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Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes.

Fan S, Meyer A - Front Genet (2014)

Bottom Line: Many of these variations affected the annotated gene regions in the genome.For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra.However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz Konstanz, Germany.

ABSTRACT
African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile Tilapia (Oreochromis niloticus), a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the Tilapia genome as a reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), inversions and deletions. In total, around 18.8, 17.7, 17.0, and 17.0 million SNPs, 2.3, 2.2, 1.4, and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710, and 2634 deletions were inferred to have evolved in N. brichardi, A. burtoni, P. nyererei, and M. zebra, respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes.

No MeSH data available.


The evolutionary patterns of SNPs, indels, inversions, and deletion during the adaptive radiation of African cichlids. The phylogeny was adopted from the cichlid genome paper (Brawand et al., submitted). The evolution of SNP, indel, inversion, and deletion were shown in (A–D). The numbers before and after slash are the number of the lineage specific variation and the divergence time (million years). The numbers of the SNPs and indels on the phylogeny were scaled by millions. The numbers of the inversions and deletion were not scaled by millions. The histogram shows the number of the variations normalized by the corresponding divergence time. Nb, Ab, Pn, and Mz indicate Neolamprologus brichardi, Astatotilapia burtoni, Pundamila nyererei, and Metriaclima zebra.
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Figure 2: The evolutionary patterns of SNPs, indels, inversions, and deletion during the adaptive radiation of African cichlids. The phylogeny was adopted from the cichlid genome paper (Brawand et al., submitted). The evolution of SNP, indel, inversion, and deletion were shown in (A–D). The numbers before and after slash are the number of the lineage specific variation and the divergence time (million years). The numbers of the SNPs and indels on the phylogeny were scaled by millions. The numbers of the inversions and deletion were not scaled by millions. The histogram shows the number of the variations normalized by the corresponding divergence time. Nb, Ab, Pn, and Mz indicate Neolamprologus brichardi, Astatotilapia burtoni, Pundamila nyererei, and Metriaclima zebra.

Mentions: Different patterns of structural genetic variation were detected during the divergence of the African cichlids (Figure 2). Large numbers of SNPs (9.8 million) can be traced back to the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra and indicate in a substantially higher rate of SNP evolution (from 1.7 TO 3.3-fold changes) in comparison to other lineages (Figure 2A) at the basis of the radiation of African cichlids. However, we did not detect similar patterns in the evolution of inversions and deletions. The rates of inversions and deletions in the common ancestor of these four species are the slowest rate in comparison to other lineages, especially in comparison to the haplochromine lineages (Figures 2C,D). The rate of indels evolved uniformly in all lineages (Figure 2B).


Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes.

Fan S, Meyer A - Front Genet (2014)

The evolutionary patterns of SNPs, indels, inversions, and deletion during the adaptive radiation of African cichlids. The phylogeny was adopted from the cichlid genome paper (Brawand et al., submitted). The evolution of SNP, indel, inversion, and deletion were shown in (A–D). The numbers before and after slash are the number of the lineage specific variation and the divergence time (million years). The numbers of the SNPs and indels on the phylogeny were scaled by millions. The numbers of the inversions and deletion were not scaled by millions. The histogram shows the number of the variations normalized by the corresponding divergence time. Nb, Ab, Pn, and Mz indicate Neolamprologus brichardi, Astatotilapia burtoni, Pundamila nyererei, and Metriaclima zebra.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4042683&req=5

Figure 2: The evolutionary patterns of SNPs, indels, inversions, and deletion during the adaptive radiation of African cichlids. The phylogeny was adopted from the cichlid genome paper (Brawand et al., submitted). The evolution of SNP, indel, inversion, and deletion were shown in (A–D). The numbers before and after slash are the number of the lineage specific variation and the divergence time (million years). The numbers of the SNPs and indels on the phylogeny were scaled by millions. The numbers of the inversions and deletion were not scaled by millions. The histogram shows the number of the variations normalized by the corresponding divergence time. Nb, Ab, Pn, and Mz indicate Neolamprologus brichardi, Astatotilapia burtoni, Pundamila nyererei, and Metriaclima zebra.
Mentions: Different patterns of structural genetic variation were detected during the divergence of the African cichlids (Figure 2). Large numbers of SNPs (9.8 million) can be traced back to the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra and indicate in a substantially higher rate of SNP evolution (from 1.7 TO 3.3-fold changes) in comparison to other lineages (Figure 2A) at the basis of the radiation of African cichlids. However, we did not detect similar patterns in the evolution of inversions and deletions. The rates of inversions and deletions in the common ancestor of these four species are the slowest rate in comparison to other lineages, especially in comparison to the haplochromine lineages (Figures 2C,D). The rate of indels evolved uniformly in all lineages (Figure 2B).

Bottom Line: Many of these variations affected the annotated gene regions in the genome.For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra.However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz Konstanz, Germany.

ABSTRACT
African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile Tilapia (Oreochromis niloticus), a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the Tilapia genome as a reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), inversions and deletions. In total, around 18.8, 17.7, 17.0, and 17.0 million SNPs, 2.3, 2.2, 1.4, and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710, and 2634 deletions were inferred to have evolved in N. brichardi, A. burtoni, P. nyererei, and M. zebra, respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes.

No MeSH data available.