Abstract
Cetaceans are the longest-lived species of mammals and the largest in the history of the planet. They have developed mechanisms against diseases like cancer, however their underlying molecular and genetic basis remain unknown. The goal of this study was to investigate the role of natural selection in the evolution of tumor suppressor genes in cetaceans. We found signal of positive selection 29 tumor suppressor genes and duplications in 197 genes. The turnover rate of tumor suppressor genes was almost 6 times faster in cetaceans when compared to other mammals. Those genes with duplications and with positive selection are involved in important cancer regulation mechanisms (e.g. chromosome break, DNA repair and biosynthesis of fatty acids). They are also related with multiple ageing and neurological disorders in humans (e.g. Alzheimer, Nijmegen breakage syndrome, and schizophrenia). These results provide evolutionary evidence that natural selection in tumor suppressor genes could act on species with large body sizes and extended life span, providing insights into the genetic basis of disease resistance. We propose that the cetaceans are an important model in cancer, ageing and neuronal, motor and behavior disorders.
Introduction
Why large organisms do not always develop more cancer than smaller ones? This is an unresolved question that was proposed by Richard Peto in 1975 and it is known as “Peto’s paradox” 1. Peto’s paradox is based on the observation that the risk of developing cancer should increase with the number of cells. Higher number of cells is associated with more cell divisions, that is one of the main causes of errors that may result in DNA damage transforming a normal cell into a cancer cell 2,3. According to the Peto’s paradox, we should expect a higher probability of developing cancer in large organisms in comparison to small ones, however, this does not occur 4–6. Recently, the availability of genomes of a wide variety of species have stimulated the search for genes that could explain Peto’s paradox. In particular, understanding the molecular basis of the anticancer mechanisms in big and long-lived species will shed light into fundamental areas like medicine, behavior and ecology.
The ways in which organisms reach and maintain larger body sizes and/or increased longevity, have puzzled scientists for decades 7. For example, the naked mole rat (Heterocephalus glaber) has an average body mass of 35g and a lifespan of 35 years 8. Long term studies suggest that their mortality rate 9 and risk of cancer does not increase with age 10. In this species special modifications in telomerase activity and sensitive contact inhibition mechanisms would be, in part, responsible for their extended lifespan 11. Among vertebrates other anti cancer-ageing mechanisms are described that could explain the maintenance of large body sizes and/or increased longevity. For example, in the little brown bat (Myotis lucifugus) it is described that telomere dynamics and changes in genes associated with growth factors are related to repair mechanisms that prevent the DNA damage with age 12,13. In the yellowmouth rockfish (Sebastes reedi) there are no signs of aging in replicative senescence 14 and in the African elephant (Loxodonta africana) it is described variation in gene copy number in TP53 and LIF genes 15. Molecular variation in tumor suppressor genes could work like a compensatory mechanism, by providing additional protection against DNA damage that could result in less probability of developing cancer 2. However, the evolutionary history of tumor suppressor genes remains unknown.
Cetaceans evolved from a terrestrial ancestor and re-entered into the oceans around 50 million years ago 16. Their adaptation to an aquatic lifestyle required large amount of morphological, physiological and behavior changes. The sub-order Cetacea is composed of two main lineages; Odontoceti (or toothed whales) and Mysticeti (or baleen whales) 16. Baleen whales and toothed whales display a huge range of body mass and maximum lifespan, ranging from the 17 years in the Pygmy sperm whale (Kogia breviceps) to 211 years in the bowhead whale (Balaena mysticetus) and from 50 kg in the Maui’s dolphin (Cephalorhynchus hectori maui) to 175 tons in the blue whale (Balaenoptera musculus) 8. Because there are species that live more than one hundred years, during their lifetime, they are exposed for a much longer time to the appearance of harmful mutations, pathogens and diseases. Then, it is expected that cetaceans developed improvements in the immune systems and DNA repair that could act favoring multiple traits. 17. In agreement with that, in the longest-living mammal, the bowhead whale (Balaena mysticetus, lifespan ≈ 211 years, weight ≈ 100 tons) and the Humpback whale, the signal of positive selection were identified in genes involved in DNA repair, cell cycle regulation, resistance to ageing and cancer 18,19. Further, recent investigations have found the signal of positive selection in genes that could be related to their variation of body size 17. Although for mammals the evidence shows that tumor suppressor genes play a key role in the evolution of body size and longevity, through decreasing the incidence of diseases such as cancer 7,20, it is still an open question which molecular variants allow cetaceans to have evolved a lower incidence of cancer 21–23.
