Population Pedigree Process of the Chatham Island Black Robin: a Case of Human-Assisted Spread of a Maladaptive Behavior in a Critically Endangered Bird

Population pedigree process of the Chatham island black robin

Population pedigree process of the Chatham island black robin: A case of human-assisted spread of a maladaptive behavior in a critically endangered bird

Raazesh Sainudiin†

†Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand Parts are Joint work with: James Briskie, Marie Hale, Melanie Massaro, Don Merton, Anthony Poole

October 24 2012,

CMAP, École Polytechnique, Palaiseau, France

1 / 100 Population pedigree process of the Chatham island black robin

Chatham Islands – Geography & Ecological History

Ecological History of Black Robins

Tests for Heritability of Rim-laying in 1980s

PVA with Behaviourially Realistic Population Pedigree Models

A Field Excursion

2 / 100 Population pedigree process of the Chatham island black robin

Part I

3 / 100 Population pedigree process of the Chatham island black robin Chatham Islands – Geography & Ecological History

Map of Antarctica (English / French)

4 / 100 Population pedigree process of the Chatham island black robin Chatham Islands – Geography & Ecological History

Chatham Islands (New Zealand) Topographical Map

5 / 100 Population pedigree process of the Chatham island black robin Chatham Islands – Geography & Ecological History

Chatham Islands (New Zealand)

I The Chatham Islands lie 767 kilometres south-east of mainland New Zealand.

I There are two main islands – Chatham Island and Pitt Island

I and many smaller islands – including Little Mangere, Mangere and Rangatira

I The islands have only emerged above sea level in the last 4 million years and are part of the Chathams rise connected below ocean to NZ.

I The climate is cool and wet with salt-laden winds all year round.

6 / 100 Population pedigree process of the Chatham island black robin Chatham Islands – Geography & Ecological History

Chatham Islands (New Zealand) Chatham Islands From Space

Chatham Is. Rangatira Pitt Is.

Mangere Little Mangare

7 / 100 Population pedigree process of the Chatham island black robin Chatham Islands – Geography & Ecological History

Chatham Islands (New Zealand)

Rangatira Island

g W n es i te d rn n

a a L r l a yd nd H in 's g ly il L My rs i n

x e ne n A W h al I is the third largest island er s W d No ha e r l h th C ss er s ro s Bay ol Echo's o t W es W W h a 's S l e outh Cross e Ik r C 's s h cey -T i q a hin is uitas S t orn in the Chatham Islands T Ji h l l's in T o ora's rn is G+G

Z o r r h o s 's u B L d on n g a D l

s r I p o I covers an area of 218 p o Marlesh r r D e g Low on r L pe p S U i Upper Marle n sh b a d 's A u's

hectares (539 acres) T r i g

m m u p s S m ' a n o w R S

U u

p p o F p r R k a e o o n r Pa n ra 's k K a S e et n u d I is a gazetted nature p m R K m o m u a k a o i w p t Pr u er io S p n P cr p e U arad e e

P k loaca are sty C a Cru O 's io ld N F or est K ix ar pend e ns oop reserve since 1953 Ap C y L F s ba a le s t n e i ta r i a c l K L r r m a s s C n e ' e - t m T ' n s a u r S o i r g e R W U p p S st e cu Scuzz E a ak z z West e h Sum m k lear rt A Ea t C s o it s

N K C I is now home to many 's endemic species

l e a r s I is home to black robins– saved from near extinction by team led by

Rangatira Island Nature Reserve Map by Dave Houston v1 - 14/07/2011 Don Merton in the 1980s 0 125 250 500 Meters Track positions +/- 10m ´ Scale 1:7,000 8 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

A Chatham island Black Robin in Rangatira today

9 / 100 I Whaling continued until 1964. It closed for economic reasons, due to over-ﬁshing by Japanese and Russian whaling ﬂeets.

I The environmental and ecological consequence on the Chatham islands was massive

I the accompanying sheep and cattle farming and the feral rabbits and pigs released by sailors resulted in over-grazing and destroyed the indigenous ﬂora

I the introduced predators such as cats, rats and stoats destroyed the indigenous fauna (especially birds that evolved in the absence of land-based predators)

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Whaling, Sealing & Farming in islands of NZ

I Seals in New Zealand had been hunted to the verge of extinction by 1830 and sealing was outlawed in 1926.

