Evolution: An Overview Based on Genetic Characters and Birds

By Nowell Stebbing

Life is a peculiar feature in the Universe. At present, we know of no place, other than our planet, where it has arisen. However life arose, the Earth has been populated by quite different species at different times. They arise with changes in climate, due ultimately to volcanic activity. Life-forms interact with the environment and with each ot

• Language: English
• Publisher: Benjamin Stebbing
• Release date: Sep 17, 2021
• ISBN: 9781904525110

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EVOLUTION

an Overview

Based on Genetic Characters and Birds

Nowell Stebbing

© Nowell Stebbing 2021

First Edition

Published 2021 by

Ben Stebbing

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PREFACE

How lineages of organisms survive sudden dramatic changes in the environment is puzzling, on the basis of the process of ‘natural selection’, as it is a very slow process. Although dramatic changes in the environment result in extinction of species, they are also associated with rapid evolution of new species. Genetic mechanisms that facilitate such changes have been revealed from investigation of some fundamental features of the molecules of living organisms. Determining DNA as the substance of inheritance, its structure and its role in specifying the types of proteins that make up the features of species, provides a basis for understanding evolutionary processes. The mechanisms change many fundamental ideas about evolution.

Even a cursory view of the natural world must lead to some consideration of the origin of all the species living today. Changes in fossil species and climate over geological times demonstrate that there have been periods when the appearance of new species is relatively sudden. Many new multi-cellular life forms arose in the ‘Cambrian Explosion’, about 540 million years ago, which led, for the first time, to significant life on land. About 125 million years ago, the cover of the Earth underwent major changes with the appearance of communities of numerous new species of flowering plants. These relatively rapid changes resulted in numerous new species appearing in what may be referred to as ‘super-radiations’. The mechanisms involved are not peculiar to super-radiations. They involve the processes by which organisms adapt to any change in their environment.

Consideration of evolution requires some ideas about the succession of species, that is their ‘phylogeny’. If DNA sequences in species are treated as ‘characters’, they can provide an unbiased basis for phylogenies, aided by their very large number. ‘Cladistics’ involves numerical methods that can determine relatedness from such characters and hence phylogenies. However, reliance on genetic characters ignores all extinct species and thus gives an incomplete view of evolutionary lineages. Moreover, cladistic methods break down when species divide very frequently. Fossils and DNA are required for establishing phylogenies.

Factors involved in evolutionary changes may be illustrated by a group of related species, and birds provide many examples. There was a world of birds before a massive meteor hit Earth 66 million years ago. Many of these birds were similar to present-day species but the fossil evidence clearly shows that they are not directly related. The adaptations of present-day species arose independently, in new lineages of birds. They have changed as the environment changed. Moreover, there was a ‘super-radiation’ in birds, immediately after the catastrophic effects of the meteor impact, which killed off many species including all the dinosaurs and most of the earlier types of birds. The focus here is on bird groups with living representatives as they can provide valuable genetic information.

It is changes in the environment that drive evolution, primarily from climate changes. Some knowledge of Earth’s changes, mainly over the last 66 million years, is necessary for understanding factors that affected the evolution of bird groups that still have living representatives. Lineages are characterised by significant dispersal of species into new environments, across the globe.

Evolution seems to be a topic of particular interest to those who oppose the whole Darwinism idea. Thus, it is appropriate to begin with the logic of scientific discovery, as this seems to be the basis of some of the misunderstandings.

