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1 Genomic footprints of selection during domestication in Old World camelids

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Veterinärmedizinische Universität Wien

(Vetmeduni Vienna)

19.01.2016

1

Robert.fitak@duke.edu, pamela.burger@vetmeduni.ac.at

Genomic footprints of selection during domestication in

Old World camelids

Fitak RR, Mohandesan E, Corander J, Yadamsuren A, Chuluunbat B, Abdelhadi O, Raziq A, Faye B, Burger PA

Vetmeduni Vienna, Austria

Plant and Animal Genome XXIV Conference, San Diego, Jan 9 2016

Special thanks to the organizers!

oldest German speaking Vetmeduni in Europe

founded in 1765

2

Introduction

3 ‘Camelid Group’

Pamela Burger, senior researcher Bob Fitak Elmira Mohandesan Huiguang Wu Pauline Charruau Emily Ruiz Collaborators

B. Faye, F. Almathen (KSA), E. Ciani (IT), O. Hanotte (UK), B. Chuluunbat, A. Yadamsuren (MAS), J. Corander (F,) A. Trinks (D), H. Jianlin (PCR), G. Konuspayeva (KZ), P. Kaczensky, C. Walzer (AT)

Funding

Austrian Science Foundation FWF, Austrian Academy of Science, Eurasia Pacific Uninet

pamela.burger@vetmeduni.ac.at

Overview

Background

domestication syndrome hypothesis

Old World camelid domestication

Old World camel genome research

International Camel Consortium for Genetic Improvement and Conservation

Results

Genetic Variation

Admixture/Demographic History

Identifying selected loci

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Vetmeduni Vienna

DOMESTICATION

GENOME RESEQUENCING

“domestication syndrome“ hypothesis

5

Vetmeduni Vienna

mild neural crest cell deficits during embryonic development

depigmentation floppy ears shorter muzzles smaller teeth curly tails docility smaller brain reproductive cycles juvenile behaviour Wilkins et al. 2014

Domestication of the Old World camelids

Camelus dromedarius

Camelus bactrianus

Camelus ferus

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Veterinärmedizinische Universität Wien

(Vetmeduni Vienna)

19.01.2016

2

Petra Kaczensky 2014 44000 km2 ≈140 km ≈140 km

Camelus ferus

Great Gobi Strictly Protected Area “A”

8 Trinks et al 2012

Bactrian camel domestication

Late Bronze and Eary Iron Age samples South-Uzbekistan, West-Siberia

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Bactrian camel domestication

wild camel domestic Bactrian

EXTINCT wild population

1.2 mio time (y)

4,000-6,000

domestication 4000-6000 ya

maybe further to the west than assumed previously

wild camels are related but not the ancestors

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dromedary domestication

Almathen, Charruau, Mohandesan et al, submitted domestication around 3000 ya

minimum of 6 maternal lineages

wild dromedaries from the Southeast coast of the Arabian Peninsula contributed to the modern gene pool

P0687

Old World Camel genome resources

11

12

Old World Camel genomes

Wang et al. 2012

Genome-wide divergent selection

overall lower heterozygosity in the domestic genome

artificial selection during domestication

Adaptation to desert environment

Lineage specific accelerated evolutionary rates

GO categories enriched genes involved in

fat and energy metabolism

salt metabolism

osmoregulation and water reservation

Oganization of the MHC complex low polymorphisms in MHC class II genes

Plasil et al. subm Wu et al. 2014

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Veterinärmedizinische Universität Wien

(Vetmeduni Vienna)

19.01.2016

3

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FAO meeting in Riyadh April, 2015: 23 participating countries

established at the 4th ISOCARD conference in Almaty, June 2015

www.icc-gic.weebly.comin preparation www.isocord.org.

Genome Resequencing

14 Vetmeduni Vienna Genome Sequences Genetic Variation Admixture Demography Selection

Dataset

Vetmeduni Vienna 15 25 Genomes ~15X coverage Mapped to C. ferus

Genetic Variation

Vetmeduni Vienna 16 Th e ta C. dromedarius C. bactrianus C. ferus

Admixture/Demography

Vetmeduni Vienna 17 A n ce st ry 0 1 C. dromedarius C. bactrianus C. ferus

Detecting Selection

Homogeneity Test • Polymorphism vs divergence • Species A vs. [species B + C] HKA Test • Gene vs. genome-wide average • Only if significant in a particular lineage

Gene-centric

approach

Heterozygosity & S2Fst

• Pairwise species comparisons • Reduced heterozygosity and high S2Fst SMILEFINDER (Guiblet et al. 2015, Oleksyk et al. 2008)

Genome-wide

approach

Vetmeduni Vienna 18

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Veterinärmedizinische Universität Wien

(Vetmeduni Vienna)

19.01.2016

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Detecting Selection

Homogeneity/HKA Test

Dromedary vs [C. ferus/bactrianus]: 6,662 genes analyzed

STARTD9: microtubule motor PRKDC: double strand break repair

CENPF: centromere-associated, transcription factor binding DNAH1: ATPase activity, microtubule motor

FAM208B: protein binding

C. ferus vs C. bactrianus

ANKYRIN2: protein kinase binding and ion channel binding OTOP1: behavior, neurological

ABCA13: ATPase activity

Vetmeduni Vienna 19

Detecting Selection

Extreme H

E

and S

2

F

ST

: C. dromedarius

Vetmeduni Vienna 20

Summary

Introgression from domestic to wild camel threatens the genomic integrity of

Camelus ferus

Population expansion of the wild camel during the last glacial maximum

followed by a rapid decline

Selection during domestication affects genes associated with

neural-physiology

“domestication syndrome”

Vetmeduni Vienna 21

Questions???

Please see posters:

P0686 P0687 P0690

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“domestication syndrome“ hypothesis

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Références

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