10 / 100 I The environmental and ecological consequence on the Chatham islands was massive

I the accompanying sheep and cattle farming and the feral rabbits and pigs released by sailors resulted in over-grazing and destroyed the indigenous ﬂora

I the introduced predators such as cats, rats and stoats destroyed the indigenous fauna (especially birds that evolved in the absence of land-based predators)

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Whaling, Sealing & Farming in islands of NZ

I Seals in New Zealand had been hunted to the verge of extinction by 1830 and sealing was outlawed in 1926.

I Whaling continued until 1964. It closed for economic reasons, due to over-ﬁshing by Japanese and Russian whaling ﬂeets.

11 / 100 I the accompanying sheep and cattle farming and the feral rabbits and pigs released by sailors resulted in over-grazing and destroyed the indigenous ﬂora

I the introduced predators such as cats, rats and stoats destroyed the indigenous fauna (especially birds that evolved in the absence of land-based predators)

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Whaling, Sealing & Farming in islands of NZ

I Seals in New Zealand had been hunted to the verge of extinction by 1830 and sealing was outlawed in 1926.

I Whaling continued until 1964. It closed for economic reasons, due to over-ﬁshing by Japanese and Russian whaling ﬂeets.

I The environmental and ecological consequence on the Chatham islands was massive

12 / 100 I the introduced predators such as cats, rats and stoats destroyed the indigenous fauna (especially birds that evolved in the absence of land-based predators)

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Whaling, Sealing & Farming in islands of NZ

I Seals in New Zealand had been hunted to the verge of extinction by 1830 and sealing was outlawed in 1926.

I Whaling continued until 1964. It closed for economic reasons, due to over-ﬁshing by Japanese and Russian whaling ﬂeets.

I The environmental and ecological consequence on the Chatham islands was massive

I the accompanying sheep and cattle farming and the feral rabbits and pigs released by sailors resulted in over-grazing and destroyed the indigenous ﬂora

13 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Whaling, Sealing & Farming in islands of NZ

I Seals in New Zealand had been hunted to the verge of extinction by 1830 and sealing was outlawed in 1926.

I Whaling continued until 1964. It closed for economic reasons, due to over-ﬁshing by Japanese and Russian whaling ﬂeets.

I The environmental and ecological consequence on the Chatham islands was massive

I the accompanying sheep and cattle farming and the feral rabbits and pigs released by sailors resulted in over-grazing and destroyed the indigenous ﬂora

I the introduced predators such as cats, rats and stoats destroyed the indigenous fauna (especially birds that evolved in the absence of land-based predators)

14 / 100 I By 1938 black robins were wiped off from all the Chatham islands except an estimated 20-35 pairs on Little Mangare (15ha) by Fleming, Turbott and Wotherspoon I Little Mangare is a rocky outcrop with a small native bush at the top that was nearly impossible for predatory mammals to reach I As per Sir Charles Flemming’s recommendation Rangatira island was purchased by the Corwn and made a nature reserve in 1954 I The more ecologically devastated Mangare island was also turned into a nature reserve with an ecological restoration effort of native ﬂora

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Discovery and Nature Reserves

I In 1871 William Travers announces the discovery of the new speciesPetroica traversi (Chatham island black robin) in Mangare island to Wellington Philosophical Society

15 / 100 I Little Mangare is a rocky outcrop with a small native bush at the top that was nearly impossible for predatory mammals to reach I As per Sir Charles Flemming’s recommendation Rangatira island was purchased by the Corwn and made a nature reserve in 1954 I The more ecologically devastated Mangare island was also turned into a nature reserve with an ecological restoration effort of native ﬂora

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Discovery and Nature Reserves

16 / 100 I As per Sir Charles Flemming’s recommendation Rangatira island was purchased by the Corwn and made a nature reserve in 1954 I The more ecologically devastated Mangare island was also turned into a nature reserve with an ecological restoration effort of native ﬂora

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Discovery and Nature Reserves

17 / 100 I The more ecologically devastated Mangare island was also turned into a nature reserve with an ecological restoration effort of native ﬂora

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Discovery and Nature Reserves

18 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Discovery and Nature Reserves

