1
|
Liao B, Wang J, Xie Y, Luo H, Min J. LINK-A: unveiling its functional role and clinical significance in human tumors. Front Cell Dev Biol 2024; 12:1354726. [PMID: 38645412 PMCID: PMC11032015 DOI: 10.3389/fcell.2024.1354726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
LINK-A, also recognized as LINC01139, has emerged as a key oncological lncRNA in cancer. LINK-A is upregulated in solid and liquid tumor samples, including breast cancer, ovarian cancer, glioma, non-small-cell lung cancer, and mantle cell lymphoma. Notably, LINK-A is involved in regulating critical cancer-related pathways, such as AKT and HIF1α signaling, and is implicated in a range of oncogenic activities, including cell proliferation, apoptosis, epithelial-mesenchymal transition (EMT), cell invasion and migration, and glycolysis reprogramming. LINK-A's differential expression and its correlation with clinical features enable it to be a promising biomarker for cancer diagnosis, prognosis, and the stratification of tumor progression. Additionally, LINK-A's contribution to the development of resistance to cancer therapies, including AKT inhibitors and immunotherapy, underscores its potential as a therapeutic target. This review provides a comprehensive overview of the available data on LINK-A, focusing on its molecular regulatory pathways and clinical significance. By exploring the multifaceted nature of LINK-A in cancer, the review aims to offer a valuable resource for future research directions, potentially guiding the development of novel therapeutic strategies targeting this lncRNA in cancer treatment.
Collapse
Affiliation(s)
- Bing Liao
- Department of Otorhinolaryngology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jialing Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Yilin Xie
- Second School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jun Min
- Department of Neurology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| |
Collapse
|
2
|
Soni V, Vos M, Eyre-Walker A. A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection. PLoS Biol 2022; 20:e3001645. [PMID: 35653351 PMCID: PMC9162324 DOI: 10.1371/journal.pbio.3001645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection.
Collapse
Affiliation(s)
- Vivak Soni
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn, United Kingdom
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- * E-mail:
| |
Collapse
|
3
|
Kumar H, Panigrahi M, Panwar A, Rajawat D, Nayak SS, Saravanan KA, Kaisa K, Parida S, Bhushan B, Dutt T. Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data. J Comput Biol 2022; 29:943-960. [PMID: 35639362 DOI: 10.1089/cmb.2021.0447] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.
Collapse
Affiliation(s)
- Harshit Kumar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Anuradha Panwar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Divya Rajawat
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Sonali Sonejita Nayak
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - K A Saravanan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Kaiho Kaisa
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Subhashree Parida
- Divisions of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Bharat Bhushan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| |
Collapse
|
4
|
Alharbi AF, Sheng N, Nicol K, Strömberg N, Hollox EJ. Balancing selection at the human salivary agglutinin gene (DMBT1) driven by host-microbe interactions. iScience 2022; 25:104189. [PMID: 35494225 PMCID: PMC9038570 DOI: 10.1016/j.isci.2022.104189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 11/19/2022] Open
Abstract
Discovering loci under balancing selection in humans can identify loci with alleles that affect response to the environment and disease. Genome variation data have identified the 5′ region of the DMBT1 gene as undergoing balancing selection in humans. DMBT1 encodes the pattern-recognition glycoprotein DMBT1, also known as SALSA, gp340, or salivary agglutinin. DMBT1 binds to a variety of pathogens through a tandemly arranged scavenger receptor cysteine-rich (SRCR) domain, with the number of domains polymorphic in humans. We show that the signal of balancing selection is driven by one haplotype usually carrying a shorter SRCR repeat and another usually carrying a longer SRCR repeat. DMBT1 encoded by a shorter SRCR repeat allele does not bind a cariogenic and invasive Streptococcus mutans strain, in contrast to the long SRCR allele that shows binding. Our results suggest that balancing selection at DMBT1 is due to host-microbe interactions of encoded SRCR tandem repeat alleles. Clear evidence from many analyses show balancing selection at DMBT1 Scavenger-receptor cysteine-rich domain array associated with balancing selection Genetic variation, not alternative splicing, responsible for protein isoforms Long, but not short, DMBT1 isoforms bind a cariogenic strain of Streptococcus mutans
Collapse
Affiliation(s)
- Adel F. Alharbi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Medina Regional Laboratory, General Directorate of Health Affairs, Ministry of Health, Medina, Saudi Arabia
| | - Nongfei Sheng
- Department of Odontology, Umeå University, Umeå, Sweden
