methods of molecular analysis and specifically through the analysis of DNA sequences, have we begun to get a picture of life on Earth that is not grossly distorted by our biased perspective as large animals living on dry land.

In this section we consider the diversity of organisms and the relationships among them. Because the genetic information for every organism is written in the universal language of DNA sequences, and the DNA sequence of any given organism can be obtained by standard biochemical techniques, it is now possible to characterize, catalogue, and compare any set of living organisms with reference to these sequences. From such comparisons we can estimate the place of each organism in the family tree of living species—the ‘tree of life’. But before describing what this approach reveals, we need first to consider the routes by which cells in different environments obtain the matter and energy they require to survive and proliferate, and the ways in which some classes of organisms depend on others for their basic chemical needs.

• Cells Can Be Powered by a Variety of Free Energy Sources

Living organisms obtain their free energy in different ways. Some, such as animals, fungi, and the bacteria that live in the human gut, get it by feeding on other living things or the organic chemicals they produce; such organisms are called organotrophic (from the Greek word trophe , meaning “food”). Others derive their energy directly from the nonliving world. These fall into two classes: those that harvest the energy of sunlight, and those that capture their energy from energy-rich systems of inorganic chemicals in the environment (chemical systems that are far from chemical equilibrium ). Organisms of the former class are called phototrophic (feeding on sunlight); those of the latter are called lithotrophic (feeding on rock). Organotrophic organisms could not exist without these primary energy converters, which constitute the largest mass of living matter on Earth.

Phototrophic organisms include many types of bacteria, as well as algae and plants, on which we—and virtually all the living things that we ordinarily see around us—depend. Phototrophic organisms have changed the whole chemistry of our environment: the oxygen in the Earth's atmosphere is a by-product of their biosynthetic activities.

Lithotrophic organisms are not such an obvious feature of our world, because they are microscopic and mostly live in habitats that humans do not frequent—deep in the ocean, buried in the Earth's crust, or in various other inhospitable environments. But they are a major part of the living world, and are especially important in any consideration of the history of life on Earth.

Some lithotrophs get energy from aerobic reactions, which use molecular oxygen from the environment; since atmospheric O 2 is ultimately the product of living organisms, these aerobic lithotrophs are, in a sense, feeding on the products of past life. There are, however, other lithotrophs that live anaerobically, in places where little or no molecular oxygen is present, in circumstances similar to those that must have existed in the early days of life on Earth, before oxygen had accumulated.

The most dramatic of these sites are the hot hydrothermal vents found deep down on the floor of the Pacific and Atlantic Oceans, in regions where the ocean floor is spreading as new portions of the Earth's crust form by a gradual upwelling of material from the Earth's interior ( Figure 1-15 ). Downward-percolating seawater is heated and driven back upward as a submarine geyser, carrying with it a current of chemicals from the hot rocks below. A typical cocktail might include H 2 S, H 2 , CO, Mn 2+ , Fe 2+ , Ni 2+ , CH 2 , NH 4 + , and phosphorus-containing compounds. A dense population of bacteria lives in the neighborhood of the vent, thriving on this austere diet and harvesting free energy from reactions between the available chemicals. Other organisms—clams, mussels, and giant marine worms—in turn live off the bacteria at the vent, forming an entire ecosystem analogous to the system of plants and animals that we belong to, but powered by geochemical energy instead of light ( Figure 1-16 ).

Figure 1-15

The geology of a hot hydrothermal vent in the ocean floor. . Water percolates down toward the hot molten rock upwelling from the Earth's interior and is heated and driven back upward, carrying minerals leached from the hot rock. A temperature gradient (more...)

Figure 1-16

Living organisms at a hot hydrothermal vent. Close to the vent, at temperatures up to about 150°C, various lithotrophic species of bacteria and archaea (archaebacteria) live, directly fuelled by geochemical energy. A little further away, where (more...)