I In 1871 William Travers announces the discovery of the new speciesPetroica traversi (Chatham island black robin) in Mangare island to Wellington Philosophical Society I By 1938 black robins were wiped off from all the Chatham islands except an estimated 20-35 pairs on Little Mangare (15ha) by Fleming, Turbott and Wotherspoon I Little Mangare is a rocky outcrop with a small native bush at the top that was nearly impossible for predatory mammals to reach I As per Sir Charles Flemming’s recommendation Rangatira island was purchased by the Corwn and made a nature reserve in 1954 I The more ecologically devastated Mangare island was also turned into a nature reserve with an ecological restoration effort of native ﬂora 19 / 100 I Eggs were removed after being laid to encourage egg-laying I the removed eggs were hatched by foster species (tomtits) I the foster-cared chicks were transferred to black robin nests for sexual imprinting I each nest was monitored, managed and logged as unintrusively as possible in its native habitat I Unfortunately, a maladaptive bavioural trait of “rim-laying” also increased with the population I Managements ceased when the population reached about 100 birds

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Recovery Program in 1980s

I Studies in 1970s by Douglas Flack on Little Mangare (15ha) tracked a handful of breeding pairs and recommended transloaction to nearby Mangere (113ha) and Rangatira islands (218ha)

20 / 100 I the removed eggs were hatched by foster species (tomtits) I the foster-cared chicks were transferred to black robin nests for sexual imprinting I each nest was monitored, managed and logged as unintrusively as possible in its native habitat I Unfortunately, a maladaptive bavioural trait of “rim-laying” also increased with the population I Managements ceased when the population reached about 100 birds

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Recovery Program in 1980s

21 / 100 I the foster-cared chicks were transferred to black robin nests for sexual imprinting I each nest was monitored, managed and logged as unintrusively as possible in its native habitat I Unfortunately, a maladaptive bavioural trait of “rim-laying” also increased with the population I Managements ceased when the population reached about 100 birds

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Recovery Program in 1980s

22 / 100 I each nest was monitored, managed and logged as unintrusively as possible in its native habitat I Unfortunately, a maladaptive bavioural trait of “rim-laying” also increased with the population I Managements ceased when the population reached about 100 birds

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Recovery Program in 1980s

23 / 100 I Unfortunately, a maladaptive bavioural trait of “rim-laying” also increased with the population I Managements ceased when the population reached about 100 birds

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Recovery Program in 1980s

24 / 100 I Managements ceased when the population reached about 100 birds

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Recovery Program in 1980s

25 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Species Recovery Program in 1980s

I Studies in 1970s by Douglas Flack on Little Mangare (15ha) tracked a handful of breeding pairs and recommended transloaction to nearby Mangere (113ha) and Rangatira islands (218ha) I Eggs were removed after being laid to encourage egg-laying I the removed eggs were hatched by foster species (tomtits) I the foster-cared chicks were transferred to black robin nests for sexual imprinting I each nest was monitored, managed and logged as unintrusively as possible in its native habitat I Unfortunately, a maladaptive bavioural trait of “rim-laying” also increased with the population I Managements ceased when the population reached about 100 birds 26 / 100 I The ﬁrst node type represents an individual in a biparental population – the vertex could be male, female or of unknown-sex I The second node type is a “marriage event” and its in-neighbours are the male and female of the union and its out-neighbours are the offspring of the union I The pedigree of a whole population is called the population pedigree I The pedigree of a subset of individuals. i.e., a sample, from a population is called a sample pedigree I In the sequel, we will add temporal and spatial aspects to the classical notion of pedigree

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

What is a Pedigree?

I A pedigree is a collection of directed graphs between two types of nodes:

27 / 100 I The second node type is a “marriage event” and its in-neighbours are the male and female of the union and its out-neighbours are the offspring of the union I The pedigree of a whole population is called the population pedigree I The pedigree of a subset of individuals. i.e., a sample, from a population is called a sample pedigree I In the sequel, we will add temporal and spatial aspects to the classical notion of pedigree

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

What is a Pedigree?

28 / 100 I The pedigree of a whole population is called the population pedigree I The pedigree of a subset of individuals. i.e., a sample, from a population is called a sample pedigree I In the sequel, we will add temporal and spatial aspects to the classical notion of pedigree

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

What is a Pedigree?

29 / 100 I The pedigree of a subset of individuals. i.e., a sample, from a population is called a sample pedigree I In the sequel, we will add temporal and spatial aspects to the classical notion of pedigree

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

What is a Pedigree?