| | - Katie Nicol
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Corresponding author
| |
Collapse
|
5
|
Nunez JCB, Rong S, Ferranti DA, Damian‐Serrano A, Neil KB, Glenner H, Elyanow RG, Brown BRP, Alm Rosenblad M, Blomberg A, Johannesson K, Rand DM. From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles. Mol Ecol 2021; 30:6417-6433. [PMID: 33960035 PMCID: PMC9292448 DOI: 10.1111/mec.15949] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/25/2022]
Abstract
The northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations to highly heterogeneous environments. Adult barnacles may be exposed to highly dissimilar levels of thermal stress depending on where they settle in the intertidal (i.e., closer to the upper or lower tidal boundary). For instance, barnacles near the upper tidal limit experience episodic summer temperatures above recorded heat coma levels. This differential stress at the microhabitat level is also dependent on the aspect of sun exposure. In the present study, we used pool-seq approaches to conduct a genome wide screen for loci responding to intertidal zonation across the North Atlantic basin (Maine, Rhode Island, and Norway). Our analysis discovered 382 genomic regions containing SNPs which are consistently zonated (i.e., SNPs whose frequencies vary depending on their position in the rocky intertidal) across all surveyed habitats. Notably, most zonated SNPs are young and private to the North Atlantic. These regions show high levels of genetic differentiation across ecologically extreme microhabitats concomitant with elevated levels of genetic variation and Tajima's D, suggesting the action of non-neutral processes. Overall, these findings support the hypothesis that spatially heterogeneous selection is a general and repeatable feature for this species, and that natural selection can maintain functional genetic variation in heterogeneous environments.
Collapse
Affiliation(s)
- Joaquin C. B. Nunez
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
- Present address:
Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
| | - Stephen Rong
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| | - David A. Ferranti
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
| | | | - Kimberly B. Neil
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
| | - Henrik Glenner
- Department of Biological SciencesUniversity of BergenBergenNorway
- Center of Macroecology and Climate, GLOBEUniversity of CopenhagenCopenhagenDenmark
| | - Rebecca G. Elyanow
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| | - Bianca R. P. Brown
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular BiologyUniversity of GothenburgLundberg LaboratoryGöteborgSweden
| | - Anders Blomberg
- Department of Chemistry and Molecular BiologyUniversity of GothenburgLundberg LaboratoryGöteborgSweden
| | - Kerstin Johannesson
- Department of Marine SciencesUniversity of GothenburgTjärnö Marine LaboratoryStrömstadSweden
| | - David M. Rand
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| |
Collapse
|
6
|
Nadachowska‐Brzyska K, Konczal M, Babik W. Navigating the temporal continuum of effective population size. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | - Wieslaw Babik
- Jagiellonian University in Kraków Faculty of Biology Institute of Environmental Sciences Kraków Poland
| |
Collapse
|
7
|
Isildak U, Stella A, Fumagalli M. Distinguishing between recent balancing selection and incomplete sweep using deep neural networks. Mol Ecol Resour 2021; 21:2706-2718. [PMID: 33749134 DOI: 10.1111/1755-0998.13379] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/12/2022]
Abstract
Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those left by ongoing positive selection. In this study, we developed and implemented two deep neural networks and tested their performance to predict loci under recent selection, either due to balancing selection or incomplete sweep, from population genomic data. Specifically, we generated forward-in-time simulations to train and test an artificial neural network (ANN) and a convolutional neural network (CNN). ANN received as input multiple summary statistics calculated on the locus of interest, while CNN was applied directly on the matrix of haplotypes. We found that both architectures have high accuracy to identify loci under recent selection. CNN generally outperformed ANN to distinguish between signals of balancing selection and incomplete sweep and was less affected by incorrect training data. We deployed both trained networks on neutral genomic regions in European populations and demonstrated a lower false-positive rate for CNN than ANN. We finally deployed CNN within the MEFV gene region and identified several common variants predicted to be under incomplete sweep in a European population. Notably, two of these variants are functional changes and could modulate susceptibility to familial Mediterranean fever, possibly as a consequence of past adaptation to pathogens. In conclusion, deep neural networks were able to characterize signals of selection on intermediate frequency variants, an analysis currently inaccessible by commonly used strategies.