• Some Cells Fix Nitrogen and Carbon Dioxide for Others

To make a living cell requires matter, as well as free energy. DNA , RNA , and protein are composed of just six elements: hydrogen, carbon, nitrogen, oxygen, sulfur, and phosphorus. These are all plentiful in the nonliving environment, in the Earth's rocks, water, and atmosphere, but not in chemical forms that allow easy incorporation into biological molecules. Atmospheric N 2 and CO 2 , in particular, are extremely unreactive, and a large amount of free energy is required to drive the reactions that use these inorganic molecules to make the organic compounds needed for further biosynthesis—that is, to fix nitrogen and carbon dioxide, so as to make N and C available to living organisms. Many types of living cells lack the biochemical machinery to achieve this fixation, and rely on other classes of cells to do the job for them. We animals depend on plants for our supplies of organic carbon and nitrogen compounds. Plants in turn, although they can fix carbon dioxide from the atmosphere, lack the ability to fix atmospheric nitrogen, and they depend in part on nitrogen-fixing bacteria to supply their need for nitrogen compounds. Plants of the pea family, for example, harbor symbiotic nitrogen-fixing bacteria in nodules in their roots.

Living cells therefore differ widely in some of the most basic aspects of their biochemistry. Not surprisingly, cells with complementary needs and capabilities have developed close associations. Some of these associations, as we see below, have evolved to the point where the partners have lost their separate identities altogether: they have joined forces to form a single composite cell.

• The Greatest Biochemical Diversity Is Seen Among Procaryotic Cells

From simple microscopy, it has long been clear that living organisms can be classified on the basis of cell structure into two groups: the eucaryotes and the procaryotes . Eucaryotes keep their DNA in a distinct membrane -bounded intracellular compartment called the nucleus . (The name is from the Greek, meaning “truly nucleated,” from the words eu , “well” or “truly,” and karyon , “kernel” or “nucleus”.) Procaryotes have no distinct nuclear compartment to house their DNA. Plants, fungi, and animals are eucaryotes; bacteria are procaryotes.

Most procaryotic cells are small and simple in outward appearance, and they live mostly as independent individuals, rather than as multicellular organisms. They are typically spherical or rod-shaped and measure a few micrometers in linear dimension ( Figure 1-17 ). They often have a tough protective coat, called a cell wall , beneath which a plasma membrane encloses a single cytoplasmic compartment containing DNA , RNA , proteins, and the many small molecules needed for life. In the electron microscope , this cell interior appears as a matrix of varying texture without any discernible organized internal structure ( Figure 1-18 ).

Figure 1-17

Shapes and sizes of some bacteria. Although most are small, as shown, there are also some giant species. An extreme example (not shown) is the cigar-shaped bacterium Epulopiscium fishelsoni , which lives in the gut of the surgeon fish and can be up to (more...)

Figure 1-18

The structure of a bacterium. (A) The bacterium Vibrio cholerae, showing its simple internal organization. Like many other species, Vibrio has a helical appendage at one end—a flagellum—that rotates as a propeller to drive the cell forward. (more...)

Procaryotic cells live in an enormous variety of ecological niches, and they are astonishingly varied in their biochemical capabilities—far more so than eucaryotic cells. There are organotrophic species that can utilize virtually any type of organic molecule as food, from sugars and amino acids to hydrocarbons and methane gas. There are many phototrophic species ( Figure 1-19 ), harvesting light energy in a variety of ways, some of them generating oxygen as a byproduct, others not. And there are lithotrophic species that can feed on a plain diet of inorganic nutrients, getting their carbon from CO 2 , and relying on H 2 S to fuel their energy needs ( Figure 1-20 )—or on H 2 , or Fe 2+ , or elemental sulfur, or any of a host of other chemicals that occur in the environment.

Figure 1-19

The phototrophic bacterium Anabaena cylindrica viewed in the light microscope. The cells of this species form long, multicellular filaments. Most of the cells (labeled V) perform photosynthesis, while others become specialized for nitrogen fixation (labeled (more...)

Figure 1-20

A lithotrophic bacterium. Beggiatoa , which lives in sulfurous environments, gets its energy by oxidizing H 2 S and can fix carbon even in the dark. Note the yellow deposits of sulfur inside the cells. (Courtesy of Ralph W. Wolfe.)

