From jungle to genome and back again. Dr Mirte Bosse, WUR - Animal Breeding and Genomics
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1 From jungle to genome and back again Dr Mirte Bosse, WUR - Animal Breeding and Genomics ELLS student conference 2018
2 A bit about me: BSc Biologie: VU Amsterdam MSc Ecology: VU Amsterdam PhD thesis: Wageningen UR Postdoc: NIOO-KNAW Postdoc: Wageningen UR Now VENI: WUR-ABG AnE VU NIOO
3 FROM ECOLOGIST
4 TO BIOINFORMATICIAN Bachelor Biology: VU Master Ecology: VU PhD thesis: WUR Postdoc: NIOO-KNAW Currently: Postdoc WUR
5 BIOINFORMATICS Bachelor Biology: VU Master Ecology: VU PhD thesis: WUR Postdoc: NIOO-KNAW Currently: Postdoc WUR
6 BIOINFORMATICS Bachelor Biology: VU Master Ecology: VU PhD thesis: WUR Postdoc: NIOO-KNAW Currently: Postdoc WUR
7 BIOINFORMATICS Bachelor Biology: VU Master Ecology: VU PhD thesis: WUR Postdoc: NIOO-KNAW Currently: Postdoc WUR
8 A bit about me: BSc Biologie: VU Amsterdam MSc Ecology: VU Amsterdam PhD thesis: Wageningen UR Postdoc: NIOO-KNAW Postdoc: Wageningen UR Now VENI: WUR-ABG AnE VU NIOO
9 Reading the genome as a history book
10 Reading the genome as a history book demography selection
11 Demographic history in pigs ~200 years ~ years Split ~1,2 million years ago Sus speciation ~ 4-2 million years ago 1. speciation
12 Suid evolution Genus Sus 12 12
13 Time of speciation in genus Sus CGTACGATTTA AGTAGGACTTT AGTAGGACTTA ACTACGACTTA
14 Sea level change and speciation in Suids
15 Sea level change and speciation in Suids
16 If it happens once... AGTAGG AGTACG AGTAGG AGTACG...it can happen again!
17 Admixture between species is common REMEMBER THIS!!!
18 Demographic history in pigs ~200 years ~ years Split ~1,2 million years ago Sus speciation ~ 4-2 million years ago 1. speciation
19 More genetic variation in Asian wild boar Dutch wild boar Larger number of regions of homozygosity (ROH) Lower nucleotide diversity Chinese wild boar
20 Genetic diversity of populations How does population size affect genetic diversity? Effective population size 20
21 Population bottleneck during last ice-age
22 Suid evolution Pygmy hog 22 22
23 The pygmy hog Porcula salvania Captive populations Background of captive population Founders unrelated? Representative? Maintain genetic diversity Use genomics for conservation -related questions 23
24 The pygmy hog Porcula salvania 24
25 The pygmy hog Porcula salvania Captive populations Which genus Background does the of captive population pygmy hog belong to? Founders unrelated? What about inbreeding Representative? in this tiny area? Maintain genetic diversity 25
26 Suid evolution Pygmy hog? 26 26
27 The pygmy hog Porcula salvania Supertree & supermatrix method
28 The pygmy hog Porcula salvania Commercial pig Europe Babyrousa Pygmy hog 28
29 The pygmy hog Porcula salvania Conservation Programme in Assam ( Durrell Wildlife Conservation Trust - >
30 A bit about me: BSc Biologie: VU Amsterdam MSc Ecology: VU Amsterdam PhD thesis: Wageningen UR Postdoc: NIOO-KNAW Postdoc: Wageningen UR Now VENI: WUR-ABG AnE VU NIOO
31 Worldwide distribution of great tits
32 Study populations Long-term study sites Wytham woods (Oxford) Veluwe & Oosterhout
33 Research questions 1. How different are great tits from Wytham and the Veluwe genetically? 2. Do great tit genomes in Wytham and the Veluwe show patterns of differential selection? 3. Can we link this to their ecology?
34 Population differentiation How different are great tits from Wytham and the Veluwe genetically? -measured with Fst Red allele rises in frequency in population 1 Blue allele rises in frequency in population 2 Before split After split
35 Fst = Population differentiation How different are great tits from Wytham and the Veluwe genetically? Fst = 0.006
36 Population differentiation
37 Research questions 1. How different are great tits from Wytham and the Veluwe genetically? 2. Do great tit genomes in Wytham and the Veluwe show patterns of differential selection? 3. Can we link this to their ecology?
38 patterns of differential selection Do great tit genomes in Wytham and the Veluwe show patterns of differential selection? -measured with Fst
39 patterns of differential selection
40 patterns of differential selection
41 patterns of differential selection What is in those peaks? Genes involved in... - Craniofacial development - Darwin finches beak shape - Collagen
42 patterns of differential selection
43 patterns of differential selection So we started measuring..
44 patterns of differential selection Bills are indeed longer, and increasing in the UK!
45 patterns of differential selection How to demonstrate selection for longer beaks? 1- from the genomics side 2- from fitness information
46 patterns of differential selection How to demonstrate selection for longer beaks? Genome-wide association study: Variants that are high frequency in the UK are associated with longer beaks!
47 patterns of differential selection How to demonstrate selection for longer beaks? 1- from the genomics side 2- from fitness information
48 patterns of differential selection How to demonstrate selection for longer beaks? More fledglings with two copies of the long-beak variant!
49 patterns of differential selection
50 patterns of differential selection
51 patterns of differential selection
52 patterns of differential selection ue=5&v=vagshcpp2eg
53 Activity at feeding site Activity at feeding site patterns of differential selection Increased activity at artificial feeder with longer beaks! Bill length
54 patterns of differential selection Increased activity at artificial feeder with longer beaks! Why????
55 patterns of differential selection Increased activity at artificial feeder with longer beaks! Why????... Results always raise more questions
56 And now... BSc Biologie: VU Amsterdam MSc Ecology: VU Amsterdam PhD thesis: Wageningen UR Postdoc: NIOO-KNAW Postdoc: Wageningen UR Now VENI: WUR-ABG AnE VU NIOO In CONSERVATION GENOMICS: What makes inbreeding so depressing
57 Acknowledgements Wageningen University & Research, Animal Breeding and Genomics Martijn Derks Martien Groenen Hendrik-Jan Megens Richard Crooijmans Ole Madsen Bioinformatics WUR Dick de Ridder CRV Christian Gross Erik Mullaart TU Delft Erwin Koenen Marcel Reinders Cobb Topigs Norsvin Randy Borg Barbara Harlizus Egbert Knol VU Amsterdam Naomi Duijvesteijn Jacintha Ellers Hendrix Genetics Dick Roelofs Katrijn Peeters Pieter van As Marco Bink CRC Antwerpen Zjef Peereboom Peter Galbusera Philippe Helsen NIOO-KNAW Marcel Visser Kees van Oers Veronika Laine Phillip Gienapp 57
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