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| ISBN-13: | 9780520947986 |
|---|---|
| Publisher: | University of California Press |
| Publication date: | 11/02/2010 |
| Sold by: | Barnes & Noble |
| Format: | eBook |
| Pages: | 216 |
| File size: | 6 MB |
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How Vertebrates Left the Water
By Michel Laurin
UNIVERSITY OF CALIFORNIA PRESS
Copyright © 2010 the Regents of the University of CaliforniaAll rights reserved.
ISBN: 978-0-520-94798-6
CHAPTER 1
How Can We Reconstruct Evolutionary History?
Our first ancestors were all aquatic. The oldest known vertebrates are about 500 Ma old, but the first potentially terrestrial vertebrates are less than 350 Ma old. For more than 150 Ma, our ancestors swam with their fins and breathed through their gills; on dry land, these structures were very inefficient. Their sensory organs worked poorly in air, if at all, and had to undergo various modifications to adapt to life on the continents. The eyes of our ancestors lacked eyelids and tear glands and could dry out rapidly; their ears did not enable them to hear most airborne sounds, such as the vocalizations of many frogs, birds, and mammals, such as the human voice. Yet all these problems were solved, and the few vertebrate species that succeeded in adapting to this new environment about 320 Ma ago diversified into the more than 25,000 extant species of land vertebrates.
To reconstruct this history, we need objective methods to use the indirect information on evolution provided by fossils or the extant biodiversity, as well as principles of nomenclature to produce classifications. These techniques and concepts are widely used in modern evolutionary biology. Thus, phylogenetics provides evolutionary trees that are the starting point of comparative or biodiversity analyses for a broad range of evolutionary problems or taxa. Biological nomenclature provides rules that enable systematists to present classifications (better called taxonomies) to summarize the evolutionary relationships between species and to sort our knowledge of the biosphere. Recent developments in phylogenetics and, to a lesser extent, in biological nomenclature have given new life to paleontology and evolutionary biology. Until approximately the 1970s, paleontologists reconstructed evolutionary trees by hand, using criteria that they did not always explain. Since then, the advent of cladistics, soon followed by software that enabled systematists to tap into the tremendous processing power of computers, introduced more objectivity into phylogenetics because the data used to produce the trees are generally published. This triggered a proliferation of phylogenetic studies and led to a re-examination of many long-held hypotheses on the phylogeny of life. As a result, we now have a much better resolved tree of life than a few decades ago, even though much of this tree will probably change as a result of future investigations. These methods are presented in a simplified manner in this chapter, and the bibliography provides an introduction to the most relevant papers where more technical information can be found.
CLASSIFICATION AND BIOLOGICAL NOMENCLATURE
Rank-Based Nomenclature
A form of classification is essential to sort information, whatever its nature. Man has classified animals since antiquity, as attested in the Bible (ESV, 2001), in which we can read: "So out of the ground the Lord God formed every beast of the field and every bird of the heavens and brought them to the man to see what he would call them. And whatever the man called every living creature, that was its name." (Genesis, 2:19). Since Aristotle (384–322 bce), many authors have proposed classifications of living beings. The subdiscipline of biology that consists of naming, defining, and delimiting the groups of living organisms (the taxa) is called "taxonomy," like the product of this activity (the taxonomies). Thus, taxonomy harks back to antiquity (under a form substantially different from today's), but, initially, only vernacular names were used. These were part of the standard vocabulary of a language, in contrast to formal names that are often known only by scientists.
The drawback of vernacular names is that their meaning can vary in space and time (this is typical of most words in any language), and there are often no exact synonyms among languages. Thus, the word "fish" once included whales (until the 19th century), although they are now excluded because we now know that whales are mammals that have returned to the seas. In English, this word has also included, at least in its broadest sense, aquatic animals that are no longer considered "fishes," such as echinoderms (e.g., "starfish"), arthropods (e.g., "crayfish"), mollusks (e.g., "cuttlefish"), or even cnidarians (e.g., "jellyfish"); but this is not true of many other European languages, such as French, in which the equivalent word "poisson" has long had a narrower sense restricted to aquatic vertebrates. These two words ("fish" and "poisson"), often considered synonyms, have thus not always referred to the same groups of animals.