Many parts of this world of microscopic organisms are virtually unexplored. Traditional methods of bacteriology have given us a fair acquaintance with those species that can be isolated and cultured in the laboratory. But DNA sequence analysis of the populations of bacteria in fresh samples from natural habitats—such as soil or ocean water, or even the human mouth—has opened our eyes to the fact that most species cannot be cultured by standard laboratory techniques. According to one estimate, at least 99% of procaryotic species remain to be characterized.

• The Tree of Life Has Three Primary Branches: Bacteria, Archaea, and Eucaryotes

The classification of living things has traditionally depended on comparisons of their outward appearances: we can see that a fish has eyes, jaws, backbone, brain, and so on, just as we do, and that a worm does not; that a rosebush is cousin to an apple tree, but less similar to a grass. We can readily interpret such close family resemblances in terms of evolution from common ancestors, and we can find the remains of many of these ancestors preserved in the fossil record. In this way, it has been possible to begin to draw a family tree of living organisms, showing the various lines of descent, as well as branch points in the history, where the ancestors of one group of species became different from those of another.

When the disparities between organisms become very great, however, these methods begin to fail. How are we to decide whether a fungus is closer kin to a plant or to an animal? When it comes to procaryotes, the task becomes harder still: one microscopic rod or sphere looks much like another. Microbiologists have therefore sought to classify procaryotes in terms of their biochemistry and nutritional requirements. But this approach also has its pitfalls. Amid the bewildering variety of biochemical behaviors, it is difficult to know which differences truly reflect differences of evolutionary history.

Genome analysis has transformed the problem, giving us a simpler, more direct, and more powerful way to determine evolutionary relationships. The complete DNA sequence of an organism defines the species with almost perfect precision and in exhaustive detail. Moreover, this specification, once we have determined it, is in a digital form—a string of letters—that can be fed directly into a computer and compared with the corresponding information for any other living thing. Because DNA is subject to random changes that accumulate over long periods of time (as we shall see shortly), the number of differences between the DNA sequences of two organisms can be used to provide a direct, objective, quantitative indication of the evolutionary distance between them.

This approach has shown that some of the organisms that were traditionally classed together as “bacteria” are as widely divergent in their evolutionary origins as is any procaryote from any eucaryote. It now appears that the procaryotes comprise two distinct groups that diverged early in the history of life on Earth, either before the ancestors of the eucaryotes diverged as a separate group or at about the same time. The two groups of procaryotes are called the bacteria (or eubacteria) and the archaea (or archaebacteria). The living world therefore has three major divisions or domains : bacteria, archaea, and eucaryotes ( Figure 1-21 ).

Figure 1-21

The three major divisions (domains) of the living world. Note that traditionally the word bacteria has been used to refer to procaryotes in general, but more recently has been redefined to refer to eubacteria specifically. Where there might be ambiguity, (more...)

Archaea were initially discovered as inhabitants of environments that we humans avoid, such as bogs, sewage farms, ocean depths, salt brines, and hot acid springs, although it is now known that they are also widespread in less extreme and more homely environments, from soils and lakes to the stomachs of cattle. In outward appearance they are not easily distinguished from the more familiar eubacteria. At a molecular level, archaea seem to resemble eucaryotes more closely in their machinery for handling genetic information (replication, transcription, and translation), but eubacteria more closely in their apparatus for metabolism and energy conversion. We discuss below how this might be explained.

• Some Genes Evolve Rapidly; Others Are Highly Conserved

Both in the storage and in the copying of genetic information, random accidents and errors occur, altering the nucleotide sequence—that is, creating mutations . Therefore, when a cell divides, its two daughters are often not quite identical to one another or to their parent. On rare occasions, the error may represent a change for the better; more probably, it will cause no significant difference in the cell's prospects; and in many cases, the error will cause serious damage—for example, by disrupting the coding sequence for a key protein . Changes due to mistakes of the first type will tend to be perpetuated, because the altered cell has an increased likelihood of reproducing itself. Changes due to mistakes of the second type— selectively neutral changes—may be perpetuated or not: in the competition for limited resources, it is a matter of chance whether the altered cell or its cousins will succeed. But changes that cause serious damage lead nowhere: the cell that suffers them dies, leaving no progeny. Through endless repetition of this cycle of error and trial—of mutation and natural selection —organisms evolve: their genetic specifications change, giving them new ways to exploit the environment more effectively, to survive in competition with others, and to reproduce successfully.