30 / 100 I In the sequel, we will add temporal and spatial aspects to the classical notion of pedigree

Population pedigree process of the Chatham island black robin Ecological History of Black Robins

What is a Pedigree?

I A pedigree is a collection of directed graphs between two types of nodes: I The ﬁrst node type represents an individual in a biparental population – the vertex could be male, female or of unknown-sex I The second node type is a “marriage event” and its in-neighbours are the male and female of the union and its out-neighbours are the offspring of the union I The pedigree of a whole population is called the population pedigree I The pedigree of a subset of individuals. i.e., a sample, from a population is called a sample pedigree

31 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

What is a Pedigree?

Highly Looped Black Robin Pedigree in 1980s

cicle = female, square = male, traingle = unknown sex, red circle = rim-layer, blue circle = non-rim-layer

33 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Female Population Tree during Field Conservation in 1980s

34 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Male Population Tree during Field Conservation in 1980s

35 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Population Pedigree during Field Conservation in 1980s

36 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Coalescent Sub-Pedigree of the 1989 population

37 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Rim-laying Behaviour during Field Conservation in 1980s

38 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Temporal Pedigree (with rim-layers) during 1980s 39 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

I Conservation Dilemma – when to cease management?

I Need managed pop. size to ↑

I But rim-laying trait also ↑

I Don Merton’s team ceased management when 50% of females were rim-layers by 1989

I Our Question: Is rim-laying a heritable Rim-laying increases in 1980s trait?

40 / 100 Population pedigree process of the Chatham island black robin Ecological History of Black Robins

Rim-laying increases in 1980s but between 2007 and 2011 (unmanaged phase) seems lower Our Question: Is rim-laying a heritable trait? 41 / 100 2. Pedigree Conditional Phenotype Randomization test I 3. Pedigree Conditional Phenotype Randomization test II

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Tests for Heritability of Rim-laying in 1980s

1. A Simple test based on mother-daughter phenotypes

42 / 100 3. Pedigree Conditional Phenotype Randomization test II

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Tests for Heritability of Rim-laying in 1980s

1. A Simple test based on mother-daughter phenotypes 2. Pedigree Conditional Phenotype Randomization test I

43 / 100 Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Tests for Heritability of Rim-laying in 1980s

1. A Simple test based on mother-daughter phenotypes 2. Pedigree Conditional Phenotype Randomization test I 3. Pedigree Conditional Phenotype Randomization test II

44 / 100 I Null Hypothesis H0: X1, X2,..., X62 i.i.d Bernoulli(p1) Random Variables

I Alternative Hypothesis H1: The Rim-laying Phenotype has a ﬁrst-order Markov dependence on Mother’s trait

p p P = 0,0 0,1 p1,0 p1,1

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Mother-daughter Phenotype based Test

I Let Egg-laying Female Xi = 1 if she is rim-layer and 0 otherwise.

45 / 100 I Alternative Hypothesis H1: The Rim-laying Phenotype has a ﬁrst-order Markov dependence on Mother’s trait

p p P = 0,0 0,1 p1,0 p1,1

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Mother-daughter Phenotype based Test

I Let Egg-laying Female Xi = 1 if she is rim-layer and 0 otherwise.

I Null Hypothesis H0: X1, X2,..., X62 i.i.d Bernoulli(p1) Random Variables

46 / 100 Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Mother-daughter Phenotype based Test

I Let Egg-laying Female Xi = 1 if she is rim-layer and 0 otherwise.

I Null Hypothesis H0: X1, X2,..., X62 i.i.d Bernoulli(p1) Random Variables

I Alternative Hypothesis H1: The Rim-laying Phenotype has a ﬁrst-order Markov dependence on Mother’s trait

p p P = 0,0 0,1 p1,0 p1,1

47 / 100 Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Mother-daughter Phenotype based Test

DATA: Mother-Daughter Phenotype Branching Diagram for Black Robins in 1980s

48 / 100 I Under H0: Maximum Likelihood Estimate (MLE) of p1 = 0.508 = fraction of rim-layers and can be seen as the independent “Markov” chain with identical rows: pˆ pˆ 0.492 0.508 Pb = 0,0 0,1 = pˆ1,0 pˆ1,1 0.492 0.508