The goal of this study was to investigate the evolution of tumor suppressor genes in cetaceans, evaluating two forms of molecular variation (dN/dS and gene copy number variation). We report a signal of positive selection in 29 tumor suppressor genes involved in multiple processes that control the cancer onset and progression. The turnover rate of tumor suppressor genes was faster in cetaceans in comparison to other mammals. We report almost two hundred genes with duplications in one or more species of cetaceans involved in ageing, motor and neuronal disorders, deficits in learning and memory and developmental disorders. This approach highlights how studying the role of natural selection in genes associated with human health could lead to advances in our understanding of the genetic basis of disease resistance.
Methods
DNA sequences and taxonomic sampling
To study the evolution of tumor suppressor genes (TSGs) in cetaceans we implemented a phylogenetic design including 15 mammalian species. Our taxonomic sampling included five Odontocetes (bottlenose dolphin, Tursiops truncatus; orca, Orcinus orca; beluga, Delphinapterus leucas; yangtze river dolphin, Lipotes vexillifer; and the sperm whale, Physeter catodon), two Mysticetes (common minke whale, Balaenoptera acutorostrata; bowhead whale, Balaena mysticetus), five other members of the superorder Laurasiatheria (cow, Bos taurus; pig, Sus scrofa; dog, Canis familiaris; horse, Equus caballus; microbat Myotis lucifugus), two Euarchontoglires (human, Homo sapiens; mouse, Mus musculus) and one Atlantogenata (African elephant, Loxodonta africana). The coding sequences of each species were downloaded from Ensembl v.96 ((http://www.ensembl.org), NCBI database 24 and the Bowhead whale genome project (http://www.bowhead-whale.org/) (supplementary table 1). To remove low quality records, sequences were clustered using CD-HITest v.4.6 25 with a sequence identity threshold of 90% and an alignment coverage control of 80%. After that, the longest open reading frame was kept using TransDecoder LongOrfs and TransDecoder-predicted in TransDecoder v3.0.1 (https://github.com/TransDecoder/TransDecoder/).
Homology inference
We inferred homologous relationships between the 1088 tumor suppressor genes described for humans, available in public databases (Tumor Suppressor Gene Database, https://bioinfo.uth.edu/TSGene/ and the Tumor Associate Gene, http://www.binfo.ncku.edu.tw/TAG/GeneDoc.php), and the other 14 species included in our study using the program OMA standalone v.2.3.1 26. We inferred two types of groupings 1) OMA Groups (OG), containing the sets of orthologous genes and 2) Hierarchical Orthologous Groups (HOGs), which are all genes that have descended from a common ancestral gene. The amino acid sequences were aligned using the L-INS-i algorithm from MAFFT v.7 27. Nucleotide alignments were generated using the amino acid alignments as a template using the function pxaa2cdn in phyx 28. Finally, to reduce the chance of false positives given for low quality alignment regions, we made a cleaning step with the codon.clean.msa algorithm of the rphast package 29, with the associated human tumor suppressor gene as reference sequence.
Natural selection analysis
To evaluate the role of natural selection in the evolution of tumor suppressor genes, we used the codon-based model in a maximum likelihood framework using the program PAML v4.9 30, as is implemented in the ETE-toolkit with the ete-evol function 31. We used the branch-site model to estimate the signature of positive selection in the last common ancestor of Cetacea, Mysticeti (baleen whales) and Odontoceti (toothed whales). We compared the null model, where the value of ω in the foreground branch was set to 1, with the model in which the omega value was estimated from the data using the likelihood ratio tests (LRT) 32 (supplementary table 2).
