Genomic Scan of Recent Positive Selection Differentiating Aggression in Chimpanzees and Bonobos Open Access

Shaw, Carmen (Summer 2020)

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Human’s closest extant relatives are chimpanzees (Pan troglodytes) and bonobos (Pan paniscus), which share roughly 99% of their genome with each other. Despite their proximate phylogenetic relationship, these two great ape species differ substantially from one another in terms of social behavior and aggression. Bonobos live in female-dominant communities, more tolerant of conspecifics in competitive social contexts, and frequently substitute sexual behavior and eroticism for aggression. Chimpanzees coexist in male-dominant social groups, actively patrolling territory boundaries between communities, where aggression and inter-group killings are commonly employed during moments of conflict. Chimpanzees are known to commit lethal aggression, whereas bonobos have no such inclinations. Identifying the genetic underpinning that predisposes an individual to aggressive behavior is largely complex due to difficulties in understanding genetic heterogeneity, diversified environmental conditions, and the unknown role evolutionary forces play on behavior. Recent studies on genome-wide transcripts and epistasis, as well as artificial selection studies and GWAS studies have revealed that a substantial portion of the genome contributes to the expression of aggressive behavior.

To further understand the neurogenetic and evolutionary underpinnings of this universal fitness trait, we have detected selection signatures across the genome in order to help elucidate mechanisms of selection and pinpoint candidate genes of interest impacting aggression. In this study, the detection of selection signatures was conducted in chimpanzees (n = 70) and bonobos (n = 13). We employed two complementary haplotype-based statistics of integrated haplotype scores (iHS) and cross-population extended haplotype homozygosity (XP-EHH) tests. From these selection scans, we were able to identify regions subjected to recent, positive selection in chimpanzees and bonobos. These genomic regions contained 15 significant genes relating to aggression including serotonin receptor 1A (HTR1A), cadherin 13 (CDH13), aldehyde dehydrogenase (ALDH2), and tryptophan hydroxylase 2 (TPH2). These genes were enriched in gene ontology terms involved in the stress response, interspecific interactions, and defense response to other organisms. These findings ultimately contribute to the identification of candidate genes of interest that impact the aggression pathway in nonhuman primates and aid in further understanding the evolutionary and biological mechanisms for differences in aggression observed between chimpanzees and bonobos.

Table of Contents


1 Abstract - 1

2 Acknowledgements - 1

3 Introduction - 4

3.1 Selective Pressures on Aggression Following Hominin-Panim Speciation - 4

3.2 Evolutionary Divergence between Chimpanzees and Bonobos - 5

3.2.1 Chimpanzee Behaviors and Inter-community Relations: ”Proactive Warfare” - 5

3.2.2 Bonobo Behaviors and Inter-community Relations: ”Free-Loving Egalitarianism” - 7

3.3 Genetic and Evolutionary Underpinnings of Aggressive Behavior - 9

3.4 Genome Scan of Recent Positive Selection in Chimpanzees and Bonobos - 10

4 Methods 10 4.1 Data and Alignment - 11

4.2 Phasing - 11

4.3 Haplotype-based Selection Scans - 12

4.4 Analysis of Putative Selection Signatures - 13

4.5 Gene Expression Profiles via Haploreg v4.1 - 13

4.6 GeneOntologyEnrichmentAnalysis - 13

5 Results - 14

5.1 Overview of iHS and XP-EHH Scans - 14

5.2 (iHS) Detection of selection signatures Intra-specifically in Bonobos and Chimpanzees - 14

5.3 (XP-EHH) Detection of selection signatures Inter-specifically of Bonobos and Chimpanzees - 15

5.4 Linkage Disequilibrium analysis via HaploReg (version4.1) - 16

5.5 Gene Ontology Enrichment Analysis of Genes in Selection Scans - 17

6 Discussion - 18

7 Conclusion - 19

8 Appendix - 21

9 References - 31

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