CONTENTS

General Introduction

PART I: The Basic Science

Phylogenies, Genes and Evolution

Introduction

Chapter

1 Presentation of Evolution Trees (Phylogenies)

2 The Molecules and Energy of Living Organisms

3 The importance of Genetic Characters

4 Naming of Bird Groups (Taxonomy)

5 Features of Evolution Trees (Anatomy of a Cladogram)

6 Relations between Major Bird Groups (Cladogram of All Birds)

7 Key Ancestral Species and the Super-radiation in Birds (Nodograms)

8 Some ‘Misfit’ Species (The Relics)

9 Major Evolution Events in Birds

PART II: Major Factors Determing Evolution

Introduction

External Factors influencing Evolution

10 Cretaceous and Tertiary Earth History

11 Breeding Systems and Social Structure in Birds

12 Origins of Distributions and Biodiversity

Genetic Factors in Evolution

13 Gene Organisation

14 Gene Expression and Regulation

15 Embryo Development: the Formation of Characters

16 Genes and Evolution: Basic Genetics

17 Genetic Differences: the Origin of Divergences

18 Eukaryotic Character Acquisition

Part III: Brief Evolutionary Histories of Bird Orders

Introduction

Section

A. The Earliest Groups

1 Phylogeny of Early Neornithines

B. Most Groups of Water and Land Birds

2 Phylogeny of Anserids

3 Phylogeny of Gallids

4 Phylogeny of the Columbea

5 Phylogeny of Early Landbirds

6 Phylogeny of the Shorebirds

7 Phylogeny of the Core Waterbirds

8 Overview: Core Landbirds

9 Phylogeny of African Landbirds

10 Phylogeny of the Falcons

11 Phylogeny of the Parrots

C. The Great Variety of Song Birds

12 Overview of Passerids

13 Phylogeny of the Sub-Oscines

14 Phylogeny of the Corvida

15 Phylogeny of the Passerida

Part IV: Background Topics

Introduction

1 The Bases of Knowledge: World-Views

2 Species Concepts and Meaning

3 Taxonomy, Group Names and Relics

4 Features of Birds

5 Fossils

6 Cladistics

7 Types of Genes, Mutations and ‘Molecular Clocks’

8 Unifying Schemes in Molecular Biology

References

Appendices

1 Abbreviations

2 Geological Times

3 Bird Order Names

4 Descriptive Terms

Glossary

Author

FIGURES, TABLES & BOXES

PARTS I and II

PART III

PART IV

GENERAL INTRODUCTION

Life and how it has changed over time must be the greatest story of planet Earth. Some changes have been very gradual but others have involved cataclysmic extinctions and rapid appearance of new life-forms. There have been enormous changes from the earliest known fossil forms, around 3.5 billion years ago, about one billion years after the Earth was formed. A science based understanding of these changes was initiated by the seminal work of Charles Darwin (1809-1882) and set out in his book, The Origin of Species. The objective here is an overview of evolution, as now understood, for interested readers even those with just a basic knowledge of science.

There are numerous fascinating features that illustrate great variety of adaptations and behaviour of living organisms, recognised as Natural History. Evolution is concerned with just one aspect, namely how this all came about. Recognising Earth changes over long periods provides the primary cause for changes in organisms and advances in molecular biology have provided understanding of mechanisms involved.

We need to begin with two ideas, one important for consideration of evolution, the other trivial but necessary. A book on the ‘origin of species’ might be expected to define what is meant by a ‘species’ but this Darwin never did. The reason for this becomes clearer as the process of ‘origin’ is examined. Understanding evolution requires various concepts of what a species is. This is the important point. Some meanings of ‘species’ are under species in the Glossary and some complexities are considered elsewhere, in Part IV 2. However, in straight-forward terms, a species may be considered as a group of individual organisms that are very similar and interbreed. Where there are similarities between different species, they may be grouped together and considered as a Genus. These can also be grouped, based on similarities. Each expanded group has a taxonomic name, as outlined in Chapter 4. From an evolution point of view, this is the trivial bit as only the succession of species needs to be considered, not how the results are then classified.

The 10,000 or so species of living birds may be included in 35 groups, which are listed in Appendix 3 with the Genus and a species considered as typifying each group. Abbreviations for frequently used terms are shown in Appendix 1. Technical terms are defined in the Glossary. They and abbreviations are shown in bold type in the text. A geological time scale is generally used when considering long-term evolution events and this is summarised in Appendix 2.

The concept of evolution is easily stated. Different species of living organisms may be readily recognised as similar and therefore considered to be related. The distinctive features of groups of birds such as owls, ducks or penguins each include species that seem clearly related. Species in these separate groups may be similar in shape, plumage and feeding habits. The relatedness of species in these groups may be attributed to their origin. There was ‘inheritance’ of features and the species arose sequentially, over time, from ancestral types. These notions underpin the concept of evolution.

There has been a revolution in biology that has increased understanding of the molecular constituents of living organisms and mechanisms involved in their production. Gregor Mendel (1822-1884) carried out breeding experiments that provided the basis for understanding the transmission of characters between generations, now recognised to be through DNA. The majority of the visible characters of organisms are now known to be made up from proteins. They constitute the huge variety of materials we see as well as internal features of metabolism, particularly enzymes, which mediate the numerous chemical transformations involved in maintaining life. Processes involved in the regulation of protein synthesis and development of structures in the embryo are topics of current molecular biology research. These processes were not originally anticipated to be as directly relevant to an understanding of evolution as is now recognised.

Darwin clearly emphasised ‘inheritance’ as a critical feature for the process of evolution and noted that nothing meaningful was known at the time about the mechanisms involved. This soon changed with an appreciation of Mendel’s breeding experiments. Genetics now provides a basis for much of our understanding of life processes and evolution. Other matters which were significant puzzles for Darwin arose from his view that evolution was slow, gradual and continuous. This made the ‘gaps’ between species, that is their differences, puzzling. There were also occasional dramatic and very rapid evolution events leading to numerous new species. An inability to explain these events was recognised as something that could undermine his whole theory. The example that worried Darwin was the sudden appearance of the flowering plants (angiosperms). In correspondence with Joseph Hooker (1817-1911), the leading botanist of the time, Darwin referred to this as the ‘abominable mystery’. These are rare events and now termed ‘super-radiations’. One occurred in the origin of a major groups of birds, 66 million years ago (mya), at the time of the K-T event (see Glossary and below).

‘Natural selection’ was considered by Darwin as the key driver of both the adaptation of species and the origin of new species. However, the survival of species, that is their fitness, and the origin of new species are now recognised as occurring by genetic mechanisms that include but are not initially dependant on natural selection. Changes in species occur from the variety of characters in individuals of a population. The variety in visible structures is due to the proteins that constitute living things and the ways these are made and assembled in the embryo and later development. The (invisible) genes, that is DNA sequences in organisms, turn out to be inherently variable and they contribute to changes in future generations. These changes adapt organisms to their environment, that is they change, over generations, when environmental features change. In this way, changes in the environment drive the ever changing forms of organisms.

Most molecules of living organisms may be considered in three major classes, namely proteins, making up structural features of organisms, the genetic information in DNA and smaller molecules involved in metabolism, including sugars of various kinds. Proteins and DNA are ‘macro-molecules’ made by linking together their subunits that are produced in metabolism. The subunits are the 21 amino acids found in proteins and four nucleotides in DNA. The interactions between the three major classes of molecules are significant determinants of evolution and also other distinctive features of life.