Vernacular words are not ideally suited to scientific use because of their variability in space and time, and because of the imperfect synonymy between names used in various languages (Minelli et al., 2005). Thus, scientists began to develop, as early as the 18th century, precise taxonomies based on names that would ideally have the same meaning for all scientists, no matter when or where they lived. Such developments were becoming increasingly important because of the exponential growth of our knowledge of the biodiversity that resulted from the scientific exploration (in which several biologists took part) of various continents in the 18th century. The Swedish botanist Linnaeus (1707–1778) was the first to propose a comprehensive taxonomy that was widely adopted among scientists. In his system, the names were based on Ancient Greek and Latin roots, an advantage because these dead languages were no longer changing, and because they were widely read by 18th-century scientists. (Most of Linnaeus' works, and even his letters to foreign colleagues, are written in Latin.) To cope with the astronomical number of species to name, he proposed to form names consisting of two words, a genus name and a specific epithet. This constituted a great nomenclatural simplification because species names had grown to Latin descriptions sometimes spanning several lines of text. Thus, our species belongs to the genus Homo and bears the epithet sapiens. Furthermore, each genus belongs to an order, each order belongs to a class, and each class fits into a kingdom. For our species, the taxa of these ranks are Primates (order), Mammalia (class), and Animalia (kingdom). Linnaeus thus used the categories species, genus, order, class, and kingdom that encompass increasingly more inclusive groups. More recently, additional categories (ranks) were introduced, such as the family between the genus and the order. For some ranks, there are now standard endings. Thus, in zoology, taxa at the family rank end in -idae. The stem of the name of a family is always formed by the name of a genus that belongs to the family. Our family name (Hominidae) derives from our genus name (Homo) and the suffix -idae. For subfamilies, the suffix is -inae, and this explains why our subfamily is named Homininae. Using such rules, the following classification of our species can be given:
Kingdom Animalia
Subkingdom Metazoa
Superphylum Deuterostomia
Phylum Chordata
Subphylum Vertebrata
Superclass Gnathostomata
Class Mammalia
Subclass Eutheria
Order Primates
Suborder Haplorhini
Superfamily Hominoidea
Family Hominidae
Subfamily Homininae
Tribe Hominini
Subtribe Hominina
Genus Homo
Species Homo sapiens
Well after Linnaeus, taxonomists proposed rules to determine how to apply names; this forms what we call "nomenclature." Such an explicit nomenclature became necessary in the 19th century because of the very rapid growth in our knowledge of biodiversity (we presently know about 2,000,000 species, and several thousand are added every year). The nomenclature used by most taxonomists is often called "Linnaean" because some of its principles were established by Linnaeus, but it differs by using types, a nomenclatural novelty introduced in the 19th century. Types are either individuals (an animal preserved in alcohol or a skeleton, for instance) used in defining species, or taxa of lower rank that are used to define taxa of higher rank. Thus, a genus is defined by a type species, and a family is defined by a type genus (Fig. 1.1). Because of these additions and the extensive use of ranks, some systematists now prefer the expression "rank-based nomenclature."
Evolution and Vertebrate Taxonomy: There Are No Fishes Anymore!
When Linnaeus proposed his taxonomy, virtually no scientists accepted any sort of theory of biological evolution (Linnaeus was initially a creationist). The theory of evolution by natural selection was proposed, discussed, and accepted (at least by scientists) in the middle to late 19th century. This theory was further elaborated in the 20th century by the discovery of genetic mutations and genetic drift. However, biologists have only recently changed their taxonomies to reflect this scientific revolution, and the rules of rank-based nomenclature have not drastically changed for more than a century.