Collapse
Affiliation(s)
- Ulas Isildak
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Alessandro Stella
- Laboratory of Medical Genetics, Department of Biomedical Sciences and Human Oncology, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus, Imperial College London, London, UK
| |
Collapse
|
8
|
|
9
|
Ebert D, Fields PD. Host-parasite co-evolution and its genomic signature. Nat Rev Genet 2020; 21:754-768. [PMID: 32860017 DOI: 10.1038/s41576-020-0269-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/14/2023]
Abstract
Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.
Collapse
Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| |
Collapse
|
10
|
Litzke V, Ottensmann M, Forcada J, Heitzmann L, Ivan Hoffman J. Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals. Ecol Evol 2019; 9:7985-7996. [PMID: 31380066 PMCID: PMC6662382 DOI: 10.1002/ece3.5317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 11/08/2022] Open
Abstract
Numerous studies have reported correlations between the heterozygosity of genetic markers and fitness. These heterozygosity-fitness correlations (HFCs) play a central role in evolutionary and conservation biology, yet their mechanistic basis remains open to debate. For example, fitness associations have been widely reported at both neutral and functional loci, yet few studies have directly compared the two, making it difficult to gauge the relative contributions of genome-wide inbreeding and specific functional genes to fitness. Here, we compared the effects of neutral and immune gene heterozygosity on death from bacterial infection in Antarctic fur seal (Arctocephalus gazella) pups. We specifically developed a panel of 13 microsatellites from expressed immune genes and genotyped these together with 48 neutral loci in 234 individuals, comprising 39 pups that were classified at necropsy as having most likely died of bacterial infection together with a five times larger matched sample of healthy surviving pups. Identity disequilibrium quantified from the neutral markers was positive and significant, indicative of variance in inbreeding within the study population. However, multilocus heterozygosity did not differ significantly between healthy and infected pups at either class of marker, and little evidence was found for fitness associations at individual loci. These results support a previous study of Antarctic fur seals that found no effects of heterozygosity at nine neutral microsatellites on neonatal survival and thereby help to refine our understanding of how HFCs vary across the life cycle. Given that nonsignificant HFCs are underreported in the literature, we also hope that our study will contribute toward a more balanced understanding of the wider importance of this phenomenon.