The properties of the molecules of living organisms confer features unlike those of other physical and chemical entities. Physical and chemical processes are characterised by ‘laws’. Living organisms are also bound by these laws but they seem to reverse the constant tendency of non-living things towards less order and lower energy states. This is the second law of thermodynamics (entropy) which living organisms may seem to reverse or circumvent. This reversal is the result of the energy manipulations that arise in metabolism. Interconversions of compounds in metabolism result in the release and transfer of energy, which is essential for the production and assembly of the constituents of living organisms. The chemical interconversions are mediated by enzymes, which seem to have been an early development in the evolution of organisms.

Progress in understanding what is, summarised above, is the subject of this book. Science progresses through ideas that may be formulated into theories and so I will begin by considering relevant concepts as they can present confusions in relation to evolution.

Theories and Related Concepts

To make sense of how we gain understanding it is necessary to consider several related ideas, particularly the meaning of ‘theory’, ‘belief’, ‘facts’, ‘proof’ and ‘truth’. A ‘theory’ is simply a proposal that places a set of observations (facts) within a broader context. A ‘theory’ generally indicates how observations may be related. It is a conjecture and it may not be right. ‘Truth’, in scientific discussions, is simply ‘correspondence with the facts’ and so a theory can be tested by determining whether it corresponds to the facts, particularly any predictions that can be made from the theory.

As it happens, there is a simple example of how a theory may be tested, that relates to birds. It is not really a theory but it illustrates some issues. ‘Theory: All swans are white’. This idea (theory) would be self evident to Europeans from seeing their native migratory species (the Mute, Whooper and Tundra or Bewick’s swans). Each sighting of these birds would confirm the theory. However, finding the Black Swan in Australia and New Zealand clearly falsified the theory. No number of observations of northern hemisphere swans, however numerous, can ‘prove’ that the theory (All swans are white) is right. In science, a theory cannot be proved. It can only be rejected, on the basis of falsification, that is by observations. A theory is considered scientific if it is ‘falsifiable’ by some observations relating to its predictions. Better theories (new conjectures, more observations) lead to more comprehensive theories and therefore greater understanding. This is the nature and basis of rational knowledge as it has developed since the Enlightenment (see Part IV 1).

A feature of rational knowledge, not found in faith systems, is that new knowledge is gained through our engagement with what we seek to understand. Knowledge increases and changes and we know the basis for the changes because we make the observations that lead to new understanding.

‘Proof’ of an idea is often considered the means whereby science furthers knowledge and establishes ‘truth’. This common misunderstanding seems to be based on a confusion of science and mathematics. Mathematics is not a science even though it may be much used in scientific endeavours. When I went to Edinburgh University to read mathematics, the Department was in the Faculty of Arts, not Science. Mathematics does include ‘proof’ of statements that can be made from the basis of a set of axioms. The knowledge is gained by ‘deduction’, a process in which the conclusions follow from the premises with logical necessity. If the premises are true, so also is the conclusion. The basic axioms of points, lines and angles lead to the theories of Euclidean geometry, which can be proved.

‘Beliefs’, particularly religious beliefs, are like mathematics in that they are based on axioms. In a belief system, its axioms may be referred to as the ‘credo’. Any theory based on a credo requires no explanation as it is seen as self-evident. The ‘theory’ may be true to all believers but it is not a science based theory.

Imbuing features of the natural world with human attributes (anthropomorphism), ‘Creationism’ and ‘Intelligent Design’, all occur in some discussions of evolution but these attributions are not based on (scientific) knowledge. They cannot provide an ‘alternative theory’ of evolution as they are subjective views or refer to axioms within a credo. The Enlightenment basis of knowledge, in the context of other world views, is considered in Part IV 1.

From this it should be clear that science has the capacity to provide understanding of relationships between species and thus their evolution. Conclusions are based on ideas, models and suppositions. There are now many theoretical ideas relating to the processes thought to determine evolutionary changes. There are numerous additional theories. For example, some relate to how new species arise on islands, others to the origin of adaptations shown by birds that catch fish. There are also many theories on the relation of molecular biology phenomena to evolution events. These may all be referred to as ‘evolutionary theories’. There are conjectures, many well founded but all open to modification. The story will change but there now seems to be a reasonable basis for understanding the process of evolution.

The Phenomenon and Process of Evolution

‘Evolution’ was first used as a descriptive term by the geologist Charles Lyell (in 1832). He referred to the existence of different but seemingly related species in successive layers of rocks. The most recent layers contained species very like living species but older rocks contained species with characters that were progressively more distinct. These changes are now well established in all groups of organisms that have been investigated. The phenomenon of evolution is a recognised fact. It is not a ‘theory’.

The processes that result in the relationships between sequential species in series such as those identified by Lyell and others, were considered by Darwin. The explanation he gave, his ‘theory of evolution’, was based on four principles, as outlined in Chapter 1. The theory may be stated as ‘descent by modification’. The natural variation amongst individuals in a species can result in some being selected so that, over many generations, their characters change. A new, different species can arise.

