Evolutionary Genomics Of Penguins' Olfaction And Ground Tit's Cooperative Breeding

Adaptive evolution is the centerpiece of the Darwin's theory of natural selection.Adaptive evolution refers to a series of variations in structures and functions resulted from adaptations to environmental changes in wild organisms.With the development of genomics techniques,a large number of genome sequences and population polymorphism data have come out,which led to overwhelming opportunities in the fields of comparative genomics,population genomics,bioinformatics,and systems biology.The development of genomics relevant fields has laid a foundation in studying the molecular mechanisms of adaptive evolution,and the next generation sequencing techonology has provided a good opportunity to promote the study of adaptive evolution.In this study,we applied comparative genomics and population genomics to undertake two genome-wide studies:1)Aquatic adaptation and the evolution of olfactory receptor genes in penguins,2)Adaptive evolution and genomic basis of cooperative breeding in the ground tit.These studies would provide scientific evidence in deep understanding of animal adaptive evolution in the age of genomics.In the chapter 2,we examined the evolution of olfactory receptor(OR)genes in penguins.We analyzed eight draft genome sequences,including 2 penguins and 6 non-penguin waterbirds that are closely related to penguins.Our genomic dataset of birds represented four avian orders,including two species of Sphenisciformes(Emperor penguin,Aptenodytes forsteri,60×coverage;Adelie penguin,Pygoscelis adeliae,60×),one species of Procellariiformes(Northern fulmar,Fulmarus glacialis,33×),four species of Pelecaniformes(Crested ibis,Nipponia Nippon,105×;Little egret,Egretta garzetta,74×;Great cormorant,Phalacrocorax carbo,24×;Dalmatian pelican,Pelecanus crispus,34×),and one species of Gaviiformes(Red-throated loon,Gavia stellata,33×).A total of 344 complete and intact ORs were identified from the draft genome sequences of the emperor penguin(gene number:32),Adelie penguin(26),northern fulmar(33),great cormorant(36),crested ibis(47),little egret(106),Dalmatian pelican(20),and red-throated loon(44).Phylogenetic analysis was performed using all intact ORs from the eight avian genomes.With the aid of phylogenetic trees,we identified 29 potentially one-to-one orthologous genes with stringent criteria.In case of missing data due to incomplete sequencing and poor assembly,we performed traditional gene sequencing by PCRs and newly generated 34 OR sequences.Through the analysis of 378 ORs,we found that,of these functionally important ORs common to other waterbirds,the percentage of nonfunctional ORs is significantly greater in penguins(18/54 = 33.3%)than in their closely related non-penguin waterbirds(3/102 = 2.9%)(p<0.0001,Fisher's exact test),which suggested a penguin-specific reduction of olfactory capability.The penguin-specific reduction of olfactory capability arose in the common ancestor of penguins between 23 and 60 Ma,which may have resulted from the aquatic specializations for underwater vision.Unlike other diving waterbirds,penguins spend the entire search,chase and capture underwater.Therefore,the aquatic specializations for underwater vision in penguins may have rendered their olfaction less important.In the chapter 3,we report a large data set of genome-wide genetic variations in a cooperatively breeding model species using a whole-genome resequencing approach,and preliminarily characterize the molecular mechanisms of the evolution of cooperative breeding in the ground tit that is endemic to the Qinghai-Tibet Plateau.We sampled the ground tit from two populations:Tianjun and Gahai,because the percentage of cooperatively breeding nests is significantly higher for TJ population(88/187=47.1%)than for GH population(15/172=8.7%).To examine the overall population variation,a total of 10 ground tits(5 from Gahai and 5 from Tianjun population)were randomly selected to construct individual libraries for genome sequencing.To increase the sample size,we randomly chose 30 ground tits(15 from Gahai and 15 from Tianjun population)to construct two pooled libraries for sequencing.This work characterized the genome-wide genetic variations in the ground tit,and developed a number of genetic markers that may be important for future use.We identified a total of 5.91 million SNPs,261,222 insertions,372,130 deletions,and 92,299 different types of structural variants from ten ground tits that were individually sequenced.Furthermore,we detected 5.98 million SNPs,335,218 insertions,458,587 deletions,and 22,154 structural variants from two pooled samples,each of which contains 15 ground tits.Two distinct population clusters,TJ(TJ1-TJ5)and GH(GH1-GH5),were identified by the neighbor-joining(NJ)method and by principal component analysis(PCA)based on all SNPs.Putatively selected genes(PSGs)were identified by screening genomic regions that show low diversity in one population but high divergence between the two populations.A total of 197 genes in TJ population and 178 genes in GH population were identified with the strongest signature of positive selection.Functional enrichment analysis of the identified PSGs revealed that functions of immunity,metabolism,and reproduction were enriched in TJ population.In contrast,functions related to development were overrepresented in GH population.This finding suggests strong genetic differentiation between the two examined populations of the ground tits with significant difference in the frequency of cooperative breeding behavior.In addition,we identified three functional pathways involved in reproduction are specifically overrepresented in TJ population,and eight putatively selected genes(PTK2,ADCY5,BTRC,UNC13B,HIPK1,KIF24,SHC1,and MAPK14)known to functionally relate to aging or longevity are enriched in the TJ population,suggesting that reproduction and lifespan may play important roles in shaping the evolution of cooperative breeding.Together,although our sampled individuals are rather limited and our findings are preliminary,the putatively selected genes highlight potential genetic basis underlying cooperative breeding behavior and underscore the important role of longevity and reproduction,which deserve to be carefully examined and tested with added individuals and populations in future.