I The Observed Likelihood ration Test Statistic is 2.97 I The p-value from parametric bootstrap is 0.083 (signiﬁcant at 10% level) I But this test ignores the pedigree within which phenoypes are expressible by genotypes in diploid individuals even under the simplest models of inherited Medelian traits

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Mother-daughter Phenotype based Test

I Under H1: the MLE of the transition probability matrix is: pˆ pˆ 0.583 0.417 Pb = 0,0 0,1 = pˆ1,0 pˆ1,1 0.360 0.640

49 / 100 I The Observed Likelihood ration Test Statistic is 2.97 I The p-value from parametric bootstrap is 0.083 (signiﬁcant at 10% level) I But this test ignores the pedigree within which phenoypes are expressible by genotypes in diploid individuals even under the simplest models of inherited Medelian traits

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Mother-daughter Phenotype based Test

I Under H1: the MLE of the transition probability matrix is: pˆ pˆ 0.583 0.417 Pb = 0,0 0,1 = pˆ1,0 pˆ1,1 0.360 0.640

I Under H0: Maximum Likelihood Estimate (MLE) of p1 = 0.508 = fraction of rim-layers and can be seen as the independent “Markov” chain with identical rows: pˆ pˆ 0.492 0.508 Pb = 0,0 0,1 = pˆ1,0 pˆ1,1 0.492 0.508

50 / 100 I The p-value from parametric bootstrap is 0.083 (signiﬁcant at 10% level) I But this test ignores the pedigree within which phenoypes are expressible by genotypes in diploid individuals even under the simplest models of inherited Medelian traits

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Mother-daughter Phenotype based Test

I Under H1: the MLE of the transition probability matrix is: pˆ pˆ 0.583 0.417 Pb = 0,0 0,1 = pˆ1,0 pˆ1,1 0.360 0.640

I The Observed Likelihood ration Test Statistic is 2.97

51 / 100 I But this test ignores the pedigree within which phenoypes are expressible by genotypes in diploid individuals even under the simplest models of inherited Medelian traits

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Mother-daughter Phenotype based Test

I Under H1: the MLE of the transition probability matrix is: pˆ pˆ 0.583 0.417 Pb = 0,0 0,1 = pˆ1,0 pˆ1,1 0.360 0.640

I The Observed Likelihood ration Test Statistic is 2.97 I The p-value from parametric bootstrap is 0.083 (signiﬁcant at 10% level)

52 / 100 Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Mother-daughter Phenotype based Test

I Under H1: the MLE of the transition probability matrix is: pˆ pˆ 0.583 0.417 Pb = 0,0 0,1 = pˆ1,0 pˆ1,1 0.360 0.640

under the simplest models of inherited Medelian traits 53 / 100 Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Pedigree Conditional Phenotype Randomization Test

Explain Idea on Board Results:

54 / 100 I The maladaptive rim-laying trait also increased with the populaiton in the absence of natural selection

I Such human-assisted spread of maladaptive traits poses the conservation dilemma

I In the case of black robins the managers seemed to have succeeded by stoppping management when half the population were rim-layers

I Merton suspected rim-laying was heritable (persn. commn. to Massaro)

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Conclusions - Part I

I Black robins were managed from just one successful breeding pair in the wild

55 / 100 I Such human-assisted spread of maladaptive traits poses the conservation dilemma

I In the case of black robins the managers seemed to have succeeded by stoppping management when half the population were rim-layers

I Merton suspected rim-laying was heritable (persn. commn. to Massaro)

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Conclusions - Part I

I Black robins were managed from just one successful breeding pair in the wild

I The maladaptive rim-laying trait also increased with the populaiton in the absence of natural selection

56 / 100 I In the case of black robins the managers seemed to have succeeded by stoppping management when half the population were rim-layers

I Merton suspected rim-laying was heritable (persn. commn. to Massaro)

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Conclusions - Part I

I Black robins were managed from just one successful breeding pair in the wild

I The maladaptive rim-laying trait also increased with the populaiton in the absence of natural selection

I Such human-assisted spread of maladaptive traits poses the conservation dilemma

57 / 100 I Merton suspected rim-laying was heritable (persn. commn. to Massaro)

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Conclusions - Part I

I Black robins were managed from just one successful breeding pair in the wild

I The maladaptive rim-laying trait also increased with the populaiton in the absence of natural selection

I Such human-assisted spread of maladaptive traits poses the conservation dilemma