Darwin proposed that any group of related species arises from a single ancestral species: in each case, sequential splitting of species leads to new groups of species. The splitting of one species from another is termed divergence. Although there are changes in characters at each divergence event, there will be many shared characters. However, after a series of divergences species can differ widely. The Families of the owls, ducks and penguins are each considered to have arisen from different ancestral species. These may have been quite unlike the present-day survivors in these Families. The factors determining changes are ones affecting the ways in which characters may be modified over generations, primarily arising from the extent to which they adapt individuals in the species to their environment. Natural selection is one process by which individuals with genes for beneficial or deleterious characters are selected or eliminated.

Evolution Trees

The successive splitting of species can be displayed in a branching, tree-like pattern and the time when splits (divergences) occurred can be estimated. In early, fossil based, analyses the time of divergences was from the age of the rocks from which the fossils were obtained. However the timing and sequence of divergences can also be determined solely from the characters displayed in living species. One method, termed cladistics, was developed in the 1960s and has progressed considerably since then. The method involves a significant break with earlier systems, based on grouping species by their similarities. Cladistics is the arrangement of species by assessment of differences in characters. The procedures are outlined in Part IV 6.

A cladistic analysis produces an evolution tree called a cladogram. This is a useful term as it indicates that it is an evolution tree based on certain principles. The general term for an evolution tree, regardless of the method used to create it, is a phylogeny. If many characters are used, the order of divergence of species can be assessed with reasonable confidence. Any ‘characters’ can be used. Morphological and behavioural features were ones originally used. Sequencing the DNA of species provides vast numbers of characters, useful for determining the succession of numerous species, however different they may appear. It is then also possible to estimate the time of divergences in groups of living species, when the rate of change in DNA sequences is known.

Relatedness may not be obvious from morphological characters and they are not always reliable indicators of divergences. DNA sequences, however, are the very stuff of inheritance and are less ambiguous in regard to evolutionary relatedness. It is genetics that connects evolving species to their environment: natural selection determines which genes are passed on to successive generations. Evolution trees are now primarily based on DNA sequence characters. However, it should be noted that the determination of evolution trees by analysis of characters is not based on any evolutionary principles other than the notion that similar characters indicate common ancestry. Nevertheless, cladistics, using genetic characters from living species, can address matters which fossils cannot and may never be able to resolve. Fossils are no longer the only route to unravelling the sequence of species in evolution.

DNA sequence based analyses are particularly useful for assessing the relationship of species considered quite distinct, based on morphological characters. This is readily illustrated by birds. Consultation of the relevant evolution tree reveals that the African Jacana is from a group related to the ancestor of the very different looking Sandpipers (see Figure III 6, 3). The ground dwelling quail-like Andalusian hemipode is, perhaps surprisingly, in a Genus (Turnix) that arose early in the lineage leading to the evolution of the gulls and terns (Figure III 6, 5 Laridae). Sighting the Coscoroba swan in Patagonia made me think about its relationship to swans and geese. Is it related to a ‘missing link’ between the two? The relevant evolution tree (Figure III 2, 1) showed that it is related to a group that is ancestral to both the swans and geese. The Jacana, the Andalusian hemipode and the Coscoroba swan are not directly the ancestors of the sandpipers, gulls and swans. They are living descendants from groups that arose from early divergences. No living species are ‘missing links’ to other living groups: all missing links are (extinct) ancestors. The concept of ‘missing links’ has become subordinate to that of sister species, the two species that arise from the splitting of a species.

A very bold idea supported by Darwin was that all organisms share one common ancestor. The evolution trees of all groups may be linked and when they are all shown together, they constitute the Tree of Life. This displays the results of evolution up to the present day and it includes all the natural world. In this view all organisms are related by descent and the components of the natural world were not created separately and not just for the benefit of Man: he is an integral part of it.

Use of Genetic Features in Evolutionary Studies

Genetic features are used in two distinct ways in studies of evolution: as ‘characters’ and as ‘mechanisms’. As just outlined, the vast number of DNA sequences, arising from the sequencing of the DNA of organisms, provides information that allows determination of divergences. This simply involves recognition of DNA sequences as characters. The outward morphological, behavioural and other characters of organisms are, to a large extent, determined by genes. These are passed on over generations and various factors may increase or decrease their frequency in the population, resulting in changes. These changes involve genetic mechanisms that occur in the replication and transmission of genes. Genetics plays an essential role in both of these types of studies and this is the reason for the emphasis given to genetics in this book.

Reliable evolution trees provide a basis for considering the evolution of any feature in a lineage of species, such as varieties of feeding mechanisms, migratory behaviour as well as the places where divergences could have occurred. There are a myriad of other fascinating features, whose evolution may be considered using the appropriate evolution trees. The purpose here is simply to consider the relations between the Orders of birds and the genetic and other mechanisms that influenced their evolution.

There have been several striking and puzzling results from genetic studies. Not only is the amount of DNA (genes) that encodes proteins small, there are also surprisingly few genes. Despite the immense differences in the appearance and ways of life amongst organisms such as humans, birds, snakes, fish and flies, the genetic differences are not great. Not all the DNA of an organism can be identified as genes, that is material that determines characters in the organism. In fact surprisingly little DNA is organised into genes associated with production of proteins. The amount of DNA in each cell of every organism that constitutes genes is less than 2%. The diversity of proteins is also far less than might be expected from the great variety of structures in living organisms.

An explanation of these observations lies, in part, in embryo development. There are genetic mechanisms that control the activity of genes that determine the formation of features during development of the embryo. These mechanisms are highly conserved and are few in number. Species differ more in how these control mechanisms operate than in the genes determining their visible and metabolic features. These matters are considered in Chapter 3 and Chapter 15.