Acceptance of the idea of organic evolution has led biologists to include all descendants of an ancestor in the same taxon as that ancestor. A group thus delimited is objective because it includes species that share a common history and inherited similarities. Such a taxon is called "monophyletic," as opposed to a "paraphyletic" group (Fig. 1.2A), which excludes part of the descendants, or a "polyphyletic" group, which contains species that are not closely related to each other (Fig. 1.2B). The taxon Pisces (the "fishes") is no longer considered valid by most biologists because it excludes some descendants of "fishes," namely, the tetrapods (Fig. 1.3). Paraphyletic taxa are artificial because their delimitation is arbitrary. They were erected long ago, when biologists classified organisms according to their similarities and along the gaps in biodiversity. Such gaps, found between "fishes" and tetrapods in the extant fauna, result from the extinction of intermediate forms. Fossils can fill these gaps, though only to an extent, because museum collections of fossils represent only a small proportion of the extinct species that once inhabited the Earth. Thus, these gaps are merely artifacts that reflect inadequacies in our knowledge of nature; they do not form justifiable borders between taxa. Indeed, why exclude only the tetrapods from the "fishes"? Why should we not also exclude the lungfishes and the coelacanth as well? The taxon Pisces is paraphyletic (Fig. 1.3), and it is preferable to replace it by a monophyletic taxon issued from the same ancestor, namely, Vertebrata, the taxon that includes all vertebrates. Monophyletic groups are considered natural and can be considered individuals in the philosophical sense: they have an origin (the appearance of the last common ancestor) and an end (the extinction of the last descendant of that ancestor). However, the rank-based codes (that presently rule the application of taxon names) do not require that taxa be monophyletic; paraphyletic and even polyphyletic taxa are allowed.
Taxonomy has been deeply transformed by the application of these principles. For instance, it was once customary to divide the limbed vertebrates (often called tetrapods, but called stegocephalians in this book) into amphibians, reptiles, birds, and mammals, but the first two of these groups are paraphyletic (Fig. 1.4). Today, some authors want to eliminate all names of paraphyletic taxa, such as Reptilia (which traditionally includes the turtles, snakes, and crocodilians, but not the birds, which are nevertheless the closest relatives of the crocodilians in the extant fauna), whereas others prefer to re-delimit these taxa to make them monophyletic. Under this latter approach, Amphibia no longer includes the first limbed vertebrates, such as the Devonian genus Ichthyostega (360 Ma old), because the latter are not more closely related to the extant amphibians (frogs, toads, salamanders, etc.) than to the mammals. The taxon Reptilia can be made monophyletic by excluding the "mammal-like reptiles" (stem synapsids) and including the birds (Fig. 1.4), as advocated by some authors.
Phylogenetic Nomenclature
Taxonomy is currently undergoing a revolution in an attempt to make biological classification less ambiguous. Use of rank-based nomenclature is increasingly unsatisfactory because taxa are delimited under that system through the use of a type and a rank (a Linnaean category, such as species, genus, or family). Since these ranks are subjective, taxonomists can—and often do—change them at will. This system also allows new taxa to be erected (to encompass the same species or individuals) and established taxa to be suppressed (by declaring them synonyms) without requiring an objective basis for any such decisions. Understandably, this results in great taxonomic instability, even if the evolutionary tree (the phylogeny) is stable. In other words, even if our ideas about the evolution of a taxon are stable (in the long term this is admittedly an idealized scenario), the classification of this taxon can be unstable, simply because taxonomists are free to expand or reduce the membership of taxa.
This problem can be illustrated by an example using the origin of mammals (Fig. 1.5). The formal name of the taxon that includes all mammals is Mammalia. This name was used by Linnaeus, who knew only placental mammals (Placentalia) and one marsupial (Marsupialia), the Virginia opossum (1). Later, we discovered monotremes, which lay eggs (unlike other mammals) but possess mammary glands. Mammalia was then expanded to encompass the monotremes (2). With the subsequent discovery of fossils similar to extant mammals, Mammalia was further expanded (3 to 6; most commonly 4 in recent times), although some authors advocate a return to an older meaning of this word (2, or occasionally even 1). Other authors extend the taxon Mammalia to encompass a much larger clade (7 to 10), although they fortunately represent a small minority.
This problem, far from affecting only the taxon Mammalia, results from the application of principles of rank-based nomenclature (see the box titled "Instability in rank-based nomenclature"), which were proposed in the 18th and 19th century, when most taxonomists considered taxa to be classes in the philosophical sense of the word. Classes can be defined by intrinsic properties that are both necessary and sufficient for an element to belong to this class. For instance, tetrapods possess four limbs, as suggested by their name, and this could be viewed as the defining property of the class Tetrapoda. However, many contemporary systematists think that taxa are individuals in the philosophical sense of the word, since they have a beginning (the appearance of a clade) and an end (the extinction of the clade) in time. Because taxa evolve, their members do not necessarily share intrinsic properties (Ereshefsky, 2007). Thus, snakes and caecilians are tetrapods, even though they have lost their limbs, because they are descended from tetrapods. For these reasons, it is preferable to define taxon names using types and the phylogeny. This is analogous to the delimitation of families (in humans) or breeds (of domestic animals), which depends on ancestry (genealogy).