Copy number variation analysis
To estimate the gene turnover rate of the tumor suppressor genes we used the software CAFE, version 4.2.1 (Computational Analysis of Gene Family Evolution) 33. Briefly, CAFE uses a stochastic birth and death model to estimate the expansions and contractions of genes using as a frame of reference the sister group relationships among species and divergence times. Using this approach we can infer the rate of evolution (λ) and the direction of the change in the size of the gene families in different lineages. We implemented two models. In the first, one λ was estimated for cetaceans as total group and other for the outgroup. In the second model, we estimated four λ values (i) the stem cetacea, (ii) the total group of Mysticeti, (iii) the total group of Odontoceti and (iv) the outgroup. All the comparisons were calculated using p<0.01 and the CAFE correction for the genome assembly and annotation random error. The divergence time between species was obtained from the TimeTree database (http://www.timetree.org/) 34. However, Odontoceti shows a polytomy, then we re-calibrate the tree using the packages APE and Phytools 33,35 in R 36, and the time-data of the most actualized time calibrated phylogeny of Odontoceti 37.
Enrichment analysis
To gain insight into the specific functions associated to the TSGs with signal of positive selection (dN/dS or CNV) we performed enrichment analyses using the gene ontology classification through DAVID bioinformatics resources -DAVID 6.7 38.
Results
Homology inference
Whales are the longest-lived mammals and the largest in the history of our planet. During their evolutionary history they developed mechanisms against ageing and diseases, however, most of them remain unknown. In this study we performed an evolutionary analysis to understand the role of natural selection, by estimating dN/dS and gene copy number variation, in the evolution of tumor suppressor genes in cetaceans. From the 1088 TSGs described for humans, we obtained 364 OrthoGroups (OG) containing the 15 mammalian species included in this study (supplementary file3) and 1044 hierarchical orthologous groups (HOG) containing two or more species (supplementary file 4, supplementary table 6).
TSGs with positive selection in cetaceans are related with multiple human disorders
According to our analyses, carried out in a set of 364 orthologous genes, we found the signal of positive selection in 29 tumor suppressor genes: 4 in the stem Cetacea, 4 in the stem of toothed whales (Odontoceti) and 21 in the stem of baleen whales (Mysticeti) (Fig.1, supplementary table 3). The TSGs with signal of positive selection are involved in multiple types of cancer and other human disorders (e.g., Fanconi anemia, Alzheimer, Nijmegen breakage syndrome and Coffin-Siris syndrome) (Table 1). The genes with a signature of positive selection were significantly enriched in 33 biological processes (supplementary table 4). In the last common ancestor of cetaceans we found enriched categories related with cancer regulation like chromosome break (BRCA2) and chemotaxis (CXCR2), but also involved in brain development that are linked with nervous system disorders in humans (PALB2 and BRCA2). In toothed whales, we found enriched categories related with the regulation of the cell cycle arrest (MYBBP1A), an important anti-cancer ageing mechanism reported before in other long-lived species (Huang et al., 2019), and also related with nervous system development (SMARCA4 and ACHE). In the last common ancestor of baleen whales, the lineage that includes the largest and long-lived species of mammals, the most represented functional categories found were related with aging and ADN repair (PRKAA1 and PRKAA2), apoptosis (SERPINB5), chromosome break (BRCA1), biosynthesis of fatty acids and cholesterol and regulation of TOR signaling (PRKAA1 and PRKAA2).
In summary, we report the signature of natural selection in TSGs involved in multiple human disorders. Since TSGs with the signature of positive selection in baleen whales and toothed whales are categorized into different biological processes, we suggest that these lineages could have evolved similar anticancer/ageing phenotype independently, reducing the risk of cancer, and favoring longevity and body mass.
