Genetics? No Problem!, First Edition. Kevin O’Dell. © 2017 John Wiley & Sons Ltd. Published 2017 by John Wiley & Sons Ltd.

Chapter 1.2

Tiger! Tiger!

You’ve always dreamed of visiting your cousin in Kolkata and you can’t quite believe you’re actually on a flight to visit her. More to the point, you can’t quite believe your parents have paid for the trip! This is a very special summer in so many respects. You’ve just finished school and, with any luck and the right exam results, you’ll be off to university in September to study genetics.

When you arrive at Netaji Subhash Chandra Bose International Airport your cousin is there to meet you. But she is not alone. ‘This is my boss, Professor Bagh,’ she says. ‘She’s wondering whether you’d like to work with us over the summer.’ You are totally lost for words. Professor Bagh is a bit of a hero of yours. She runs the Bengal Tiger Conservation Project and nobody knows more about tigers than she does.

The professor smiles at you and says, ‘Your cousin tells me you’re a budding geneticist. Every good conservation project needs a talented geneticist.’ You begin to fear your cousin has been rather exaggerating. You are somewhat reassured when Professor Bagh smiles and says, ‘We have several talented geneticists working with us. Would you like to become part of our genetics team?’

Over the next few days, whilst you get used to your new surroundings, you find out as much as you can about the Bengal tiger. You soon discover that even though it is the most numerous of the world’s tiger subspecies, there are still fewer than 2500 Bengal tigers in the wild. Its current and historic range is shown in Fig. 1.2.1. Apparently most Bengal tigers live in eastern India, with smaller populations in Bangladesh, Bhutan and Nepal. The Bengal tiger is classified as an endangered species by the International Union for Conservation of Nature (IUCN), and Professor Bagh is developing a strategy to help the species survive.

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Your cousin explains that there are several reasons why tiger populations are declining. Apparently, humans cause most of the problems, either through the destruction of habitat or by poaching. This means that the remaining tiger populations are fairly isolated and inbred. So there is a real risk of extinction.

Question 1: Why is inbreeding often a problem for wild animals? (10%)

Question 2: What kind of plan could conservation project leaders, such as Professor Bagh, follow to avoid issues with inbreeding? (10%)

SriLanka

Chennai

Bangalore

Madurai

HyderabadPune

Mumbai

I n d i aAhmedabad

JaipurKanpur

Kolkata

Bangladesh

BhutanPatna

Varanasi

Myanmar

Maximum known habitat

Current habitat

Nepal

New Delhi

Pakistan

Amritsar

Nagpur

Figure 1.2.1 Map showing the current and historical range of the Bengal tiger.

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Tiger! Tiger! 9

On your first day at work your cousin introduces you to the Professor’s team and you’re very excited when she asks you to put on some protective clothing. You presume this must be because you’re going to start some analysis of tiger DNA samples, so the protective clothing will prevent exposure to the dangerous chemicals you’ll be using to do this.

You are therefore slightly surprised when your cousin also hands you a bucket and spade and takes you outside. ‘The tigers have been moved to another enclosure,’ she says very confidently. ‘All you have to do is collect tiger poo and put it in the bucket, whilst I mark the position of the poo on my map so we know which tiger it came from’. She notices the horrified look on your face. ‘It’s a lot safer than asking a tiger to give you a blood sample,’ she says. Whilst you are still somewhat horrified, you have to concede that she has a valid point. Over the summer you become quite an expert at collecting, bagging and labelling tiger poo.

Back in the laboratory, Professor Bagh explains what she wants you to do. ‘We occasion-ally see white Bengal tigers,’ she says, ‘and we’d like you to help us determine the genetic basis of this variant.’ The two versions of Bengal tiger, the common orange form and the very rare white form, are shown in Fig. 1.2.2. Your first thought is that the white tiger is an albino.

You ask Professor Bagh to provide you with some tiger pedigree data so you can determine whether the white colour is genetically inherited. One of the tiger pedigrees is shown in Fig. 1.2.3.

Figure 1.2.2 The wild‐type orange and rare white varieties of Bengal tiger. Professor Bagh’s team use these cartoons to identify individual orange tigers as each individual has a slightly different orange and black pattern. The white tigers only differ in their black patterning.

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10 Chapter 1.2

Question 3: Looking at the image of the mutant white tiger in Fig. 1.2.2, give two reasons why the white Bengal tiger is not a true albino. (10%)

Question 4: What is the evidence that the white colour is caused by a recessive mutation? (10%)

Question 5: Redraw the pedigree showing the genotypes of each individual. (10%)

Question 6: There may be some individuals whose genotypes cannot be absolutely deter-mined. Who are they and why can’t their genotypes be determined? (10%)

Question 7: How could you determine the precise genotypes of the problem animals identified in your answer to question 6? (10%)

A few days later your cousin rushes into the laboratory in a bit of a panic. ‘Your theory must be wrong,’ she says. ‘Two white Bengal tigers have just given birth to three orange cubs!’ You ask her to explain further. ‘We’ve been following tiger movements within the conservation project area for months,’ she replies, ‘and we’re fairly sure Sunetra mated with Arindam.’ You note that she uses the phrase fairly sure rather than absolutely certain, and you realise that it’s time to test the parentage of the three orange cubs using DNA profiling. Images of these and of other tigers you have encountered are shown in Fig. 1.2.4.

5

1

3 4 62

2

2 31 4 765 8 9 10

1 7

I

II

III

Figure 1.2.3 Inheritance of white and orange Bengal tiger colour in a typical tiger family. By convention, females are circles and males are squares. Generations are indicated by roman numerals (I, II, III and IV), whilst individuals within that generation are numbered 1, 2, etc.

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Tiger! Tiger! 11

You remember your biology teacher explaining how DNA tests using short tandem repeats (STRs) can be used to determine parentage. So you look at your notes and investigate how STRs are inherited.

Question 8: What is the genetic basis of STRs and how can they be used to determine parent-age? (10%)

It’s now that you appreciate the value of the work you’ve been doing in the summer. Your data-base immediately tells you which samples of tiger poo came from the mother and her three cubs, as well as which samples came from each of the four possible fathers. You collect the appropriate tiger poo samples from the freezer and you prepare DNA samples. For each of the eight tigers, you determine the length of a particularly variable STR on chromosome 4. This data is presented in Table 1.2.1.

Figure 1.2.4 Images of your time working at the Bengal Tiger Conservation Project with your new best friend Del.

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12 Chapter 1.2

Question  9: Who are the parents of the three orange cubs, Clementine, Satsuma and Tangerine? (10%)

Question 10: What is the most plausible explanation for Clementine, Satsuma and Tangerine being orange? (10%)

Table 1.2.1 The STR status and coat colour of the mother and her three cubs, as well as the STR status and coat colour of the four males who could be the father of the cubs. All of the adults were originally caught in the wild at least a year ago, so their place of capture is also shown. As the gestation period of tigers is approximately 100 days, the cubs must have been conceived since Sunetra arrived at the Bengal Conservation Project.

Name Colour Status Place of capture STRs

Sunetra white mother West Bengal 22 & 27Clementine orange cub 27 & 31Satsuma orange cub 22 & 31Tangerine orange cub 27 & 34Arindam white father? West Bengal 22 & 28Shantanu orange father? West Bengal 20 & 27Sourav white father? Assam 31 & 34Utpal orange father? Bihar 18 & 26

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