A candidate multimodal functional genetic network for thermal adaptation

Abstract

Vertebrate ectotherms such as reptiles provide ideal organisms for the study of adaptation to environmental thermal change. Comparative genomic and exomic studies can recover markers that diverge between warm and cold adapted lineages, but the genes that are functionally related to thermal adaptation may be difficult to identify. We here used a bioinformatics genome-mining approach to predict and identify functions for suitable candidate markers for thermal adaptation in the chicken. We first established a framework of candidate functions for such markers, and then compiled the literature on genes known to adapt to the thermal environment in different lineages of vertebrates. We then identified them in the genomes of human, chicken, and the lizard Anolis carolinensis, and established a functional genetic interaction network in the chicken. Surprisingly, markers initially identified from diverse lineages of vertebrates such as human and fish were all in close functional relationship with each other and more associated than expected by chance. This indicates that the general genetic functional network for thermoregulation and/or thermal adaptation to the environment might be regulated via similar evolutionarily conserved pathways in different vertebrate lineages. We were able to identify seven functions that were statistically overrepresented in this network, corresponding to four of our originally predicted functions plus three unpredicted functions. We describe this network as multimodal: central regulator genes with the function of relaying thermal signal (1), affect genes with different cellular functions, namely (2) lipoprotein metabolism, (3) membrane channels, (4) stress response, (5) response to oxidative stress, (6) muscle contraction and relaxation, and (7) vasodilation, vasoconstriction and regulation of blood pressure. This network constitutes a novel resource for the study of thermal adaptation in the closely related nonavian reptiles and other vertebrate ectotherms.

Keywords: Adaptation; Anolis; Ectotherms; Functional network; Genome mining; Reptiles; Thermal adaptation; Thermoregulation.

Figure 1. Flow chart of the process of identifying candidate functional pathways that are likely adaptive to changes in the thermal environment across vertebrates. Question marks denote hypothesis testing.

Candidate genes for thermal adaptation: Genes that have been found to be adaptive (either by sequence modification or by changes in expression levels) related to changes in the thermal environment. Functional Genetic Pathways: All DNA segments in an organism that directly or indirectly interact with each other to perform a cellular function. Genetically Overrepresented (GO) functions: Abbreviation for Genetically Overrepresented Gene Ontology, which describes which functions are common in a genetic regulatory network. This includes the functions performed by single genes, as well as functions performed by interacting genes. Vertebrate Ectotherms: Fish, Amphibians, and Reptiles. Yellow boxes denote research resources provided in this paper.

Figure 2. Amniote phylogeny based on 3,994 one-to-one orthologous synonymous protein sites showing major features of amniote evolution.

Printed with permission from Alföldi et al., Nature 2011.

Figure 3. Large functional network of a subset of candidate marker genes for thermal adaptation.

Candidate markers are indicated in green, links to other networks (depicted in Figs. 4 and 5) in pink. Hypothetical connections manually inferred from human genes to connect parts of chicken networks (NPS) are shown in the hexagonal box. A detailed version of this figure can be accessed in Fig. S1.

Figure 4. Aquaporin and Heat shock protein gene functional networks of a subset of candidate marker genes for thermal adaptation.

Candidate markers are indicated in green. Hypothetical connections manually inferred from human genes to connect parts of chicken networks (NPPA, SUMO1) are shown in hexagonal boxes. Dashed lines—hypothetical functional association with the large network depicted in Fig. 3.

Figure 5. Functional networks of the ADORA Functional Network.

Candidate markers in green. Dashed line—functional association with the large network depicted in Fig. 3.

Figure 6. Comparison of (A) clustering coefficients, (B) network heterogeneity, (C) network density and (D) average closeness centrality of candidate and 50 randomized networks.

Candidate gene network neighbors (bar) are significantly less connected, nodes are equally heterogeneous, the network is significantly more dense (= functionally related), and has a significantly larger closeness centrality than the randomized neighbor networks (columns).