The Process of Evolution

There are many factors that seem to determine evolution in any group of organisms. There are internal factors, that is ones dependant on life processes and the genetic make-up of organisms. There are also numerous external, that is, environmental factors that determine where organisms can find food, shelter, breed and survive. Consideration of internal and external factors determining evolution are core parts of this book (Part II).

Internal factors include mutations. These were originally identified as rare changes in the appearance of an organism. An early use of the term was for some gross anatomical changes. It is now recognised that mutations arise from changes in DNA and that these are not rare but a common and a general feature of all DNA. Individually they generally have negligible effects. With recognition that changes in DNA cause mutations, the term changed to a feature of DNA.

Mendel proposed that there are two forms of the factor that determine inheritance of any character. For example, garden peas could be yellow or green. The two determinants are termed alleles, one acquired from each parent. Together they constitute the gene for colour of the peas. There may be other variant alleles present in other individuals for different colours of peas. Thus, the population can contain many alleles for each character but only two occur in any individual. The shape of peas, for example ‘wrinkled’ or ‘smooth’, is determined by another gene. Again, there may be a variety of alleles in the population determining a variety of shapes.

Each reproduction event results in new combinations of genes in the offspring. Although two forms of each gene (alleles) occur in individuals, the available alleles contribute to variations in the number of possible pairs of alleles in individuals in a population. This number is significant. If there are 10 variant alleles for a particular gene in a population, then the number of possible pairs of these alleles is 2¹⁰ = 1,024. As we shall see, this results in enormous numbers of possible gene combinations when all the genes in a species are considered.

Just one of the two alleles at a gene position may determine a character in an organism. The other allele will be a ‘variant’ that may not contribute to determination of the character. Genetic mechanisms in organisms with bi-parental reproduction allow species to maintain such inactive variant alleles. These may confer negligible or no advantage but at some time, in future generations, they can become active and provide a useful adaptation. The allele may then increase in frequency in the population, by natural selection, over further generations. Several such changes can result in production of new characters. This provides a basis for evolution arising from development of variant alleles which originally played no role in determination of a character.

If we now consider the environment in which organisms live, it should be noted that the Earth itself is constantly changing. It is not static. The most significant long-term Earth feature is the movement of land masses (tectonic plates), associated with volcanic activity. These events greatly affect climate in successive geological ages. We are in a time when tectonic plates generally are moving apart, as a result of mid-ocean volcanic activity. Over geological time periods this causes changes in the distribution of continents and the course of ocean currents over the globe and therefore huge changes in climate. Tropical regions have expanded and contracted with dramatic effects on the evolution and distribution of species, including birds. Creation of the Southern Ocean greatly changed world climate. It contributed to the recent Ice Ages and also produced new rich feeding grounds in the Antarctic region.

Cataclysmic events have characterised and affected Earth history. They arise, for example, from sudden bursts of volcanic activity or external events such as the one that led to extinction of the dinosaurs and many other organisms (the K-T event). This event was the impact of a massive meteor in Central America about 66 mya and it marks the end of the Mesozoic era and beginning of the Tertiary period. It is also the time from which we have knowledge of the groups of birds that live today.

The time scale over which evolutionary changes occur in organisms varies widely. Single-celled organisms such as bacteria, with generation times measured in minutes, evolve rapidly but larger organisms, such as vertebrates, with generation times measured in years, may evolve more slowly. Evolution of a new species of vertebrates may occur over many generations and take 50 to 100 thousand years. A new species may then persist for several million years. Clearly, environmental changes occur at a much slower rate than the evolution rate of bacteria. However, the above greatly simplified comparison serves to indicate that evolution of vertebrates is more in line with the time scale of geological changes.

A consequence is that this must make vertebrates susceptible to the rate of changes in their environment especially to any cataclysmic events. This is illustrated by the recent Ice Ages, which affected the distribution and survival of many bird species (see Part III C). A tendency to extinction will also occur if the intrinsic rate of genetic change (mutations) is low and this seems to be the case, for example, in the falcons (see Part III 10).

Carbon dioxide dominated the atmosphere of early Earth. It is now a minor component (0.04%) but very significant in terms of current life forms. Early life forms did not utilise oxygen for metabolic activities and some released oxygen into the atmosphere. The initial effect was a mass extinction of many life forms, termed the ‘oxygen catastrophe’, which began about 2.4 bya (billion years ago). However, significant new life forms utilising oxygen arose. An atmosphere containing significant amounts of oxygen developed very gradually. In a period of over one billion years there evolved all the complexities of land-dwelling species, for whom oxygen is essential. Multi-cellular organisms evolved. From around 600 mya they came to occupy all land masses. For the previous two billion years life had been confined to water without dependance on respiration of oxygen.

Life has also changed the Earth. Evolution and Earth changes are inter-related. Plants and other life on land have affected the composition of the atmosphere. Oxygen is now a significant component, as is water. Water results in the weathering of rocks and reshaping of land by erosion and deposition of the sediments produced. The remains of life have also contributed significantly to the nature of the Earth’s crust, in deposits such as coal and limestones. The changes that resulted from erosion of rocks are readily seen by comparing the surface of the Moon with that of the Earth. Formation of craters from bombardment by asteroids have been equal but hardly any remain visible on Earth. Even the very large crater formed by the K-T event, 66 mya, can now only be deduced from scattered evidence.

