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Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

ABSTRACT: The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages.

SUBMITTER: Figueiro HV

PROVIDER: S-EPMC5517113 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

Figueiró Henrique V HV Li Gang G Trindade Fernanda J FJ Assis Juliana J Pais Fabiano F Fernandes Gabriel G Santos Sarah H D SHD Hughes Graham M GM Komissarov Aleksey A Antunes Agostinho A Trinca Cristine S CS Rodrigues Maíra R MR Linderoth Tyler T Bi Ke K Silveira Leandro L Azevedo Fernando C C FCC Kantek Daniel D Ramalho Emiliano E Brassaloti Ricardo A RA Villela Priscilla M S PMS Nunes Adauto L V ALV Teixeira Rodrigo H F RHF Morato Ronaldo G RG Loska Damian D Saragüeta Patricia P Gabaldón Toni T Teeling Emma C EC O'Brien Stephen J SJ Nielsen Rasmus R Coutinho Luiz L LL Oliveira Guilherme G Murphy William J WJ Eizirik Eduardo E

Science advances 20170719 7

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all liv ...[more]

PMID: 28776029

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Project description:BACKGROUND: Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them. RESULTS: We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low-abundance organisms. Genome signatures, in the form of tetranucleotide frequencies analyzed by emergent self-organizing maps, segregated sequences from all known populations sharing < 50 to 60% average amino acid identity and revealed previously unknown genomic clusters corresponding to low-abundance organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters were resolved because intra-genome differences resulting from translational selection or protein adaptation to the intracellular (pH approximately 5) versus extracellular (pH approximately 1) environment were small relative to inter-genome differences. We found that these genome signatures stem from multiple influences but are primarily manifested through codon composition, which we propose is the result of genome-specific mutational biases. CONCLUSIONS: An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities.

Dataset Information

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

Publications

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

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