To replace rank-based nomenclature (at least above the species level), several systematists have developed a phylogenetic nomenclature. In that system, the taxon name Mammalia could be defined (for instance) as the smallest clade that includes monotremes, marsupials, and placentals (Fig. 1.5, node 2). If we wish to discuss more or less inclusive clades than this one, we have to use other names for them (each name must have a single definition). Phylogenetic nomenclature should clarify the meaning of taxon names since each name will correspond to a single clade on a given tree. For this reason, it is adopted in this book. It differs from rank-based nomenclature by using at least two types, called "specifiers," to define taxon names. In phylogenetic nomenclature, three main kinds of definitions can be given to these names (Fig. 1.6): 1, node-based (for instance, the smallest clade that includes species A and B, in pale gray); 2, apomorphy-based (an apomorphy is a new character state; such a definition can be, for instance, the clade delimited by apomorphy M shared with species A, shown in white); 3, branch-based (the largest clade that includes species A but not species Z in dark gray). (See the box titled "Nodes, apomorphies, and branches.")
(Continues...)
Excerpted from How Vertebrates Left the Water by Michel Laurin. Copyright © 2010 the Regents of the University of California. Excerpted by permission of UNIVERSITY OF CALIFORNIA PRESS.
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Table of Contents
Contents
Preface, xi,ONE HOW CAN WE RECONSTRUCT EVOLUTIONARY HISTORY?, 1,
Classification and Biological Nomenclature, 2,
Modern Phylogenetics, 16,
Homology and Analogy: Lungs, Swim Bladders, and Gills, 37,
Geological Time Scale and the Chronology of a Few Key Events, 39,
A Few Relevant Paleontological Localities, 40,
TWO CONQUEST OF LAND: DATA FROM EXTANT VERTEBRATES, 45,
Are Animals Still Conquering the Land Today?, 45,
The Coelacanth, a Living Fossil?, 47,
Dipnoans: Our Closest Extant Finned Cousins, 49,
Reproduction among Tetrapods: Amphibians Are Not All Amphibious!, 51,
THREE PALEONTOLOGICAL CONTEXT, 55,
The Conquest of Land in Various Taxa, 55,
The History of Our Ideas about the Conquest of Land by Vertebrates, 63,
The Lateral-Line Organ and the Lifestyle of Paleozoic Stegocephalians, 68,
FOUR VERTEBRATE LIMB EVOLUTION, 73,
The Vertebrate Skeleton, 73,
Hox Genes and the Origin of Digits, 75,
Sarcopterygian Fins and the Origin of Digits, 79,
Fragmentary Fossils, Phylogeny, and the First Digits, 82,
The Gills of Acanthostega and the Original Function ofthe Tetrapod Limb, 88,
Bone Microanatomy and Lifestyle, 89,
FIVE DIVERSITY OF PALEOZOIC STEGOCEPHALIANS, 99,
Temnospondyls, 99,
Embolomeres, 106,
Seymouriamorphs, 109,
Amphibians, 116,
Diadectomorphs, 121,
Amniotes, 125,
Stegocephalian Phylogeny, 127,
SIX ADAPTATIONS TO LIFE ON LAND, 135,
Limbs and Girdles, 136,
Vertebral Centrum and Axial Skeleton, 140,
Breathing, 142,
The Skin and Water Exchange, 147,
Sensory Organs, 150,
SEVEN SYNTHESIS AND CONCLUSION, 161,
Conquest of Land and the First Returns to the Aquatic Environment, 161,
Why Come onto Land?, 163,
Modern Paleontology and the "Indiana Jones" Stereotype, 166,
Glossary, 169,
Bibliography, 175,
Index, 187,
What People are Saying About This
"Summarizes key concepts of modern paleontological research."—The Guardian
"I recommend the book to students especially, although the book certainly would be a welcome addition into any natural historian's library."—Systematic Biology
"The text is detailed, well referenced, and. . . readable."—Choice
"It is a fantastic summary of the fossil record of our vertebrate ancestors and brethren as well as a general introduction to the science of paleontology."—Systematic Biology
"Well-written and -illustrated synthesis of an interesting evolutionary topic, crafted from the perspective of a talented and qualified paleontologist."—Bioscience