Clearly, some parts of the genome change more easily than others in the course of evolution. A segment of DNA that does not code for protein and has no significant regulatory role is free to change at a rate limited only by the frequency of random errors. In contrast, a gene that codes for a highly optimized essential protein or RNA molecule cannot alter so easily: when mistakes occur, the faulty cells are almost always eliminated. Genes of this latter sort are therefore highly conserved . Through 3.5 billion years or more of evolutionary history, many features of the genome have changed beyond all recognition; but the most highly conserved genes remain perfectly recognizable in all living species.

These latter genes are the ones that must be examined if we wish to trace family relationships between the most distantly related organisms in the tree of life. The studies that led to the classification of the living world into the three domains of bacteria, archaea, and eucaryotes were based chiefly on analysis of one of the ribosomal RNA subunits—the so-called 16S RNA, which is about 1500 nucleotides long. Because the process of translation is fundamental to all living cells, this component of the ribosome has been well conserved since early in the history of life on Earth ( Figure 1-22 ).

Figure 1-22

Genetic information conserved since the beginnings of life. A part of the gene for the smaller of the two main RNA components of the ribosome is shown. Corresponding segments of nucleotide sequence from an archaean (Methanococcus jannaschii), a eubacterium (more...)

Most Bacteria and Archaea Have 1000–4000 Genes

Natural selection has generally favored those procaryotic cells that can reproduce the fastest by taking up raw materials from their environment and replicating themselves most efficiently, at the maximal rate permitted by the available food supplies. Small size implies a large ratio of surface area to volume, thereby helping to maximize the uptake of nutrients across the plasma membrane and boosting a cell's reproductive rate.

Presumably for these reasons, most procaryotic cells carry very little superfluous baggage; their genomes are small and compact, with genes packed closely together and minimal quantities of regulatory DNA between them. The small genome size makes it relatively easy to determine the complete DNA sequence. We now have this information for many species of eubacteria and archaea, and a few species of eucaryotes. As shown in Table 1-1 , most eubacterial and archaean genomes contain between 10 6 and 10 7 nucleotide pairs, encoding 1000–4000 genes.

Some Genomes That Have Been Completely Sequenced.

A complete DNA sequence reveals both the genes an organism possesses and the genes it lacks. When we compare the three domains of the living world, we can begin to see which genes are common to all of them and must therefore have been present in the cell that was ancestral to all present-day living things, and which genes are peculiar to a single branch in the tree of life. To explain the findings, however, we need to consider a little more closely how new genes arise and genomes evolve.

• New Genes Are Generated from Preexisting Genes
• Intragenic mutation : an existing gene can be modified by mutations in its DNA sequence.
• Gene duplication : an existing gene can be duplicated so as to create a pair of closely related genes within a single cell.
• Segment shuffling : two or more existing genes can be broken and rejoined to make a hybrid gene consisting of DNA segments that originally belonged to separate genes.
• Horizontal (intercellular) transfer : a piece of DNA can be transferred from the genome of one cell to that of another—even to that of another species. This process is in contrast with the usual vertical transfer of genetic information from parent to progeny.

Figure 1-23

Four modes of genetic innovation and their effects on the DNA sequence of an organism.

Each of these types of change leaves a characteristic trace in the DNA sequence of the organism, providing clear evidence that all four processes have occurred. In later chapters we discuss the underlying mechanisms, but for the present we focus on the consequences.