Birds as Exemplifiers of Evolution

Any group of organisms may be chosen to exemplify the processes of evolution. There are several reasons for choosing one group of species and making this birds. Birds are a well studied group with some relevant information on most of the living species and they are found across the entire globe, occupying many different environments. Thus, birds provide opportunities for studying evolutionary factors affecting adaptations to many different habitats. A disadvantage may be that there are so many of them. Working out their evolutionary relationships does involve coming to grips with over 10,000 living species. Birds are vertebrates in the larger assembly of organisms known as eukaryotes. These are organisms with two sets of genes derived from the two parents involved in reproduction. This group of organisms also includes jellyfish, worms, flies and crustaceans as well as plants. The mechanisms for generating sex cells (eggs and sperm) are complex and ancient. These organisms share many genetic features relevant to their evolution and this is the reason for focusing on genetic characters and mechanisms and a vertebrate group (birds) in this broad overview of evolution.

Features of human evolution attract attention and some examples are referred to here. These relate to human diseases where the genetics has been extensively investigated. However, humans are in a very small group of vertebrates. From an evolutionary perspective, humans are of relevance more because of the impact they have had on the fate of other species than the factors that have affected their own evolution. In contrast, there are many lineages of birds that illustrate dramatic evolutionary changes over long periods. These include the remarkable explosion in the number of new species after the K-T event and adaptations to life on water as well as land. They involve factors demonstrating the interplay of genetics and environmental features that are not so clearly demonstrated when evolution is simply illustrated by examples selected from a few organisms or environmental circumstances.

Back to birds: throughout the Cretaceous there were several distinct groups of bird-like species. Understanding of evolution in this period is dependent on fossils. The discovery of Archaeopteryx in the 1860s, just after the publication of Darwin’s book on evolution, was rightly hailed as significant evidence in favour of evolution and specifically the origin of birds. Archaeopteryx was a Mesozoic bird-like creature with feathers, wings and a long tail as well as teeth and clawed digits. It was about the size of a crow. It is a prime example of a ‘missing link’, in this case between birds and dinosaur-related reptilian ancestors. This bird lived in the time of the dinosaurs, from about 150 million years ago. There are now 10 known specimens, one in the British Museum, and they have come from a quarry in southern Germany that produced the fine-grained stone required for the engraving used in making lithographs, hence the bird’s full name; Archaeopteryx lithographica. The fossil site was one favourable for preservation of details of structures: the fine structure of feathers is apparent.

Some recently discovered fossils, mainly from China, have greatly enhanced understanding of the evolution of reptiles, birds and mammals. In addition to Archaeopteryx, many bird-like species have been discovered from the Mesozoic era. These discoveries were widely reported, particularly the existence of feathered reptiles. Initially the feathers seemed to be for keeping warm, not flying. More recently there has been evidence for colours in these feathers, a feature found in many species of living birds, indicating ‘display’ as a function of feathers. That modern birds are descendants of reptiles is widely recognised. It is often stated that birds are surviving dinosaurs. There may have been a common ancestor in a lineage preceding birds and dinosaurs. However, direct descent of birds from dinosaurs seems, once again, uncertain. These matters are considered here only in so far as they relate to the origin of Neornithines.

Another fossil discovery of significance was a report of a new type of Cretaceous bird, by Walker (1981) (Cyril Walker, 1939-2009). The bird was curious in that the bones forming the knob and concavity of the shoulder joint were reversed, compared with the joint in modern birds. These birds were therefore referred to as the ‘opposite’ birds and many other distinguishing features are now recognised for these birds, formally now referred to as the Enantiornithines. Review of numerous fossil specimens resulted in the recognition that Enantiornithines were the predominant birds of the Cretaceous, at that time found throughout the world with diverse forms remarkably similar in general appearance to the range of modern surviving birds. A surprising result was that there were no fossils of any modern birds in the Cretaceous. Walker’s brief report has revolutionised understanding of the origin and evolution of surviving birds.

Of all the Cretaceous birds, only one group has survived. The surviving species are referred to as Neornithines (Neo=new; ornithine=bird) and they are the species used here to exemplify evolution. Because they have living representatives, it is possible to use genetic characters in evolution studies of Neornithines. This is the reason for focusing on Neornithines in the present overview of evolution, with only limited consideration of Cretaceous bird groups. Thus, the origin of birds in general is given only brief attention.

Neornithines became numerous only from about 66 mya. Since then many new species of these birds have arisen with major changes in the types to be found across the globe. Some groups of Neornithines are now also entirely extinct. Several of the extinct groups were remarkably different from those living today. Evolution has resulted in some dramatic changes in Neornithines.

We do not today view birds as the dominant herbivore or carnivore in any environment. The hawks and falcons may be apex carnivorous species but they feed on relatively small prey, unlike ground dwelling mammals in the same environment. There, the large Carnivora, including wolves and lions feed also on the native herbivorous mammals, regardless of size. Prey for Carnivora include deer, horses and antelope. However, the situation was quite different just 2.5 million years ago. Large birds (Neornithines) were then the dominant herbivores and carnivores in several regions.

The huge flightless Mihirungs (Dromornithines) were the dominant herbivore of Australia, where they had occupied this role from the Oligocene. Different very large herbivorous birds were dominant in smaller isolated regions, such as the Moas in New Zealand and the Mao-nalos on Hawaii. Some Moas weighed up to 500 kg. In the case of New Zealand, the dominant carnivore was also a bird: the mighty Haarst’s Eagle, that hunted Moas.