Collapse
Affiliation(s)
- Vivienne Litzke
- Department of Animal BehaviourBielefeld UniversityBielefeldGermany
| | | | | | | | - Joseph Ivan Hoffman
- Department of Animal BehaviourBielefeld UniversityBielefeldGermany
- British Antarctic Survey, High CrossCambridgeUK
| |
Collapse
|
11
|
Altman MO, Gagneux P. Absence of Neu5Gc and Presence of Anti-Neu5Gc Antibodies in Humans-An Evolutionary Perspective. Front Immunol 2019; 10:789. [PMID: 31134048 PMCID: PMC6524697 DOI: 10.3389/fimmu.2019.00789] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/25/2019] [Indexed: 12/31/2022] Open
Abstract
The glycocalyx of human cells differs from that of many other mammals by the lack of the sialic acid N-glycolylneuraminic acid (Neu5Gc) and increased abundance of its precursor N-acetylneuraminic acid (Neu5Ac). Most humans also have circulating antibodies specifically targeting the non-human sialic acid Neu5Gc. Recently, several additional mammalian species have been found to also lack Neu5Gc. In all cases, loss-of-function mutations in the gene encoding the sialic acid-modifying enzyme CMAH are responsible for the drastic change in these species. Unlike other glycan antigens, Neu5Gc apparently cannot be produced by microbes, raising the question about the origin of these antibodies in humans. Dietary exposure and presentation on bacteria coating themselves with Neu5Gc from the diet are distinct possibilities. However, the majority of the non-human species that lack Neu5Gc do not consume diets rich in Neu5Gc, making it unlikely that they will have been immunized against this sialic acid. A notable exception are mustelids (ferrets, martens and their relatives) known for preying on various small mammal species rich in Neu5Gc. No studies exist on levels of anti-Neu5Gc antibodies in non-human species. Evolutionary scenarios for the repeated, independent fixation of CMAH loss-of-function mutations at various time points in the past include strong selection by parasites, especially enveloped viruses, stochastic effects of genetic drift, and directional selection via female immunity to paternal Neu5Gc. Convergent evolution of losses of the vertebrate-specific self-glycan Neu5Gc are puzzling and may represent a prominent way in which glycans become agents of evolutionary change in their own right. Such change may include the reconfiguration of innate immune lectins that use self-sialic acids as recognition patterns.
Collapse
Affiliation(s)
- Meghan O Altman
- Department of Pathology, Biomedical Research and Training Facility 2, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, United States
| | - Pascal Gagneux
- Department of Pathology, Biomedical Research and Training Facility 2, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, United States.,Department of Anthropology, University of California, San Diego, La Jolla, CA, United States
| |
Collapse
|
12
|
Bitarello BD, de Filippo C, Teixeira JC, Schmidt JM, Kleinert P, Meyer D, Andrés AM. Signatures of Long-Term Balancing Selection in Human Genomes. Genome Biol Evol 2018; 10:939-955. [PMID: 29608730 PMCID: PMC5952967 DOI: 10.1093/gbe/evy054] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Balancing selection maintains advantageous diversity in populations through various mechanisms. Although extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here, we describe the Non-central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: ∼0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (P < 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap ∼8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.
Collapse
Affiliation(s)
- Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - João C Teixeira
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Joshua M Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philip Kleinert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| |
Collapse
|
13
|
Keller MC. Evolutionary Perspectives on Genetic and Environmental Risk Factors for Psychiatric Disorders. Annu Rev Clin Psychol 2018; 14:471-493. [DOI: 10.1146/annurev-clinpsy-050817-084854] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew C. Keller
- Department of Psychology and Neuroscience and the Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| |
Collapse
|
14
|
Siewert KM, Voight BF. Detecting Long-Term Balancing Selection Using Allele Frequency Correlation. Mol Biol Evol 2018; 34:2996-3005. [PMID: 28981714 PMCID: PMC5850717 DOI: 10.1093/molbev/msx209] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Balancing selection occurs when multiple alleles are maintained in a population, which can result in their preservation over long evolutionary time periods. A characteristic signature of this long-term balancing selection is an excess number of intermediate frequency polymorphisms near the balanced variant. However, the expected distribution of allele frequencies at these loci has not been extensively detailed, and therefore existing summary statistic methods do not explicitly take it into account. Using simulations, we show that new mutations which arise in close proximity to a site targeted by balancing selection accumulate at frequencies nearly identical to that of the balanced allele. In order to scan the genome for balancing selection, we propose a new summary statistic, β, which detects these clusters of alleles at similar frequencies. Simulation studies show that compared with existing summary statistics, our measure has improved power to detect balancing selection, and is reasonably powered in non-equilibrium demographic models and under a range of recombination and mutation rates. We compute β on 1000 Genomes Project data to identify loci potentially subjected to long-term balancing selection in humans. We report two balanced haplotypes-localized to the genes WFS1 and CADM2-that are strongly linked to association signals for complex traits. Our approach is computationally efficient and applicable to species that lack appropriate outgroup sequences, allowing for well-powered analysis of selection in the wide variety of species for which population data are rapidly being generated.
