Dataset Information

A genome wide study of genetic adaptation to high altitude in feral Andean Horses of the paramo.

ABSTRACT: BACKGROUND: Life at high altitude results in physiological and metabolic challenges that put strong evolutionary pressure on performance due to oxidative stress, UV radiation and other factors dependent on the natural history of the species. To look for genes involved in altitude adaptation in a large herbivore, this study explored genome differentiation between a feral population of Andean horses introduced by the Spanish in the 1500s to the high Andes and their Iberian breed relatives. RESULTS: Using allelic genetic models and Fst analyses of ~50 K single nucleotide polymorphisms (SNPs) across the horse genome, 131 candidate genes for altitude adaptation were revealed (Bonferoni of p???2?×?10(-7)). Significant signals included the EPAS1 in the hypoxia-induction-pathway (HIF) that was previously discovered in human studies (p?=?9.27?×?10(-8)); validating the approach and emphasizing the importance of this gene to hypoxia adaptation. Strong signals in the cytochrome P450 3A gene family (p?=?1.5 ×10(-8)) indicate that other factors, such as highly endemic vegetation in altitude environments are also important in adaptation. Signals in tenuerin 2 (TENM2, p?=?7.9?×?10(-14)) along with several other genes in the nervous system (gene categories representation p?=?5.1?×?10(-5)) indicate the nervous system is important in altitude adaptation. CONCLUSIONS: In this study of a large introduced herbivore, it becomes apparent that some gene pathways, such as the HIF pathway are universally important for high altitude adaptation in mammals, but several others may be selected upon based on the natural history of a species and the unique ecology of the altitude environment.

SUBMITTER: Hendrickson SL

PROVIDER: S-EPMC3878729 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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A genome wide study of genetic adaptation to high altitude in feral Andean Horses of the páramo.

Hendrickson Sher L SL

BMC evolutionary biology 20131217

<h4>Background</h4>Life at high altitude results in physiological and metabolic challenges that put strong evolutionary pressure on performance due to oxidative stress, UV radiation and other factors dependent on the natural history of the species. To look for genes involved in altitude adaptation in a large herbivore, this study explored genome differentiation between a feral population of Andean horses introduced by the Spanish in the 1500s to the high Andes and their Iberian breed relatives.< ...[more]

PMID: 24344830

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Project description:Humans living at high altitude (≥ 2,500 meters above sea level) have acquired unique abilities to survive the associated extreme environmental conditions, including hypoxia, cold temperature, limited food availability and high levels of free radicals and oxidants. Long-term inhabitants of the most elevated regions of the world have undergone extensive physiological and/or genetic changes, particularly in the regulation of respiration and circulation, when compared to lowland populations. Genome scans have identified candidate genes involved in altitude adaption in the Tibetan Plateau and the Ethiopian highlands, in contrast to populations from the Andes, which have not been as intensively investigated. In the present study, we focused on three indigenous populations from Bolivia: two groups of Andean natives, Aymara and Quechua, and the low-altitude control group of Guarani from the Gran Chaco lowlands. Using pooled samples, we identified a number of SNPs exhibiting large allele frequency differences over 900,000 genotyped SNPs. A region in chromosome 10 (within the cytogenetic bands q22.3 and q23.1) was significantly differentiated between highland and lowland groups. We resequenced ~1.5 Mb surrounding the candidate region and identified strong signals of positive selection in the highland populations. A composite of multiple signals like test localized the signal to FAM213A and a related enhancer; the product of this gene acts as an antioxidant to lower oxidative stress and may help to maintain bone mass. The results suggest that positive selection on the enhancer might increase the expression of this antioxidant, and thereby prevent oxidative damage. In addition, the most significant signal in a relative extended haplotype homozygosity analysis was localized to the SFTPD gene, which encodes a surfactant pulmonary-associated protein involved in normal respiration and innate host defense. Our study thus identifies two novel candidate genes and associated pathways that may be involved in high-altitude adaptation in Andean populations.