For millions of years the dominant carnivores of S America were birds, namely the numerous and colossal ‘terror-birds’ (Phorusrhacids). Some of these entered N America when the isthmus of Panama arose. These dominant carnivorous birds could kill and devour a horse. S America was the location of the largest flying birds to have existed. They were a group related to the NW Vultures with wing-spans of about 6 m and body weight of over 70 kg. These were not birds with muscle-powered flight. They were soaring birds that took-off and landed into the relentless westerly winds that occurred across S America before the rise of the Andes. All these types, along with the unrelated but better known Dodos, have disappeared as a result of changes in climate or interactions with competitive mammals, particularly humans. Today, an ability to fly is a key means of escape for most groups of birds and this places constraints on size. Birds today are mostly small creatures.

Scientific Terms

There is a general view that molecular biology is a completely foreign field for the general public. In fact, some basic concepts are widely used. People use ‘DNA’ to refer to the essential unchanging feature of a type of motor car. There is also the general notion that ‘genes’ are bits of DNA that determine the various characters of individuals. Genes are widely recognised as agents that can determine diseases and affect many athletic and cultural abilities. ‘Enzymes’, which are fundamental catalysts of chemical interconversions in living organisms, are generally recognised as the agents that carry out brewing of beer and used even in some cleaning agents. A ‘clone’ of organisms is recognised as being made up of all the individuals arising from one donor, such as Dolly the sheep. The concepts and discoveries of molecular biology are in general use even if specific terminology is largely restricted to scientists.

Technical terms have been reduced to a minimum in this Introduction. The Glossary is tailored to the subjects of this book and therefore less circumspect than might be found in a standard biology text. The odd-looking words and terms found in scientific texts are often off-putting to those unfamiliar with the reasons for their use. Some understanding of Greek and Latin is helpful but not necessary and this seems to have declined steadily since the Bible was translated into English, in 1526. Technical terms are supposed to provide clarity and simplicity. This they do. However, their meaning and relation to common English needs a little explanation.

Some plain English words are used here and they may seem technical but are not. They are just not widely used. Examples are pelagic, vagile, extant and endemic, used in relation to living organisms because their dictionary meanings are directly relevant and correct. Other English words are used and their meaning is understandable once the context is explained. This is the case for a number of processes for which quite long descriptions would be required each time reference is made to them. Transcription and translation are examples. The molecular mechanisms to which they refer are elaborate. They are, respectively, the processes of replication of DNA (or production of RNA) and the transfer of genetic information in DNA into amino acids in proteins. Once explained, the common English words convey the meanings concisely without the need to repeat the molecular story each time reference is made to the processes.

Common English words are often used with the meaning unaltered but slightly circumscribed. The term nested, referring to a group of birds, does not describe how the birds sit on their nests but how one or a group of species sits between others in the tree-like branching pattern that relate to their evolution. So, when used in the context of evolution trees, the narrower meaning renders nested a technical term but one readily understandable. Sister, for describing the two daughters (species or subsequent lineages) from an evolution event (divergence), also has a defined meaning slightly different from common understanding, but not obscure.

Even easier to understand, in terms of technical meaning, are dominant and recessive to describe the character expression of genes. With two genes for a character (technically alleles, one from each parent), a dominant gene is one whose character is manifest regardless of the other which is described as recessive. Brown eyes in humans is dominant and blue eyes, recessive. Similarly, linkage of genes is straight-forward once it is understood that genes are lengths of DNA and they are strung along the length of chromosomes. Hermes was the messenger of the Greek Gods, conveying information from Olympus to those below: without even resorting to the Greek, messenger RNA can be used and understood, for conveying information in DNA to the site of protein synthesis. There, transfer RNA uses a triplet code (codon) in its sequence of bases to transfer the specified amino acid into a growing protein sequence. The reader is now familiar with the guts of molecular biology before even consulting the Glossary. When necessary, just read the definitions to understand the science.

Moving on to foreign words, mainly Greek and Latin, they do seem odd if only because they are unfamiliar. This is the intention. If one common word, like ‘translation’ would suffice, it would be used. In these cases it is the potential for misunderstanding that is the reason for their use, particularly when several words would have to be strung together to convey the meaning. It is then helpful to use an unfamiliar looking word. For example, sympatric: living-in-the-same-area and allopatric: living-in-different-areas. Extensive use of foreign words occurs in the ‘Latin’ names for species (‘Latin’ is in quotes as it is intended to convey the fact that some are actually Greek). A few terms, widely used in reference to species, are listed in Appendix 4. Just two words are used to convey a description of species. The full description has a lot of words, available by consulting an ornithological text. In the ‘Latin’ species name, the first (Genus) term is intended to describe a key character of a group of species and the second term, a peculiarity of one species. This may be where it is found: africanus (Africa), chiliensis (Chile), novaehollandiae (Australia, the old name), pratensis (in meadows), alpinus (alpine). In many cases the terms are simply the Greek or Latin names given in ancient texts: nothing mysterious is intended. The ‘Latin’ name is just the common name in a different language, Latin or Greek. As examples, consider the names of four birds, the Great Tit, the Spotted Sandpiper, the White-headed Stilt and the Raven: Parus (tit) major (great); Actitis (coast-dweller=sandpiper) macularius (spotted); Himantopus (strap-to-leg=stilt) leucocephalus (white-headed) and one double-dose, Latin then Greek, Corvus (crow) corax (raven). Oddities have slipped through, such as Caprimulgus, literally the goat sucking birds. This was once thought to be the night-time activity of the nightjars: the name has stuck. Troglodytes, the wren, was wrongly thought to live in caves: the species name has not changed.

