Genomic signatures of divergent selection are associated with social behavior for spinner dolphin ecotypes

Genomic signatures of divergent selection and speciation patterns in a ‘natural experiment’, the young parallel radiations of Nicaraguan crater lake cichlid fishes

Molecular Ecology ◽

10.1111/j.1365-294x.2012.05738.x ◽

2012 ◽

Vol 21 (19) ◽

pp. 4770-4786 ◽

Cited By ~ 51

Author(s):

Andreas F. Kautt ◽

Kathryn R. Elmer ◽

Axel Meyer

Keyword(s):

Natural Experiment ◽

Crater Lake ◽

Divergent Selection ◽

Cichlid Fishes ◽

Genomic Signatures

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Genomic signatures of divergent selection for production and adaptation in domestic goats (Capra hircus)

10.21203/rs.2.15925/v1 ◽

2019 ◽

Author(s):

Joram M Mwacharo ◽

Eui-Soo Kim ◽

Ahmed R Elbeltagy ◽

Adel M Aboul-Naga ◽

Barbara A Rischkowsky ◽

...

Keyword(s):

Genetic Improvement ◽

Cellular Response ◽

Mammalian Species ◽

Acid Synthesis ◽

Divergent Selection ◽

Autoimmune Response ◽

Capra Hircus ◽

Thermal Nociception ◽

Genomic Signatures ◽

Candidate Regions

Abstract Background : Goats are distributed worldwide and include many breeds with marked phenotypic variation. Both natural and human driven processes have shaped their genomes. Here, 52K genome-wide SNP genotypes were used to investigate signatures of divergent selection between indigenous goats from an arid hot environment in Egypt and breeds developed under temperate environments in Europe. Three selection signature approaches were used, the di derivative of F ST , iHS and Rsb. Results: Out of a total of 36 candidate regions that were detected to be under selection by the three approaches, the analysis detected nine regions with the strongest selection signatures spanning 134 genes of which 68 were the most significantly functionally enriched. In addition to well-known genes affecting dairy traits ( LAP3 , ABCG2 , MEPE , IBSP , MED28 ) and body weight and stature ( LCORL , NCAPG , CCSER1 , DCAF16 ) in several mammalian species, we found evidence for selection in regions spanning genes implicated in the regulation of fatty acid synthesis and metabolic pathways ( PI4K2B and PPARGC1A ), inflammatory gene expression and autoimmune response pathways ( CXCL8 , HERC5 , RGS18 , TROVE2 ) and spermatogenesis ( SPATA18 , LAP3 ). Other genes not reported before in goats included SLIT2 , PACRGL , GRP125 , DHX15 , SOD3 and KCNIP4 which have been associated with thermal nociception in mice. We also detected a paralog of TBC1D12 , namely TBC1D14 , in one of the candidate regions. TBC1D12 has been linked to environmental adaptation in sheep. Gene ontology analysis revealed the 68 candidate genes were highly enriched in two biological processes viz regulation of G protein-coupled receptor signaling pathway (GO:0045744) and cellular response to stress (GO:0033554). Conclusions: Our results provide evidence that goat genomes have evolved, in part, via diverse positive selection directed at breed formation, at past and recent genetic improvement and adaptation to environments. Based on their uniqueness, these breed-group specific signatures of selection can be considered to be footprints of divergence which may be useful in characterizing genome architecture and diversity in domestic animals and for targeted genetic improvement.

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Genomic signatures of spatially divergent selection at clownfish range margins

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.0407 ◽

2021 ◽

Vol 288 (1952) ◽

pp. 20210407

Author(s):

René D. Clark ◽

Matthew L. Aardema ◽

Peter Andolfatto ◽

Paul H. Barber ◽

Akihisa Hattori ◽

...

Keyword(s):

Gene Flow ◽

Candidate Genes ◽

Local Adaptation ◽

Genetic Drift ◽

Divergent Selection ◽

Species Range ◽

Evolutionary Forces ◽

The Core ◽

Range Edge ◽

Genomic Signatures

Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.

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