Project description:BackgroundThe páramo is a high-elevation biogeographical province in the northern Andes, known for its great biodiversity and ecosystem services. Because there have been very few biogeographic studies encompassing the entire province to date, this study aimed at conducting a phytogeographical regionalisation of the páramo. Specifically, (1) clustering analyses were conducted to identify the main phytogeographical units in the three altitudinal belts: sub-páramo, mid-páramo and super-páramo, and examine their diagnostic flora, (2) an ordination complemented the geo-climatic characterization of the obtained units and (3) a hierarchical classification transformation was obtained to evaluate the relationships between units.MethodsThe study area included the entire Andean páramo range in northern Peru, Ecuador, Colombia and Venezuela. The analyses were based on 1,647 phytosociological plots from the VegPáramo database. The K-means non-hierarchical clustering technique was used to obtain clusters identifiable as phytogeographical units, and the Ochiai fidelity index was calculated to identify their diagnostic species. A principal component analysis was conducted to obtain the geo-climatic characterization of each unit. Finally, the relationships between clusters were traced using a hierarchical plot-based classification.ResultsFifteen clusters were obtained, 13 natural and two artificial, of which two represented the sub-páramo, nine the mid-páramo and four the super-páramo. Even though data representativeness was a potential limitation to segregate certain sub-páramo and super-páramo units, the overall bioregionalisation was robust and represented important latitudinal, altitudinal and climatic gradients.DiscussionThis study is the first to bioregionalise the páramo province based on a substantial widely distributed biological dataset, and therefore provides important novel scientific insight on its biogeography. The obtained phytogeographical units can be used to support further research on the páramo at smaller scale and on the humid Neotropical high-elevation ecosystems at broader-scale. Finally, several units were highlighted in our results as particularly worthy of further scientific and conservation focus.

Project description:High altitudes (>8,000 ft or 2,500 m) provide an experiment of nature for measuring adaptation and the physiological processes involved. Studies conducted over the past ~25 years in Andeans, Tibetans, and, less often, Ethiopians show varied but distinct O2 transport traits from those of acclimatized newcomers, providing indirect evidence for genetic adaptation to high altitude. Short-term (acclimatization, developmental) and long-term (genetic) responses to high altitude exhibit a temporal gradient such that, although all influence O2 content, the latter also improve O2 delivery and metabolism. Much has been learned concerning the underlying physiological processes, but additional studies are needed on the regulation of blood flow and O2 utilization. Direct evidence of genetic adaptation comes from single-nucleotide polymorphism (SNP)-based genome scans and whole genome sequencing studies that have identified gene regions acted upon by natural selection. Efforts have begun to understand the connections between the two with Andean studies on the genetic factors raising uterine blood flow, fetal growth, and susceptibility to Chronic Mountain Sickness and Tibetan studies on genes serving to lower hemoglobin and pulmonary arterial pressure. Critical for future studies will be the selection of phenotypes with demonstrable effects on reproductive success, the calculation of actual fitness costs, and greater inclusion of women among the subjects being studied. The well-characterized nature of the O2 transport system, the presence of multiple long-resident populations, and relevance for understanding hypoxic disorders in all persons underscore the importance of understanding how evolutionary adaptation to high altitude has occurred.NEW & NOTEWORTHY Variation in O2 transport characteristics among Andean, Tibetan, and, when available, Ethiopian high-altitude residents supports the existence of genetic adaptations that improve the distribution of blood flow to vital organs and the efficiency of O2 utilization. Genome scans and whole genome sequencing studies implicate a broad range of gene regions. Future studies are needed using phenotypes of clear relevance for reproductive success for determining the mechanisms by which naturally selected genes are acting.

Dataset Information

A genome wide study of genetic adaptation to high altitude in feral Andean Horses of the paramo.

Publications

A genome wide study of genetic adaptation to high altitude in feral Andean Horses of the páramo.

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