• Gene Duplications Give Rise to Families of Related Genes Within a Single Cell

A cell must duplicate its entire genome each time it divides into two daughter cells. However, accidents occasionally result in the duplication of just part of the genome, with retention of original and duplicate segments in a single cell. Once a gene has been duplicated in this way, one of the two gene copies is free to mutate and become specialized to perform a different function within the same cell. Repeated rounds of this process of duplication and divergence, over many millions of years, have enabled one gene to give rise to a whole family of genes within a single genome. Analysis of the DNA sequence of procaryotic genomes reveals many examples of such gene families: in Bacillus subtilis , for example, 47% of the genes have one or more obvious relatives ( Figure 1-24 ).

Figure 1-24

Families of evolutionarily related genes in the genome of Bacillus subtilis. The biggest family consists of 77 genes coding for varieties of ABC transporters—a class of membrane transport proteins found in all three domains of the living world. (more...)

When genes duplicate and diverge in this way, the individuals of one species become endowed with multiple variants of a primordial gene . This evolutionary process has to be distinguished from the genetic divergence that occurs when one species of organism splits into two separate lines of descent at a branch point in the family tree—when the human line of descent became separate from that of chimpanzees, for example. There, the genes gradually become different in the course of evolution, but they are likely to continue to have corresponding functions in the two sister species. Genes that are related in this way—that is, genes in two separate species that derive from the same ancestral gene in the last common ancestor of those two species—are said to be orthologs . Related genes that have resulted from a gene duplication event within a single genome —and are likely to have diverged in their function—are said to be paralogs . Genes that are related by descent in either way are called homologs , a general term used to cover both types of relationship ( Figure 1-25 ).

Figure 1-25

Paralogous genes and orthologous genes: two types of gene homology based on different evolutionary pathways. (A) and (B) The most basic possibilities. (C) A more complex pattern of events that can occur.

The family relationships between genes can become quite complex ( Figure 1-26 ). For example, an organism that possesses a family of paralogous genes (for example, the seven hemoglobin genes α, β, γ, δ, ε, ζ, and θ) may evolve into two separate species (such as humans and chimpanzees) each possessing the entire set of paralogs. All 14 genes are homologs, with the human hemoglobin α orthologous to the chimpanzee hemoglobin α, but paralogous to the human or chimpanzee hemoglobin β, and so on. Moreover, the vertebrate hemoglobins (the oxygen-binding proteins of blood) are homologous to the vertebrate myoglobins (the oxygen-binding proteins of muscle), as well as to more distant genes that code for oxygen-binding proteins in invertebrates and plants. From the DNA sequences, it is usually easy to recognize that two genes in different species are homologous; it is much more difficult to decide, without other information, whether they are orthologs.

Figure 1-26

A complex family of homologous genes. This diagram shows the pedigree of the hemoglobin (Hb), myoglobin, and globin genes of human, chick, shark, and Drosophila . The lengths of the lines represent the amount of divergence in amino acid sequence.

• Genes Can Be Transferred Between Organisms, Both in the Laboratory and in Nature

Procaryotes also provide examples of the horizontal transfer of genes from one species of cell to another. The most obvious tell-tale signs are sequences recognizable as being derived from bacterial viruses , also called bacteriophages ( Figure 1-27 ). These small packets of genetic material have evolved as parasites on the reproductive and biosynthetic machinery of host cells. They replicate in one cell, emerge from it with a protective wrapping, and then enter and infect another cell, which may be of the same or a different species. Inside a cell, they may either remain as separate fragments of DNA , known as plasmids , or insert themselves into the DNA of the host cell and become part of its regular genome . In their travels, viruses can accidentally pick up fragments of DNA from the genome of one host cell and ferry them into another cell. Such transfers of genetic material frequently occur in procaryotes, and they are common between eucaryotic cells of the same species.

Figure 1-27

The viral transfer of DNA from one cell to another. . (A) An electron micrograph of particles of a bacterial virus, the T4 bacteriophage. The head of this virus contains the viral DNA; the tail contains apparatus for injecting the DNA into a host bacterium. (more...)