Cetaceans have an accelerated gene turnover rate in comparison to other mammals
Our results revealed that the turnover rate of TSGs of cetaceans, as a total group, is more than five times faster (λc = 0.0037) in comparison to the rest of the tree (λo = 0.0007) (Fig. 2a). In the second model, in which we specified four rates of gene family evolution, we found that the turnover rate values estimated for the last common ancestor of baleen whales (λmy= 0.0036) and the last common ancestor of cetaceans (λC= 0.0037) are similar, but lower in comparison to the estimate of the last common ancestor of toothed whales (λod= 0.0046) (Fig. 2b). In all cases the gene turnover rate is almost 6 times faster in comparison to the outgroup (Fig. 2b).
To gain insights into the mechanisms related to ageing and disease resistance that are related to the tumor suppressor gene families, we identified the TSGs with specific duplications in cetaceans. According to our analyses we identified 197 TSGs with specific duplications in one or more cetacean species (Fig 3a, supplementary table 7). These duplicate genes are related with ageing (21 TSGs, supplementary table 8), immune system, vision and neurological, cardiovascular, metabolic and developmental disorders in humans (Fig 3b). Also they are involved in multiple biological processes (supplementary table 9) which are directly associated with the regulation of cancer, like cell proliferation (DAB2, FES, YAP1, BIN1), cell migration (EFNA1, PTPRK), apoptosis (LITAF, EPB41L3. KIF1B) and metabolism pathways (NEO1, PAX6, PTPRD and PTPRK). In our analysis, we also report extensive variation in the expansion and contraction of TSGs families in cetaceans and in the African elephant (Loxodonta africana) and the little brown bat (Myotis lucifugus), mammalian species that are well known for being cancer resistant (Gorbunova et al., 2014) (Fig. 4).
In summary, we found an accelerated rate of evolution of TSGs in cetaceans in comparison to other mammals. The gene families with an accelerated rate of evolution are related with important anticancer process that has also been reported in other long-lived species, like DNA repair, cell cycle and replicative senescence. Finally, we report almost two hundred genes duplicated just in one or more cetaceans, that are involved in multiple human disorders that comes from immune system and ageing to neurological disorders.
Discussion
TSGs with the signature of positive selection are related to cancer and Falcony anemia
To understand the evolution of tumor suppressor genes in cetaceans, we studied the role of positive selection in genes involved in detection and repair of genetic damage, because this could be an important process in preventing the appearance of mutations that promote the spread of cancer cells in the organism. In the ancestor of cetaceans we report the signature of positive selection in the CXCR2 gene, that is a chemotaxis receptor, that regulates the recruitment of leukocytes during the inflammation processes and has also been described as a crucial factor in the tumor cell dissemination 39. The MYBBP1A gene had the signature of positive selection in the ancestor of toothed whales, and is involved in p53 activation playing a fundamental role in programmed cell death 40. In baleen whales we also found genes that could protect against the tumor growth, like the SERPINB5 gene, that has an important role in angiogenesis and metastasis 41. Considering the evolution of the enormous body size in cetaceans, molecular variants in CXCR2, MYBBP1A and SERPINB5 could arise as a protective mechanism against the development of tumors.
We also found the signature of positive selection in the BRCA2 gene (marginally significant p-value of 0.06) in the ancestor of cetaceans and BRCA1 and PALB2 in the ancestor of baleen whales. BRCA1-2 genes are strongly associated with breast, ovarian and prostate cancer, the most common malignancy among the human population 42. These genes have a central role in the maintenance of genomic stability and are also involved with chromosome breakage and cell cycle control 43. Previous studies have also shown the signature of positive selection in BRCA2 in long-lived species of bats 13, suggesting that BRCA2, in association with their paralog BRCA1, could improve the DNA repair process protecting against the accumulation of DNA damage in cetaceans.