I In the case of black robins the managers seemed to have succeeded by stoppping management when half the population were rim-layers

58 / 100 Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Conclusions - Part I

I Black robins were managed from just one successful breeding pair in the wild

I The maladaptive rim-laying trait also increased with the populaiton in the absence of natural selection

I Such human-assisted spread of maladaptive traits poses the conservation dilemma

I In the case of black robins the managers seemed to have succeeded by stoppping management when half the population were rim-layers

I Merton suspected rim-laying was heritable (persn. commn. to Massaro)

59 / 100 I We have also shown that the trait is at a low frequency in the unmanaged population between 2007-2011 perhaps due to strong natural selection since management ceased in 1990 I One can also develop a theory of periodic environmental extremes under which rim-layers will have an advantage by successfully raising only one chick as opposed to none (but difﬁcult to test without long-term data) I To appreciate the intensity of ﬁeld operations and limitations of biomathematical models read: The black robin: saving the world’s most endangered bird, David Butler and Don Merton, Oxford University Press, 1994.

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Conclusions - Part I contd...

I Our research group at Canterbury (with Briskie, Hale, Massaro and Poole) have developed tests to establish that rim-laying during 1980s is likely to be a heritable trait

60 / 100 I One can also develop a theory of periodic environmental extremes under which rim-layers will have an advantage by successfully raising only one chick as opposed to none (but difﬁcult to test without long-term data) I To appreciate the intensity of ﬁeld operations and limitations of biomathematical models read: The black robin: saving the world’s most endangered bird, David Butler and Don Merton, Oxford University Press, 1994.

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Conclusions - Part I contd...

61 / 100 I To appreciate the intensity of ﬁeld operations and limitations of biomathematical models read: The black robin: saving the world’s most endangered bird, David Butler and Don Merton, Oxford University Press, 1994.

Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Conclusions - Part I contd...

62 / 100 Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Conclusions - Part I contd...

I Our research group at Canterbury (with Briskie, Hale, Massaro and Poole) have developed tests to establish that rim-laying during 1980s is likely to be a heritable trait I We have also shown that the trait is at a low frequency in the unmanaged population between 2007-2011 perhaps due to strong natural selection since management ceased in 1990 I One can also develop a theory of periodic environmental extremes under which rim-layers will have an advantage by successfully raising only one chick as opposed to none (but difﬁcult to test without long-term data) I To appreciate the intensity of ﬁeld operations and limitations of biomathematical models read: The black robin: saving the world’s most endangered bird, David Butler and Don Merton, Oxford University Press, 1994. 63 / 100 Population pedigree process of the Chatham island black robin Tests for Heritability of Rim-laying in 1980s

Part II

64 / 100 I Punchline: Observe First, Model Later I Unfortunately now: Convenient Software of “Math-statical” Models dictate Interpreting Rich Field Observations I Field Biology is in collaboration with Melanie Massaro I Mathematical insights from the field are invaluable! I Theory is under development with Amandine Veber I This talk will focus on visualizations of field observations to convey the combinatorial complexity of interactions that may not be ignored in small populations by taking probabilistically convenient limits of large population sizes I i.e., I’ll try to show that every “turf-holding”, “mate-alluring”, “love-making” and “chick-rearing” event counts in the field!!!

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Current Research - disclaimers

I This is a highly empirical story

65 / 100 I Unfortunately now: Convenient Software of “Math-statical” Models dictate Interpreting Rich Field Observations I Field Biology is in collaboration with Melanie Massaro I Mathematical insights from the field are invaluable! I Theory is under development with Amandine Veber I This talk will focus on visualizations of field observations to convey the combinatorial complexity of interactions that may not be ignored in small populations by taking probabilistically convenient limits of large population sizes I i.e., I’ll try to show that every “turf-holding”, “mate-alluring”, “love-making” and “chick-rearing” event counts in the field!!!

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Current Research - disclaimers

I This is a highly empirical story I Punchline: Observe First, Model Later

66 / 100 I Field Biology is in collaboration with Melanie Massaro I Mathematical insights from the field are invaluable! I Theory is under development with Amandine Veber I This talk will focus on visualizations of field observations to convey the combinatorial complexity of interactions that may not be ignored in small populations by taking probabilistically convenient limits of large population sizes I i.e., I’ll try to show that every “turf-holding”, “mate-alluring”, “love-making” and “chick-rearing” event counts in the field!!!

