Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites

Yan-hu Liu; Lu Wang; Tao Xu; Xiaomin Guo; Yang Li; Ting-ting Yin; He-chuan Yang; Yang Hu; Adeniyi C Adeola; Oscar J Sanke; Newton O Otecko; Meng Wang; Yaping Ma; Olaogun S Charles; Mikkel-holger S Sinding; Shyam Gopalakrishnan; José Alfredo Samaniego; Anders J Hansen; Carlos Fernandes; Philippe Gaubert; Jane Budd; Philip M Dawuda; Eli Knispel Rueness; Lubin Jiang; Weiwei Zhai; M Thomas P Gilbert; Min-sheng Peng; Xiaopeng Qi; Guo-dong Wang; Ya-ping Zhang

doi:10.1093/molbev/msx258

Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites

Yan-hu Liu, Lu Wang, Tao Xu, Xiaomin Guo, Yang Li, Ting-ting Yin, He-chuan Yang, Yang Hu, Adeniyi C Adeola, Oscar J Sanke, Newton O Otecko, Meng Wang, Yaping Ma, Olaogun S Charles, Mikkel-holger S Sinding, Shyam Gopalakrishnan, José Alfredo Samaniego, Anders J Hansen, Carlos Fernandes, Philippe GaubertJane Budd, Philip M Dawuda, Eli Knispel Rueness, Lubin Jiang, Weiwei Zhai, M Thomas P Gilbert, Min-sheng Peng, Xiaopeng Qi, Guo-dong Wang, Ya-ping Zhang

15 Citations (Scopus)

Abstract

Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to diverse environments. Here, we explored their demographic history and genetic basis of adaptation to the tropical African environment using whole genome analyses of 19 African indigenous dogs from Nigeria. Demographic analysis suggests that the ancestors of these dogs migrated into Africa from Eurasia 14,000 years ago and underwent a severe founder effect before population expansion. Admixture analysis further reveals that African dog genomes contain about 1.88–3.50% introgression from African golden wolves (Canis anthus). Population genetic analysis identifies 50 positively selected genes linked with immunity, angiogenesis, ultraviolet protection, as well as insulin secretion and sensitivity that may contribute to adaptation to tropical conditions. One of the positively selected genes, adhesion G protein-coupled receptor E1 (ADGRE1), has also been found to be association with severe malaria resistance in African human populations. Functional assessments showed that ADGRE1 provides protective host defense against Plasmodium infections. This result, together with the fact that the inflammatory response to canine babesiosis is similar to complicated falciparum malaria in humans, support the dogs as a model for the study of malaria control and treatment.

Original language	English
Journal	MOLECULAR BIOLOGY AND EVOLUTION
Volume	35
Issue number	2
Pages (from-to)	287-298
ISSN	0737-4038
DOIs	https://doi.org/10.1093/molbev/msx258
Publication status	Published - 1 Feb 2018

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Liu, Y., Wang, L., Xu, T., Guo, X., Li, Y., Yin, T., Yang, H., Hu, Y., Adeola, A. C., Sanke, O. J., Otecko, N. O., Wang, M., Ma, Y., Charles, O. S., Sinding, M. S., Gopalakrishnan, S., Alfredo Samaniego, J., Hansen, A. J., Fernandes, C., ... Zhang, Y. (2018). Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites. MOLECULAR BIOLOGY AND EVOLUTION , 35(2), 287-298. https://doi.org/10.1093/molbev/msx258

Liu, Y, Wang, L, Xu, T, Guo, X, Li, Y, Yin, T, Yang, H, Hu, Y, Adeola, AC, Sanke, OJ, Otecko, NO, Wang, M, Ma, Y, Charles, OS, Sinding, MS , Gopalakrishnan, S, Alfredo Samaniego, J, Hansen, AJ, Fernandes, C, Gaubert, P, Budd, J, Dawuda, PM, Knispel Rueness, E, Jiang, L, Zhai, W, Gilbert, MTP, Peng, M, Qi, X, Wang, G & Zhang, Y 2018, 'Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites', MOLECULAR BIOLOGY AND EVOLUTION , vol. 35, no. 2, pp. 287-298. https://doi.org/10.1093/molbev/msx258