In humans, the BRCA1-2 and PALB2 genes are also related with Fanconi anemia, a genetic disease that is involved in bone-marrow failure and congenital malformation, which made patients more susceptible to cancer at younger ages. Damages in those genes cause an increased cancer predisposition by DNA repair deficiency 44. Patients with Fanconi anemia also have accelerated telomere shortening, product of the DNA damage and oxidative stress 45, which are determinants of ageing and cell senescence. In cetaceans, the combination of new molecular variants (e.g. BRCA1/2 and PALB2) could reduce the incidence of cancer and lead us to understand new routes that could improve the mechanisms of DNA damage, cancer and ageing.
TSGs with the signature of positive selection are related with ageing
Ageing is the biggest risk factor for developing cancer and is characterized by the progressive accumulation of cellular damage, but the mechanisms linking these two processes -ageing and cancer-remain unclear 46. One of the mechanisms that define how well we age, is the regulation of energy flow in the cells 47. The genes PRKAA1 and PRKAA2 had signature of positive selection in baleen whales, and are part of the AMP-activated protein kinase (AMPK) complex, one of the primary regulators of energy homeostasis in eukaryotic cells and is considered as “a metabolic master-switch” 48. The AMPK modulators have an important role in cardiac disorders (e.g. Wolff-Parkinson-White) 49, metabolic diseases (e.g. diabetes type II and obesity) 50 and also preventing the proliferation of cancer cells 51. This pro-longevity mechanism has been used as therapeutic targets for age-related disorders in mammals 52,53 and it could be an important ageing mechanism in the evolution of baleen whales, who can live more than two hundred years. In baleen whales, the mechanisms associated with cancer resistance may have responded to selective pressures related to the increase in body size. Then, new pathways that improved their repair mechanisms of DNA damage, product of the metabolism of fatty acids and cholesterol, could arise in response to variants of these genes.
Previous studies with the bowhead whale genome (the longest-lived mammal) found a link between genes involved in metabolism and the evolution of longevity 19. A number of studies have supported associations between sindroms related with metabolism and cardiovascular diseases, diabetes and schizophrenia 54. For example, Hansen et al., (2011) studied 410 Danish patients with type II diabetes, 4089 with schizophrenia and others 17,597 european patients as controls. They found that the patients with type II diabetes increases the risk of developing schizophrenia and the genetic risk factor is associated mutations in the gene TCF7L2 55. In our study, we found ten copies of this gene in the killer whale and seven in beluga, however, the physiological consequences of having an increased number of copies and its relation with diabetes and schizophrenia remains unknown. Comparative studies in genes related with ageing and cancer, will provide insights into the evolution of physiological, morphological and behavioural traits.
Another anticancer and ageing mechanism is replicative senescence. This process is in charge of stopping cell proliferation 56 and in species that evolved large body sizes is considered as an important tumour suppressor mechanism 11. In our study we report four copies of the IRF5 gene in the orca and three copies of the PTPRD gene in the orca and in the sperm whale, both of them promoters of replicative senescence. The PTPRD gene has been associated with different types of cancer, including laryngeal, head and neck squamous cell carcinomas 57. The fact that cases of oral squamous cell carcinoma have been diagnosed in dolphins of the genus Tursiops 58, coincides with the fact that they only have one copy of the PTPRD gene. In contrast, we report five copies of the PTPRD gene in beluga and minke whale and two copies in the killer whale and the river dolphin. An increase in the copy number of TSGs (e.g PTPRD and IRF5) could work as an extra protection against the development of squamous cell carcinomas in cetaceans, since it has been suggested that increasing the number of copies would act as “guardians” to prevent somatic mutations spreading in the cell population 4,59. This result is in agreement with previous studies, where it has been shown that longevity-associated gene families evolve faster (increase the number of gene family members) in long-lived species 60.