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Current Research - disclaimers

I This is a highly empirical story I Punchline: Observe First, Model Later I Unfortunately now: Convenient Software of “Math-statical” Models dictate Interpreting Rich Field Observations

67 / 100 I Mathematical insights from the field are invaluable! I Theory is under development with Amandine Veber I This talk will focus on visualizations of field observations to convey the combinatorial complexity of interactions that may not be ignored in small populations by taking probabilistically convenient limits of large population sizes I i.e., I’ll try to show that every “turf-holding”, “mate-alluring”, “love-making” and “chick-rearing” event counts in the field!!!

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Current Research - disclaimers

68 / 100 I Theory is under development with Amandine Veber I This talk will focus on visualizations of ﬁeld observations to convey the combinatorial complexity of interactions that may not be ignored in small populations by taking probabilistically convenient limits of large population sizes I i.e., I’ll try to show that every “turf-holding”, “mate-alluring”, “love-making” and “chick-rearing” event counts in the ﬁeld!!!

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Current Research - disclaimers

69 / 100 I This talk will focus on visualizations of ﬁeld observations to convey the combinatorial complexity of interactions that may not be ignored in small populations by taking probabilistically convenient limits of large population sizes I i.e., I’ll try to show that every “turf-holding”, “mate-alluring”, “love-making” and “chick-rearing” event counts in the ﬁeld!!!

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Current Research - disclaimers

70 / 100 I i.e., I’ll try to show that every “turf-holding”, “mate-alluring”, “love-making” and “chick-rearing” event counts in the ﬁeld!!!

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Current Research - disclaimers

71 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Current Research - disclaimers

I This is a highly empirical story I Punchline: Observe First, Model Later I Unfortunately now: Convenient Software of “Math-statical” Models dictate Interpreting Rich Field Observations I Field Biology is in collaboration with Melanie Massaro I Mathematical insights from the field are invaluable! I Theory is under development with Amandine Veber I This talk will focus on visualizations of field observations to convey the combinatorial complexity of interactions that may not be ignored in small populations by taking probabilistically convenient limits of large population sizes I i.e., I’ll try to show that every “turf-holding”, “mate-alluring”, “love-making” and “chick-rearing” event counts in the field!!! 72 / 100 I Problems with current PVA: driven by mathematical convenience as opposed to biological realism I PVA Models often assume branching process under random mating for a set of parameters assumed or estimated for the species in question I PVA models are used by international bodies to assign threatened / endangered status to a species I PLAN: use field data on the Black Robin Population to build behaviourally realistic pedigree models for bi-parental territorial species for use in more realistic PVA I VISION: Integrate behavioural ecology with population pedigrees for subsequent molecular evolutionary genetics

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Population Viability Analysis (PVA) in Conservation

I PVA = computer program that uses Monte Carlo methods to guess the probability of extinction of a population under a given management scenario for a given species

73 / 100 I PVA Models often assume branching process under random mating for a set of parameters assumed or estimated for the species in question I PVA models are used by international bodies to assign threatened / endangered status to a species I PLAN: use ﬁeld data on the Black Robin Population to build behaviourally realistic pedigree models for bi-parental territorial species for use in more realistic PVA I VISION: Integrate behavioural ecology with population pedigrees for subsequent molecular evolutionary genetics

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Population Viability Analysis (PVA) in Conservation

74 / 100 I PVA models are used by international bodies to assign threatened / endangered status to a species I PLAN: use ﬁeld data on the Black Robin Population to build behaviourally realistic pedigree models for bi-parental territorial species for use in more realistic PVA I VISION: Integrate behavioural ecology with population pedigrees for subsequent molecular evolutionary genetics

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Population Viability Analysis (PVA) in Conservation

75 / 100 I PLAN: use ﬁeld data on the Black Robin Population to build behaviourally realistic pedigree models for bi-parental territorial species for use in more realistic PVA I VISION: Integrate behavioural ecology with population pedigrees for subsequent molecular evolutionary genetics

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Population Viability Analysis (PVA) in Conservation

76 / 100 I VISION: Integrate behavioural ecology with population pedigrees for subsequent molecular evolutionary genetics

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Population Viability Analysis (PVA) in Conservation