Horizontal transfers of genes between eucaryotic cells of different species are very rare, and they do not seem to have played a significant part in eucaryote evolution. In contrast, horizontal gene transfers occur much more frequently between different species of procaryotes. Many procaryotes have a remarkable capacity to take up even nonviral DNA molecules from their surroundings and thereby capture the genetic information these molecules carry. This enables bacteria in the wild to acquire genes from neighboring cells relatively easily. Genes that confer resistance to an antibiotic or an ability to produce a toxin, for example, can be transferred from species to species and provide the recipient bacterium with a selective advantage. In this way, new and sometimes dangerous strains of bacteria have been observed to evolve in the bacterial ecosystems that inhabit hospitals or the various niches in the human body. For example, horizontal gene transfer is responsible for the spread over the past 40 years, of penicillin-resistant strains of Neisseria gonorrheae, the bacterium that causes gonorrhea. On a longer time scale, the results can be even more profound; it has been estimated that at least 18% of all of the genes in the present-day genome of E. coli have been acquired by horizontal transfer from another species within the past 100 million years.

• Horizontal Exchanges of Genetic Information Within a Species Are Brought About by Sex

Horizontal exchanges of genetic information have an important role in bacterial evolution in today's world, and they may have occurred even more frequently and promiscuously in the early days of life on Earth. Indeed, it has been suggested that the genomes of present-day eubacteria, archaea, and eucaryotes originated not by divergent lines of descent from a single genome in a single ancestral type of cell, but rather as three independent anthologies of genes that have survived from the pool of genes in a primordial community of diverse cells in which genes were frequently exchanged ( Figure 1-28 ). This could explain the otherwise puzzling observation that the eucaryotes seem more similar to archaea in their genes for the basic information-handling processes of DNA replication, transcription, and translation, but more similar to eubacteria in their genes for metabolic processes.

Figure 1-28

Horizontal gene transfers in early evolution. In the early days of life on Earth, cells may have been less capable of maintaining their separate identities and may have exchanged genes much more readily than now. In this way, the archaean, eubacterial, (more...)

Horizontal gene transfer among bacteria may seem a surprising process, but it has a parallel in a phenomenon familiar to us all: sex. Sexual reproduction causes a large-scale horizontal transfer of genetic information between two initially separate cell lineages—those of the father and the mother. A key feature of sex, of course, is that the genetic exchange normally occurs only between individuals of the same species. But no matter whether they occur within a species or between species, horizontal gene transfers leave a characteristic imprint: they result in individuals who are related more closely to one set of relatives with respect to some genes, and more closely to another set of relatives with respect to others. By comparing the DNA sequences of individual human genomes, an intelligent visitor from outer space could deduce that humans reproduce sexually, even if it knew nothing about human behavior.

Sexual reproduction is a widespread (although not universal) phenomenon, especially among eucaryotes. Even bacteria indulge from time to time in controlled sexual exchanges of DNA with other members of their own species. Natural selection has clearly favored organisms that are capable of this behavior, although evolutionary theorists still dispute precisely what the selective advantage of sex is.

• The Function of a Gene Can Often Be Deduced from Its Sequence

Family relationships among genes are important not just for their historical interest, but because they lead to a spectacular simplification in the task of deciphering gene functions. Once the sequence of a newly discovered gene has been determined , it is now possible, by tapping a few keys on a computer, to search the entire database of known gene sequences for genes related to it. In many cases, the function of one or more of these homologs will have been already determined experimentally, and thus, since gene sequence determines gene function, one can frequently make a good guess at the function of the new gene: it is likely to be similar to that of the already-known homologs.

In this way, it becomes possible to decipher a great deal of the biology of an organism simply by analyzing the DNA sequence of its genome and using the information we already have about the functions of genes in other organisms that have been more intensively studied. Mycobacterium tuberculosis , the eubacterium that causes tuberculosis, is extremely difficult to study experimentally in the laboratory and provides an example of the power of comparative genomics . DNA sequencing has revealed that this organism has a genome of 4,411,529 nucleotide pairs, containing approximately 4000 genes. Of these genes, 40% were immediately recognizable (when the genome was sequenced, in 1998) as homologs of known genes in other species, and could be tentatively assigned a function on that basis. Another 44% showed some informative similarity to other known genes—for example, containing a conserved protein domain within a longer amino acid sequence. Only 16% of the 4000 genes were totally unfamiliar. As we saw also for Bacillus subtilis (see Figure 1-24 ), about half the genes have sequences closely similar to those of other genes in the M. tuberculosis genome, showing that they must have arisen through relatively recent gene duplications. Compared with other bacteria, M. tuberculosis contains an exceptionally large number of genes coding for enzymes involved in the synthesis and degradation of lipid (fatty) molecules. This presumably reflects this bacterium's production of an unusual outer coat that is rich in these substances; the coat, and the enzymes that produce it, may explain how M. tuberculosis escapes destruction by the immune system of tuberculosis patients.