TSGs with the signature of positive selection are related with neurological disorders
Given that whales, porpoises and dolphins have developed complex neurological systems and have the greatest absolute brain size among animals 61, it is expectable that they possess molecular variants to reduce the development of nervous system disorders (e.g. Alzheimer’s, Nijmegen breakage syndrome, Coffin-Siris syndrome and spatial learning and motor coordination diseases). For example, the EPB41L3 gene is involved in meningiomas development 62, that is the most common central nervous system tumors in humans 63. In our study we found 13 copies in the minke whale, eight in the beluga, four in the river dolphin and two in the killer whale and the sperm whale. On the other hand, BRCA2 gene (with positive selection in the stem of cetaceans) has also an important role in maintaining neural homeostasis in the central nervous system 64. Experiments in mice have shown that the deletion of the BRCA2 gene affect their embryonic and postnatal neural development 65, while in humans, mutations in this gene could cause microcephaly 66. Other duplicated gene in cetaceans related with neurological disorders, like depression and schizophrenia, is the DLG1 gene 67, and we identified three to five copies in five cetaceans species. Thus, amino acid changes in the BRCA2 gene in addition extra copies of the EPB41L3 and DLG1 genes, could be seen as an adaptive process improving the DNA repair system and providing an improved protection against cancer and neurological disorders, a hypothesis that needs to be tested.
Alzheimer’s disease is another neurodegenerative disorder developed mainly in old ages that affects the cognitive functions and generating slow memory loss 68. In cetaceans, we report multiple copies of genes that has been recognized as a genetic risk factors in human Alzheimer’s. Some of those genes are EPHA1, that is a positive regulator of angiogenesis, and metastases 69; the ACHE gene, that encodes for the enzyme acetylcholinesterase, which is a catabolic enzyme for the neurotransmitter acetylcholine that is involved in the nervous system development pathways 70 and the BIN1 gene, that is a neuroinflammation related gene 71. Particularly, for the BIN1 gene we found eleven copies in the beluga, eight in the river dolphin and four in the killer whale. The extra copies could serve as a complement to prevent the emergence of diseases that can cause memory loss that could affect the social abilities of the group. Then, in toothed whales, the anticancer mechanism could have evolved in response to the cognitive demands associated with complex cognitive system, sociability and use of echolocation. Thus TSGs may have been positively selected by natural selection by improving the mechanisms that lead to the appearance of diseases such as Alzheimer’s.
In the ancestor of toothed whales, we found TSGs with positive selection involved in neurodevelopmental disorders like Nijmegen breakage syndrome (NBS) and Coffin-Siris syndrome (CSS). NBS is a genetic disorder characterized by severe microcephaly leaded by growth retardation, short stature, and malfunctioning of the immune system, making the individuals with more predisposition to cancer 72. The NBS is associated with mutations in the gene MDC1, that is involved in the signalling, detection and reparation of DNA damage 73. The gene MDC1 could be an important anticancer mechanism in toothed whales. On the other hand, Coffin-Siris syndrome (CSS) is a rare neurodevelopmental disorder, characterized by cognitive and developmental disability 74. CSS is related with mutations in the SMARCA4 gene in the 11% of patients 75. SMARCA4 is part of the ATP-dependent chromatin remodelling complex BAF (or SWI\SNF complex) 76. This complex is in charge of the regulation of gene expression and cell differentiation and maintenance of stem cell pluripotency 77. Particularly, SMARCA4 has been also associated with small-cell carcinoma of the ovary hypercalcemic type (SCCOHT), a malignant tumour with poor response to chemotherapy 78. Overall, these genes which are related to neurodevelopmental disorders in humans, in species that developed complex cognitive systems, like the toothed whales, could underlie new discoveries and gene pathways that could have an impact in human medicine.