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abstract = "Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to diverse environments. Here, we explored their demographic history and genetic basis of adaptation to the tropical African environment using whole genome analyses of 19 African indigenous dogs from Nigeria. Demographic analysis suggests that the ancestors of these dogs migrated into Africa from Eurasia 14,000 years ago and underwent a severe founder effect before population expansion. Admixture analysis further reveals that African dog genomes contain about 1.88–3.50% introgression from African golden wolves (Canis anthus). Population genetic analysis identifies 50 positively selected genes linked with immunity, angiogenesis, ultraviolet protection, as well as insulin secretion and sensitivity that may contribute to adaptation to tropical conditions. One of the positively selected genes, adhesion G protein-coupled receptor E1 (ADGRE1), has also been found to be association with severe malaria resistance in African human populations. Functional assessments showed that ADGRE1 provides protective host defense against Plasmodium infections. This result, together with the fact that the inflammatory response to canine babesiosis is similar to complicated falciparum malaria in humans, support the dogs as a model for the study of malaria control and treatment.",

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AU - Liu, Yan-hu

AU - Wang, Lu

AU - Xu, Tao

AU - Guo, Xiaomin

AU - Li, Yang

AU - Yin, Ting-ting

AU - Yang, He-chuan

AU - Hu, Yang

AU - Adeola, Adeniyi C

AU - Sanke, Oscar J

AU - Otecko, Newton O

AU - Wang, Meng

AU - Ma, Yaping

AU - Charles, Olaogun S

AU - Sinding, Mikkel-holger S

AU - Gopalakrishnan, Shyam

AU - Alfredo Samaniego, José

AU - Hansen, Anders J

AU - Fernandes, Carlos

AU - Gaubert, Philippe

AU - Budd, Jane

AU - Dawuda, Philip M

AU - Knispel Rueness, Eli

AU - Jiang, Lubin

AU - Zhai, Weiwei

AU - Gilbert, M Thomas P

AU - Peng, Min-sheng

AU - Qi, Xiaopeng

AU - Wang, Guo-dong

AU - Zhang, Ya-ping

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N2 - Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to diverse environments. Here, we explored their demographic history and genetic basis of adaptation to the tropical African environment using whole genome analyses of 19 African indigenous dogs from Nigeria. Demographic analysis suggests that the ancestors of these dogs migrated into Africa from Eurasia 14,000 years ago and underwent a severe founder effect before population expansion. Admixture analysis further reveals that African dog genomes contain about 1.88–3.50% introgression from African golden wolves (Canis anthus). Population genetic analysis identifies 50 positively selected genes linked with immunity, angiogenesis, ultraviolet protection, as well as insulin secretion and sensitivity that may contribute to adaptation to tropical conditions. One of the positively selected genes, adhesion G protein-coupled receptor E1 (ADGRE1), has also been found to be association with severe malaria resistance in African human populations. Functional assessments showed that ADGRE1 provides protective host defense against Plasmodium infections. This result, together with the fact that the inflammatory response to canine babesiosis is similar to complicated falciparum malaria in humans, support the dogs as a model for the study of malaria control and treatment.

AB - Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to diverse environments. Here, we explored their demographic history and genetic basis of adaptation to the tropical African environment using whole genome analyses of 19 African indigenous dogs from Nigeria. Demographic analysis suggests that the ancestors of these dogs migrated into Africa from Eurasia 14,000 years ago and underwent a severe founder effect before population expansion. Admixture analysis further reveals that African dog genomes contain about 1.88–3.50% introgression from African golden wolves (Canis anthus). Population genetic analysis identifies 50 positively selected genes linked with immunity, angiogenesis, ultraviolet protection, as well as insulin secretion and sensitivity that may contribute to adaptation to tropical conditions. One of the positively selected genes, adhesion G protein-coupled receptor E1 (ADGRE1), has also been found to be association with severe malaria resistance in African human populations. Functional assessments showed that ADGRE1 provides protective host defense against Plasmodium infections. This result, together with the fact that the inflammatory response to canine babesiosis is similar to complicated falciparum malaria in humans, support the dogs as a model for the study of malaria control and treatment.

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JO - MOLECULAR BIOLOGY AND EVOLUTION

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ER -

Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites

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