• More Than 200 Gene Families Are Common to All Three Primary Branches of the Tree of Life

Given the complete genome sequences of representative organisms from all three domains—archaea, eubacteria, and eucaryotes—one can search systematically for homologies that span this enormous evolutionary divide. In this way we can begin to take stock of the common inheritance of all living things. There are considerable difficulties in this enterprise. For example, individual species have often lost some of the ancestral genes; other genes have probably been acquired by horizontal transfer from another species and therefore may not be truly ancestral, even though shared. Recent genome comparisons strongly suggest that both lineage-specific gene loss and horizontal gene transfer, in some cases between evolutionarily distant species, have been major factors of evolution, at least in the procaryotic world. Finally, in the course of 2 or 3 billion years, some genes that were initially shared will have changed beyond recognition by current methods.

Because of all these vagaries of the evolutionary process, it seems that only a small proportion of ancestral gene families have been universally retained in a recognizable form. Thus, out of 2264 protein -coding gene families recently defined by comparing the genomes of 18 bacteria, 6 archaeans and 1 eucaryote ( yeast ), only 76 are truly ubiquitous (that is, represented in all the genomes analyzed). The great majority of these universal families include components of the translation and transcription systems. This is not likely to be a realistic approximation of an ancestral gene set. A better—though still crude—idea of the latter can be obtained by tallying the gene families that have representatives in multiple, but not necessarily all, species from all three major kingdoms. Such an analysis reveals 239 ancient conserved families. With a single exception, these families can be assigned a function (at least in terms of general biochemical activity, but usually with more precision), with the largest number of shared gene families being involved in translation and ribosome production and in amino acid metabolism and transport ( Table 1-2 ). This set of highly conserved gene families represents only a very rough sketch of the common inheritance of all modern life; a more precise reconstruction of the gene complement of the last universal common ancestor might be feasible with further genome sequencing and more careful comparative analysis.

The Numbers of Gene Families, Classified by Function, That Are Common to All Three Domains of the Living World.

• Mutations Reveal the Functions of Genes

Without additional information, no amount of gazing at genome sequences will reveal the functions of genes. We may recognize that gene B is like gene A, but how do we discover the function of gene A in the first place? And even if we know the function of gene A, how do we test whether the function of gene B is truly the same as the sequence similarity suggests? How do we make the connection between the world of abstract genetic information and the world of real living organisms?

The analysis of gene functions depends heavily on two complementary approaches: genetics and biochemistry. Genetics starts with the study of mutants: we either find or make an organism in which a gene is altered, and examine the effects on the organism's structure and performance ( Figure 1-29 ). Biochemistry examines the functions of molecules: we extract molecules from an organism and then study their chemical activities. By putting genetics and biochemistry together and examining the chemical abnormalities in a mutant organism, it is possible to find those molecules whose production depends on a given gene. At the same time, studies of the performance of the mutant organism show us what role those molecules have in the operation of the organism as a whole. Thus, genetics and biochemistry in combination provide a way to work out the connection between genes, molecules, and the structure and function of the organism.

Figure 1-29

A mutant phenotype reflecting the function of a gene. A normal yeast (of the species Schizosaccharomyces pombe) is compared with a mutant in which a change in a single gene has converted the cell from a cigar shape (left) to a T shape (right). The mutant (more...)

