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Material Copyrighted - Preview 1 1 Great Clarendon Street, Oxford, OX2 6DP, United Kingdom Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide. Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries © Lindell Bromham 2016 The moral rights of the author have been asserted First edition 2008 Impression: 1 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, by licence or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this work in any other form and you must impose this same condition on any acquirer Published in the United States of America by Oxford University Press 198 Madison Avenue, New York, NY 10016, United States of America British Library Cataloguing in Publication Data Data available Material Library of Congress Control Number: 2015943760 ISBN 978–0–19–873636–3 Printed in Great Britain by Bell & Bain Ltd., Glasgow Links to third party websites are provided by Oxford in good faith and for information only. Oxford disclaims any responsibility for the materials contained in any third party website referenced in this work. Copyrighted - Preview Introduction The story in DNA 1 “In nature’s infinite book of secrecy A little I can read” William Shakespeare (1623) Antony and Cleopatra. What this chapter is about This chapter gives an overview of the kind of information that can be gained from analysing DNA sequences, such as identifying individuals, il- luminating social interactions, understanding the evolution of major ad-Material aptations, tracing the evolutionary origins of lineages, and investigating the tempo and mode of evolution over all timescales. By taking a brief look at the use of DNA sequences in evolution and ecology, we will set the scene for topics covered in more detail in later chapters. Key concepts • Evolutionary biology connects changes in individualCopyrighted genomes to population-level processes to the generation- of biodiversity • Information on all of these levels is available in the genome Preview 2 Introduction Reading the Story in DNA The mystery of the Chilean blob As reported on Unexplained-Mysteries.com: ‘One In July 2003, a 13 tonne blob washed up on a Chilean of the myths of the sea has been skewered by gene beach (Figure 1.1). With no bones, no skin, not even researchers’. any cells, there was nothing obvious to identify the The DNA sample taken from the Chilean blob was origin of the mystery blob. Theories abounded: it was enough to unambiguously identify it as the remains of a giant squid, a new species of octopus, an unknown a sperm whale. But that DNA sample could do far more. monster from the deep, an alien. This was not the first From that one tiny sample we could identify not only appearance of a giant ‘globster’. In 1896, an 18 metre the species it came from but also, given enough data, blob washed up on St Augustine beach in Florida (USA). which individual whale. We could use that DNA sample The identification of the blob varied from giant squid to to predict where that individual whale was born and to whale blubber. However, when it was formally described understand its relationship to other whales within its in the scientific literature (albeit sight unseen), it was immediate family and to members of its social group. given the scientific name Octopus giganteus. There have That sample of DNA could help us to track whale move- been at least half a dozen other reported globsters, in- ments across the globe, both in space and in time. We cluding the 1960 Tasmanian West Coast Monster, thirty could use it to trace this whale’s family history back feet long and eight feet tall, which, although badly de- through the ages, exploring how the whales responded composed, was described as being hairy. to a changing world as ice ages came and went. The The mystery of the Chilean blob was solved in 2004 DNA sample could help us to reconstruct the evolution when researchers sequenced DNA samples from the of important whaleMaterial adaptations such as echolocation, globster, and compared them to DNA sequences held and identify the nearest mammalian relatives of the in the gigantic public database GenBank (TechBox 1.1). whales, a question that had perplexed biologists for The sequences matched that of a sperm whale (scien- centuries. By comparing this whale DNA to the DNA tific namePhyseter catadon: Figure 1.2). The globster of other mammals, we could ask whether the rise of was nothing but blubber (Case Study 1.1). The team modern mammals was contingent on the extinction of also retrospectively solved previous sea monster mys- the dinosaurs. Deeper still, this DNA could help us look teries. For example, DNA extracted from samples of the ‘Nantucket Blob’ of 1996 showed that it had beenCopyrighted the remains of a fin whale (Baleonoptera physalus- ). Preview Figure 1.2 Sperm whales (Physeter catadon, also known as Physeter macrocephalus) derive their common name from spermaceti, a waxy, milky white substance that is found in abundance in sperm whales’ heads. The exact function of Figure 1.1 The blob that washed up on a Chilean beach spermaceti is not known: it might act as a sounding medium had people guessing: squid? octopus? kraken? DNA analysis for echolocation or to aid buoyancy or possibly to give the proved beyond doubt that the blob was the remains of a head extra heft for headbutts in male-to-male combat. sperm whale. Similar blobs have been found on beaches all When whaling was a global industry, whale oil, derived from over the world. A prolonged period at sea may break down spermaceti, had a variety of industrial uses, including the whale carcasses and turn their innards into unrecognizable production of candles. blobs which eventually wash ashore. Image courtesy of Gabriel Barathieu, licensed under the Creative Image courtesy of Elsa Cabrera/CCC. Commons Attribution Share Alike 2.0 Generic license. Individuals, families, and populations 3 back into deep time, shedding light on one of the great- individuals share particular sequence changes, bi- est biological mysteries, the explosive beginnings of the ologists can use DNA sequences to reveal the rela- animals, and even back to the origin of the kingdoms. tionships between individual whales. Since DNA is This chapter will use sperm whale DNA to briefly illus- inherited from both father and mother with relatively trate the kind of information we can get from analysing few changes, it is possible to use DNA sequences to DNA sequences. The rest of the book will show you how. conclusively identify an individual’s parents. The inheritance of specific DNA differences can also be traced back through a whale’s family tree, to its par- Individuals, families, and populations ents, grandparents and great-grandparents, and so The genome of a sperm whale contains over on. So, in addition to identifying specific individu- 3,000,000,000 nucleotides of DNA. Nucleotides are the als, if you take DNA sequences from a whole group basic units of DNA, and they come in four types, which of whales, you can tell who is whose mother or sis- are given the single-letter codes A, C, G and T. These four ter or cousin. More generally, you can start to under- letters make up the DNA alphabet. All of the informa- stand how populations of sperm whales interact and tion needed to make the essential parts of a whale, such interbreed. as the skin, the eyes, the blubber, and the blood, is coded in these four letters. Chapter 4 explains how DNA replication results in related individuals being more genetically similar The structure of DNA is covered in Chapter 2 Sperm whales travel in social groups that co-operate to Most of the genome is exactly the same for all sperm defend and protect each other and may even share suck- whales, because all whales must be able to make func- ling of calves.Material It is difficult to determine the membership tional skin, eyes, blubber and blood in order to sur- of these groups from sightings alone because of the prac- vive. But some of the DNA letters can change without tical difficulties of observing whale behaviour, most of destroying the information needed to make a work- which happens underwater. To make things even more ing whale. Because of this, some DNA sequences vary difficult, sperm whales can travel across entire oceans and slightly between individual sperm whales. Most of can dive to a depth of a kilometre. Biologists who study these differences between genomes arise when DNA is whale behaviour have traditionally had to be content copied from the parent’s genome to make the eggs or with hanging around in boats, waiting for their subjects sperm that will go on to form a new individual. DNA to surface. But when they do surface, in addition to tak- copying is astoundingly accurate, but it is not perfect. In Copyrighteding photos which allow individual whales to be identified, fact, you could probably expect around 100 differences - biologists can zip over in worryingly small boats and try in the nucleotide sequence of the sperm whale genome to take a small biopsy or pick up the bits of skin that the between a parent whale and its calf, due to mutation.