TGSs duplications in cetaceans are related with spatial learning and motor disorders in humans
As in humans, cetaceans possess a fascinating evolution of behavior, with a complex social structure, developinging language comprehension and self-recognition ability 79. Dolphins and whales are characterized for having few fully developed young, which develop a faster self-recognition ability and are capable of following the mother shortly after birth in a behavior that is known as a “infant carrying” 80. During lactancy and infant carrying, the morphological and physiological hydrodynamic development of the young impacts in the swimming performance 81. Newborns with diseases, motor malformations or poorly self-recognition ability usually are killed or left to die as they do not have enough skills to survive in nature 82. In our study we identify duplicated genes in cetaceans that are related with spatial learning and motor disorders in humans. For example, EPB41 gene is involved in involved in the actomyosin structure organization that is a machinery that works in the contractile apparatus in muscle cells and neuronal membrane receptor complexes 83. Experiments with EPB41 knockout mice also revealed erythroid disorders and others neuronal defects related with spatial learning and motor coordination 84. In our study we found four copies of the EPB41 gene in the minke whale and beluga and five copies in the river dolphin. An increase in the copy number of EPB41 could represent a way to develop new pathways to regulate the machinerie that controls the muscle contractions in an aquatic environment and also control and/or avoid neuronal disorders.
Another gene duplicated in cetaceans is the PAX6 gene, that is involved in the central nervous system and eye development across the tree of life 85,86. Mutations in the PAX6 gene cause ocular pathologies, like aniridia in humans 87 or malformed retina and lens in frogs (Xenopus tropicalis) 88. Also, it has been related with neurological phenotypes (e.g autism and mental retardation) 89,90. In zebrafish (Danio rerio) has been identified two PAX6 genes, as a consequence of the teleost-specific genome duplication, suggesting a division of labor between the two copies during the development of brain and eye structures 91. In our study we report four copies in beluga and four copies in the common minke whale. Studying human ageing under a comparative evolutionary perspective offers an avenue that could provide information about the role of natural selection in the evolution of species that found another way to avoid ageing diseases like cancer.
In the same direction, ABI2 gene is a regulator of cell migration and when is mutated generates aberrant dendritic spine morphogenesis and deficits in learning and memory 92.
ABI2 has a paralog, ABI1, which positively regulates lung metastasis of aggressive breast cancer 93. Regua et al., (2008) suggest that in the absence of ABI1, its paralog could play a compensatory role that may support primary tumor growth. In our study, we report seven copies of ABI2 in the killer whale, four in the beluga, six in the river dolphin, two in the sperm whale, and two in the minke whale. Charcot Marie Tooth disease (CMT) is a hereditary motor and sensory neuropathy. The CMT type 1C cause abnormalities in myelin and affect the health of the nerve fiber, this disorder is associated with mutations in the LITAF gene 94. In CMT type 2A the sensory peripheral nerves are malfunction, developing alterations in the sensorial capacity, atrophy and muscle weakness. The CMT type 2A? has been related related with mutations in the KIF1B gene that is a precursor in the axon from the cell body to the synapse 95. However, even when affect an important morphological and physiological traits, it seems that the CMT disease do not decrease the lifespan of the individuals 96. In our study, we report four copies of the LITAF gene in the river dolphin and three copies in the bowhead whale found an increased number of copies of the KIF1B gene in four cetaceans species: six in the minke whale, four in beluga, four in the sperm whale and two in the river dolphin. The role of the expanded repertoire of LITAF and KIF1B in cetaceans remain unknown, however, they could play a role at neuronal and motor level, taking into account that the organs of senses (including the sonar) and the development of hydrodynamic body shape were ones of the most remarkable morphological modifications in the evolution of the cetaceans.
In big, social and long-lived organisms, natural selection could favor disease resistant mechanisms for the improvement of the immune system, DNA repair mechanisms and metabolic pathway, but could also select positively molecular variants associated to avoid neuronal and motor pathologies.