I PVA = computer program that uses Monte Carlo methods to guess the probability of extinction of a population under a given management scenario for a given species I Problems with current PVA: driven by mathematical convenience as opposed to biological realism I PVA Models often assume branching process under random mating for a set of parameters assumed or estimated for the species in question I PVA models are used by international bodies to assign threatened / endangered status to a species I PLAN: use ﬁeld data on the Black Robin Population to build behaviourally realistic pedigree models for bi-parental territorial species for use in more realistic PVA

77 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Population Viability Analysis (PVA) in Conservation

Notions of Molecular continuums within Population Pedigrees a homotopy between Kingman Coalescent Trees and Chang’s Pedigree (RS & Bhalchandra Thatte)

Zygotic, cytoplasmic, karyotic and sub-karyotic pedigrees of a Wright-Fisher population with ﬁve eukaryotic diploid individuals 79 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

39 Connected Components (sub-pedigrees) in Pedigree Survey 2007-2011

80 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

All 39 Connected Components (sub-pedigrees) in Pedigree Survey 2007-2011

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111 Maternal Life-Line Components in Pedigree Survey 2007-2011

82 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Life-Lines of all 107 Mothers in Pedigree Survey 2007-2011

83 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

117 Paternal Life-Line Components in Pedigree Survey 2007-2011

84 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Life-Lines of all 113 Fathers in Pedigree Survey 2007-2011

85 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Male Territory Graphs by year

2009 (eye-balled by a ball graph)

86 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Male Territory Graphs by year

2010 (eye-balled by a ball graph)

87 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Male Territory Graphs by year

2011 (eye-balled by a ball graph)

88 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Male Territorial Dynamics – yearly nest site relocation

89 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Male/ Female yearly nest to nest distance

sex-speciﬁc distance between home nest and ﬁrst nest

90 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Male/ Female yearly nest to nest distance

sex-speciﬁc distance between nest at age ≥ 1 and next nest

91 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Male/ Female yearly nest to nest distance

I Permutation Test to Reject H0 : male dist = female dist (105 MC samples)

I Strongly reject H0 for home to ﬁrst nest (pv = 0.00025)

I Fail to reject H0 for nest at age ≥ 1 to next nest (pv = 0.14) male/ female distance from home nest to ﬁrst nest male/ female distance from nest at age ≥ 1 to next nest

92 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Need Models of Spatio-temporal Population Pedigrees

93 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Need Models of Spatio-temporal Population Pedigrees

94 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Need Models of Spatio-temporal Population Pedigrees

95 / 100 I I hope to have convinced you that the ﬁeld data for small threatened populations is far from simplistic mathematical assumptions such as random mating I The effect of such assumptions on extinction probability computations in PVA is the natural judge I Besides possibly robustifying PVA using realistic models of pedigree processes we believe such models will pave the way for the fusion of behavioural ecology and evolutionary genetics

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Conclusions - Part II

I Population viability Analyses use Branching Process Models and Simulations to determine the status of a threatened species

I PLAN: continue to work on Part 2 next year during my visit to CMAP in 2013 96 / 100 I The effect of such assumptions on extinction probability computations in PVA is the natural judge I Besides possibly robustifying PVA using realistic models of pedigree processes we believe such models will pave the way for the fusion of behavioural ecology and evolutionary genetics

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Conclusions - Part II

I PLAN: continue to work on Part 2 next year during my visit to CMAP in 2013 97 / 100 I Besides possibly robustifying PVA using realistic models of pedigree processes we believe such models will pave the way for the fusion of behavioural ecology and evolutionary genetics

Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Conclusions - Part II

I PLAN: continue to work on Part 2 next year during my visit to CMAP in 2013 98 / 100 Population pedigree process of the Chatham island black robin PVA with Behaviourially Realistic Population Pedigree Models

Conclusions - Part II

I Population viability Analyses use Branching Process Models and Simulations to determine the status of a threatened species I I hope to have convinced you that the ﬁeld data for small threatened populations is far from simplistic mathematical assumptions such as random mating I The effect of such assumptions on extinction probability computations in PVA is the natural judge I Besides possibly robustifying PVA using realistic models of pedigree processes we believe such models will pave the way for the fusion of behavioural ecology and evolutionary genetics I PLAN: continue to work on Part 2 next year during my visit to CMAP in 2013 99 / 100 Population pedigree process of the Chatham island black robin A Field Excursion

Thank you!

100 / 100