It is the case that technical terms can get messy, particularly when unforeseen complexities arise or terms become applied to slightly different phenomena. An example is the term ‘species’ as used in taxonomy and evolution. This is reviewed here, in Part IV 2. In such cases changes in terminology or re-definition of meaning can be helpful. As outlined above, ‘mutation’ is a term now used for the frequent changes that occur in all DNA and no change in the basic definition has been needed since DNA was seen as the basis of mutations.

The Organisation of Subjects

The objective here is to consider recent scientific developments in relation to evolution so that a broad if rather cursory overview is obtained. This means that there is much that has been greatly simplified. Therefore, this is more a hand-book than a textbook. Each section attempts to be more-or-less ‘stand alone’. This results in some repetition of key concepts and frequent reference to the Glossary. Conciseness is sought by separating out topics (into Part IV) that are relevant to more than one field or basic to an understanding of evolution. These topics include the concept of a ‘species’, taxonomy and features of birds, including fossils. There are also sections referring to some necessary technical matters, particularly cladistics and puzzles that still remain in understanding relationships in the very earliest groups of birds that have survived.

There are large fields of science covered here but more specialist texts for these are cited. Those seriously interested should include some older pivotal works such as Darwin’s Origin of Species: it is still in publication and needs to be considered as it is a basic text for evolution. Wallace’s book The Geographical Distribution of Animals is still informative, relevant and also available online. Fortunately, several scientific organisations have open access policies but many key scientific papers are essentially inaccessible to the ordinary reader because of the policies of publishing companies. Where possible, references to technical works are to texts that can be found without too much difficulty by internet searches. Historically important papers are more readily available, from searching subjects and the scientists that made early discoveries. These are often excellent introductions to scientific developments.

Part I of this book provides the basics necessary for understanding the main narrative presented in more detail, in Part II. Some major events in the evolution of Neornithines are briefly reviewed in Part I as are important descriptive terms used in evolution trees. DNA sequences are now the primary characters used in producing evolution trees but they are then used simply as ‘characters’. There is no consideration of genetic mechanisms. Key features that influence evolution are the genetic mechanism and other ‘internal’ processes, referred to above. An overview of these topics, in Part I, attempts to link key factors which affect evolution that are derived from quite different disciplines.

Each Chapter includes a summary and each Part begins with an Introduction that sets out the relevance and relationships between the topics presented.

PART I

The Basic Science

Phylogenies, Genes and Evolution

Introduction

Part I provides some basics necessary for understanding the two main narratives of this book, namely factors that determine evolution and the evolutionary history of a group of related species, which here is birds.

The sequential splitting of species can be portrayed in a tree-like pattern which displays the sequence of their evolution. Such an evolution tree is called a phylogeny. All groups of organisms are branches in such a tree which, collectively, is referred to as the Tree of Life. Types of phylogenies are reviewed in the Chapter 1.

The major molecular constituents of organisms are reviewed in Chapter 2. These are proteins, produced as a great variety of materials with distinct properties. Proteins and the genetic material, DNA, are large ‘macro-molecules’ with particular structures that enable organisms to grow and reproduce. The synthesis of macromolecules is from carbon containing compounds. These originate primarily from photosynthesis in plants. This process incorporates energy into carbon containing compounds that are used in metabolic reactions to reverse the general reduction in orderliness that occurs in all other, non-living materials.

The introduction of new characters is mediated by the genetic make-up of organisms. There will be selection of individuals with characters that confer adaptive advantage. Their genes will be passed on generation by generation. This is how even initially minor characters can change and become significant in the evolution of new species. The huge number of genetic characters that have arisen from sequencing the DNA of organisms is now the basis for comprehensive phylogenies. The nature of genetic characters is considered in Chapter 3.

Use of birds to exemplify the sequential evolution of species determined from genetic characters, requires consideration of their taxonomy. This is not a book on taxonomy but use of agreed bird group names is necessary and this requires some consideration. Chapter 4 deals with the relevant taxonomy issues.

The relatedness of species may be assessed by differences in their characters, as outlined in Chapter 5. The method is ‘cladistics’ and the phylogenies it yields are distinguished by use of certain principles and use of characters from just living species. Such phylogenies are termed cladograms.

With some simplification of names and appropriate grouping of bird species, they can all be encompassed in one cladogram, as outlined in Chapter 6. This All Birds cladogram relates all the major groups of living birds. It is thus an overview and introduction to later sections on evolution of bird groups (Part III).

There is now general agreement on bird phylogenies particularly those considered in Part III. However, some principles of cladistic analyses do not apply to the origin of some of the Orders of birds, many of which arose relatively suddenly around the time of the K-T event, the effect of a massive meteor that hit Earth 66 million years ago. Features of such extraordinary proliferations of species are unusual and termed super-radiations. The super-radiation that occurred in the production of many Orders of birds are considered in Chapter 7, by analysis of events at the nodes (branch points) in the All Birds cladogram.

The cladistic analyses leading to the All Birds cladogram reveals that a few odd species are peculiarly related to the major groups (Orders). The characteristics of some of these species (Relic Clades as they are