Conclusions
The main goal of this study was to shed light into the evolution of tumor suppressor genes in cetaceans. We reported signal of positive selection in 29 TSGs and an accelerated gene turnover rate in comparison to other mammals, with duplications in 197 genes in one or more cetacean species. These genes were involved in important process in ageing (e.g. PTPRD, PRKAA1 and PRKAA2) and cancer regulation like chromosome break, chemotaxis, programmed cell death and metabolism of fatty acids and cholesterol. In cetaceans, natural selection could favor new molecular variants that could improve the mechanism of DNA repair, energy consumption and ageing. We also report TSGs with positive selection and/or gene duplications related with multiple human disorders like Fanconi anemia (BRCA1-2 and PALB2), Alzheimer (EPHA1, ACHE), diabetes and schizophrenia (TCF7L2, DLG1), Nijmegen breakage syndrome (MDC1), Coffin-Siris syndrome (SMARCA4). Other TGSs with duplications in cetaceans were related with spatial learning and motor disorders in humans (EPB41, ABI2, KIF1B, LITAF). Studying genes that are related to human malignancies from a comparative perspective offers a novel avenue that could provide clues about the role of natural selection in the evolution of species that found a way to beat diseases. This study provide evolutionary evidence that natural selection in tumor suppressor genes could act on species with large body sizes and extended life span, providing insights into the genetic basis associated with the evolution of disease resistance. We propose that the cetaceans are an important model to understand longevity, neuronal, motor and behavioral disorders in humans and other animals.
Author contributions
DTM and JCO conceived the project; DTM performed the bioinformatic analysis. DTM wrote the manuscript; JCO and JPM edited the manuscript and were the project advisors.
Acknowledgements
Members of the Integrative Genomics of Ageing Group at the University of Liverpool, for all the support and advice during DTM’s internship. To Richard Gregory in the Centre for Genomic Research (CGR) and Ian C. Smith in the Advanced Research Computing at the University of Liverpool for their help with computing resources. This work was supported by Comisión Nacional de Investigación Científica y Tecnológica (CONICYT) - Chile through the doctoral studentship number N°21170433 and the scholarship from MECESUP AUS 2003 to DTM, Millennium Nucleus of Ion Channels Associated Diseases (MiNICAD), Iniciativa Científica Milenio, Ministry of Economy, Development and Tourism, Chile to JCO. Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) grant 1160627 to JCO. To Dr. Andres Parada, for the academic discussions and programming advice. To Alejandra Tejada-Martinez for the graphic designs. Finally to Jesus Tejada and Gloria Martinez for their unconditional support. AnAge is supported by funding from the Biotechnology and Biological Sciences Research Council (BB/R014949/1) to JPM.
References
- 1.↵
- 2.↵
- 3.↵
- 4.↵
- 5.
- 6.↵
- 7.↵
- 8.↵
- 9.↵
- 10.↵
- 11.↵
- 12.↵
- 13.↵
- 14.↵
- 15.↵
- 16.↵
- 17.↵
- 18.↵
- 19.↵
- 20.↵
- 21.↵
- 22.
- 23.↵
- 24.↵
- 25.↵
- 26.↵
- 27.↵
- 28.↵
- 29.↵
- 30.↵
- 31.↵
- 32.↵
- 33.↵
- 34.↵
- 35.↵
- 36.↵
- 37.↵
- 38.↵
- 39.↵
- 40.↵
- 41.↵
- 42.↵
- 43.↵
- 44.↵
- 45.↵
- 46.↵
- 47.↵
- 48.↵
- 49.↵
- 50.↵
- 51.↵
- 52.↵
- 53.↵
- 54.↵
- 55.↵
- 56.↵
- 57.↵
- 58.↵
- 59.↵
- 60.↵
- 61.↵
- 62.↵
- 63.↵
- 64.↵
- 65.↵
- 66.↵
- 67.↵
- 68.↵
- 69.↵
- 70.↵
- 71.↵
- 72.↵
- 73.↵
- 74.↵
- 75.↵
- 76.↵
- 77.↵
- 78.↵
- 79.↵
- 80.↵
- 81.↵
- 82.↵
- 83.↵
- 84.↵
- 85.↵
- 86.↵
- 87.↵
- 88.↵
- 89.↵
- 90.↵
- 91.↵
- 92.↵
- 93.↵
- 94.↵
- 95.↵
- 96.↵