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Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors.

Paudel Y, Madsen O, Megens HJ, Frantz LA, Bosse M, Crooijmans RP, Groenen MA - BMC Genomics (2015)

Bottom Line: Unraveling the genetic mechanisms associated with reduced gene flow between genetically differentiated populations is key to understand speciation.Different types of structural variations (SVs) have been found as a source of genetic diversity in a wide range of species.These CNVRs encompass 624 genes and were found to evolve ~2.5 times faster than single nucleotide polymorphisms (SNPs).

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. paudelyogesh@gmail.com.

ABSTRACT

Background: Unraveling the genetic mechanisms associated with reduced gene flow between genetically differentiated populations is key to understand speciation. Different types of structural variations (SVs) have been found as a source of genetic diversity in a wide range of species. Previous studies provided detailed knowledge on the potential evolutionary role of SVs, especially copy number variations (CNVs), between well diverged species of e.g. primates. However, our understanding of their significance during ongoing speciation processes is limited due to the lack of CNV data from closely related species. The genus Sus (pig and its close relatives) which started to diverge ~4 Mya presents an excellent model for studying the role of CNVs during ongoing speciation.

Results: In this study, we identified 1408 CNV regions (CNVRs) across the genus Sus. These CNVRs encompass 624 genes and were found to evolve ~2.5 times faster than single nucleotide polymorphisms (SNPs). The majority of these copy number variable genes are olfactory receptors (ORs) known to play a prominent role in food foraging and mate recognition in Sus. Phylogenetic analyses, including novel Bayesian analysis, based on CNVRs that overlap ORs retain the well-accepted topology of the genus Sus whereas CNVRs overlapping genes other than ORs show evidence for random drift and/or admixture.

Conclusion: We hypothesize that inter-specific variation in copy number of ORs provided the means for rapid adaptation to different environments during the diversification of the genus Sus in the Pliocene. Furthermore, these regions might have acted as barriers preventing massive gene flow between these species during the multiple hybridization events that took place later in the Pleistocene suggesting a possible prominent role of ORs in the ongoing Sus speciation.

No MeSH data available.


Cluster and phylogenetic tree analysis. A: Cluster analysis. The phylogenetic tree on the left side is obtained from Frantz et al. [31] and the cluster tree on the right side is obtained by cluster analysis using the actual CN of CNVRs from different populations. The branch length does not correspond to the evolutionary distance. B: NJ-Phylogenetic tree obtained by using the pairwise difference based on SNPs (Abb. see Table 1). C: NJ-Phylogenetic tree obtained by using the pairwise CNDs of all possible pairs for CNVRs overlapping ORs (Abb. see Table 1).
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Fig4: Cluster and phylogenetic tree analysis. A: Cluster analysis. The phylogenetic tree on the left side is obtained from Frantz et al. [31] and the cluster tree on the right side is obtained by cluster analysis using the actual CN of CNVRs from different populations. The branch length does not correspond to the evolutionary distance. B: NJ-Phylogenetic tree obtained by using the pairwise difference based on SNPs (Abb. see Table 1). C: NJ-Phylogenetic tree obtained by using the pairwise CNDs of all possible pairs for CNVRs overlapping ORs (Abb. see Table 1).

Mentions: To investigate whether the observed CNVRs were congruent with the known phylogeny of the species, we performed a cluster analysis based on the CN at each CNV locus. The resulting tree is highly congruent to the phylogenomic analyses based on SNPs [31] (Figure 4A). However, some inconsistencies are observed in the resolution of branching order within Sus-ISEA, which is not surprising as recurring hybridization was common in the evolutionary history of Sus-ISEA [31].Figure 4


Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors.

Paudel Y, Madsen O, Megens HJ, Frantz LA, Bosse M, Crooijmans RP, Groenen MA - BMC Genomics (2015)

Cluster and phylogenetic tree analysis. A: Cluster analysis. The phylogenetic tree on the left side is obtained from Frantz et al. [31] and the cluster tree on the right side is obtained by cluster analysis using the actual CN of CNVRs from different populations. The branch length does not correspond to the evolutionary distance. B: NJ-Phylogenetic tree obtained by using the pairwise difference based on SNPs (Abb. see Table 1). C: NJ-Phylogenetic tree obtained by using the pairwise CNDs of all possible pairs for CNVRs overlapping ORs (Abb. see Table 1).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4413995&req=5

Fig4: Cluster and phylogenetic tree analysis. A: Cluster analysis. The phylogenetic tree on the left side is obtained from Frantz et al. [31] and the cluster tree on the right side is obtained by cluster analysis using the actual CN of CNVRs from different populations. The branch length does not correspond to the evolutionary distance. B: NJ-Phylogenetic tree obtained by using the pairwise difference based on SNPs (Abb. see Table 1). C: NJ-Phylogenetic tree obtained by using the pairwise CNDs of all possible pairs for CNVRs overlapping ORs (Abb. see Table 1).
Mentions: To investigate whether the observed CNVRs were congruent with the known phylogeny of the species, we performed a cluster analysis based on the CN at each CNV locus. The resulting tree is highly congruent to the phylogenomic analyses based on SNPs [31] (Figure 4A). However, some inconsistencies are observed in the resolution of branching order within Sus-ISEA, which is not surprising as recurring hybridization was common in the evolutionary history of Sus-ISEA [31].Figure 4

Bottom Line: Unraveling the genetic mechanisms associated with reduced gene flow between genetically differentiated populations is key to understand speciation.Different types of structural variations (SVs) have been found as a source of genetic diversity in a wide range of species.These CNVRs encompass 624 genes and were found to evolve ~2.5 times faster than single nucleotide polymorphisms (SNPs).

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. paudelyogesh@gmail.com.

ABSTRACT

Background: Unraveling the genetic mechanisms associated with reduced gene flow between genetically differentiated populations is key to understand speciation. Different types of structural variations (SVs) have been found as a source of genetic diversity in a wide range of species. Previous studies provided detailed knowledge on the potential evolutionary role of SVs, especially copy number variations (CNVs), between well diverged species of e.g. primates. However, our understanding of their significance during ongoing speciation processes is limited due to the lack of CNV data from closely related species. The genus Sus (pig and its close relatives) which started to diverge ~4 Mya presents an excellent model for studying the role of CNVs during ongoing speciation.

Results: In this study, we identified 1408 CNV regions (CNVRs) across the genus Sus. These CNVRs encompass 624 genes and were found to evolve ~2.5 times faster than single nucleotide polymorphisms (SNPs). The majority of these copy number variable genes are olfactory receptors (ORs) known to play a prominent role in food foraging and mate recognition in Sus. Phylogenetic analyses, including novel Bayesian analysis, based on CNVRs that overlap ORs retain the well-accepted topology of the genus Sus whereas CNVRs overlapping genes other than ORs show evidence for random drift and/or admixture.

Conclusion: We hypothesize that inter-specific variation in copy number of ORs provided the means for rapid adaptation to different environments during the diversification of the genus Sus in the Pliocene. Furthermore, these regions might have acted as barriers preventing massive gene flow between these species during the multiple hybridization events that took place later in the Pleistocene suggesting a possible prominent role of ORs in the ongoing Sus speciation.

No MeSH data available.