In recent years, DNA sequence information and the powerful tools of molecular biology have allowed rapid progress. From sequence comparisons, one can often identify particular domains within a gene that have been preserved nearly unchanged over the course of evolution. These conserved domains are likely to be the most important parts of the gene in terms of function. We can test their individual contributions to the activity of the gene product by creating in the laboratory mutations of specific sites within the gene, or by constructing artificial hybrid genes that combine part of one gene with part of another. Organisms can be engineered to make either the RNA or the protein specified by the gene in large quantities to facilitate biochemical analysis. Specialists in molecular structure can determine the three-dimensional conformation of the gene product, revealing the exact position of every atom in it. Biochemists can determine how each of the parts of the genetically specified molecule contributes to its chemical behavior. Cell biologists can analyze the behavior of cells that are engineered to express a mutant version of the gene.

There is, however, no one simple recipe for discovering a gene 's function, and no simple standard universal format for describing it. We may discover, for example, that the product of a given gene catalyzes a certain chemical reaction , and yet have no idea how or why that reaction is important to the organism. The functional characterization of each new family of gene products, unlike the description of the gene sequences, presents a fresh challenge to the biologist's ingenuity. Moreover, the function of a gene is never fully understood until we learn its role in the life of the organism as a whole. To make ultimate sense of gene functions, therefore, we have to study whole organisms, not just molecules or cells.

• Molecular Biologists Have Focused a Spotlight on E. coli

Because living organisms are so complex , the more we learn about any particular species, the more attractive it becomes as an object for further study. Each discovery raises new questions and provides new tools with which to tackle questions in the context of the chosen organism. For this reason, large communities of biologists have become dedicated to studying different aspects of the same model organism .

In the enormously varied world of bacteria, the spotlight of molecular biology has for a long time focused intensely on just one species: Escherichia coli , or E. coli (see Figures 1-17 and 1-18 ). This small, rod-shaped eubacterial cell normally lives in the gut of humans and other vertebrates, but it can be grown easily in a simple nutrient broth in a culture bottle. Evolution has optimized it to cope with variable chemical conditions and to reproduce rapidly. Its genetic instructions are contained in a single, circular molecule of DNA that is 4,639,221 nucleotide -pairs long, and it makes approximately 4300 different kinds of proteins ( Figure 1-30 ).

Figure 1-30

The genome of E. coli. (A) A cluster of E. coli cells. (B) A diagram of the E. coli genome of 4,639,221 nucleotide pairs (for E. coli strain K-12). The diagram is circular because the DNA of E. coli , like that of other procaryotes, forms a single, closed (more...)

In molecular terms, we have a more thorough knowledge of the workings of E. coli than of any other living organism. Most of our understanding of the fundamental mechanisms of life—for example, how cells replicate their DNA to pass on the genetic instructions to their progeny, or how they decode the instructions represented in the DNA to direct the synthesis of specific proteins—has come from studies of E. coli . The basic genetic mechanisms have turned out to be highly conserved throughout evolution: these mechanisms are therefore essentially the same in our own cells as in E. coli .

Procaryotes (cells without a distinct nucleus ) are biochemically the most diverse organisms and include species that can obtain all their energy and nutrients from inorganic chemical sources, such as the reactive mixtures of minerals released at hydrothermal vents on the ocean floor—the sort of diet that may have nourished the first living cells 3.5 billion years ago. DNA sequence comparisons reveal the family relationships of living organisms and show that the procaryotes fall into two groups that diverged early in the course of evolution: the bacteria (or eubacteria) and the archaea. Together with the eucaryotes (cells with a membrane -bounded nucleus), these constitute the three primary branches of the tree of life. Most bacteria and archaea are small unicellular organisms with compact genomes comprising 1000–4000 genes. Many of the genes within a single organism show strong family resemblances in their DNA sequences, implying that they originated from the same ancestral gene through gene duplication and divergence. Family resemblances (homologies) are also clear when gene sequences are compared between different species, and more than 200 gene families have been so highly conserved that they can be recognized as common to all three domains of the living world. Thus, given the DNA sequence of a newly discovered gene, it is often possible to deduce the gene's function from the known function of a homologous gene in an intensively studied model organism , such as the bacterium E. coli.

• Cite this Page Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. The Diversity of Genomes and the Tree of Life.
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