Collapse
Affiliation(s)
- Katherine M Siewert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin F Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
15
|
Ma Y, Zhang J, Wen L, Lin A. Membrane-lipid associated lncRNA: A new regulator in cancer signaling. Cancer Lett 2018; 419:27-29. [PMID: 29330108 DOI: 10.1016/j.canlet.2018.01.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 01/09/2023]
Abstract
Long noncoding RNAs (LncRNAs) are one of the emerging regulators which are involved in diverse biological processes. LncRNAs can participate in the regulation of gene expression via various ways in the cytoplasm and the nucleus. The function of the nuclear lncRNAs has been studied a lot. Recent studies have shown that the regulatory roles of cytoplasmic lncRNA, including membrane lipid associated lncRNA, which may open an unexplored mechanistic territory. LncRNA dysregulated expression represents a common event in pathogenesis of a variety of human genetic diseases including cancer. Lipid-associated lncRNA is capable of modulating critical cellular functions by directly interacting with phospholipids on the plasma membrane. Besides, it also could be a predictor for the poor prognosis of cancer. In this review, we sum up the roles of cytoplasmic lncRNA, especially lipid-associated lncRNA in cancer.
Collapse
Affiliation(s)
- Yanxiu Ma
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Junmei Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lixia Wen
- Institute of Immunology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Aifu Lin
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| |
Collapse
|
16
|
Lin A, Hu Q, Li C, Xing Z, Ma G, Wang C, Li J, Ye Y, Yao J, Liang K, Wang S, Park PK, Marks JR, Zhou Y, Zhou J, Hung MC, Liang H, Hu Z, Shen H, Hawke DH, Han L, Zhou Y, Lin C, Yang L. The LINK-A lncRNA interacts with PtdIns(3,4,5)P 3 to hyperactivate AKT and confer resistance to AKT inhibitors. Nat Cell Biol 2017; 19:238-251. [PMID: 28218907 PMCID: PMC5332298 DOI: 10.1038/ncb3473] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/12/2017] [Indexed: 12/13/2022]
Abstract
Phosphatidylinositol-3,4,5-trisphosphate (PIP3) mediates signaling pathways as a second messenger in response to extracellular signals. Although primordial functions of phospholipids and RNAs have been hypothesized in the “RNA world”, physiological RNA-phospholipid interactions and their involvement in essential cellular processes has remained a mystery. We explicate the contribution of lipid-binding long non-coding RNAs (lncRNAs) in cancer cells. Among them, Long Intergenic Noncoding RNA for Kinase Activation (LINK-A) directly interacts with AKT pleckstrin homology domain and PIP3 at the single nucleotide level, facilitating AKT-PIP3 interaction and consequent enzymatic activation. LINK-A-dependent AKT hyperactivation leads to tumorigenesis and resistance to AKT inhibitors. Genomic deletions of the LINK-A PIP3-binding motif dramatically sensitized breast cancer cells to AKT inhibitors. Furthermore, meta-analysis showed the correlation between LINK-A expression and incidence of a SNP (rs12095274: A>G), AKT phosphorylation status, and poor outcomes for breast and lung cancer patients. PIP3-binding lncRNA modulates AKT activation with broad clinical implications.
Collapse
Affiliation(s)
- Aifu Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Qingsong Hu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Chunlai Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zhen Xing
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Guolin Ma
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Cheng Wang
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of System Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yin Ye
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ke Liang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shouyu Wang
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Peter K Park
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jeffrey R Marks
- Department of Surgery, Division of Surgical Science, Duke University, School of Medicine, Durham, North Carolina 27710, USA
| | - Yan Zhou
- Department of Oncology, Yixing People's Hospital, Yixing 214200, China
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of System Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - David H Hawke
- Department of System Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
17
|
Croze M, Wollstein A, Božičević V, Živković D, Stephan W, Hutter S. A genome-wide scan for genes under balancing selection in Drosophila melanogaster. BMC Evol Biol 2017; 17:15. [PMID: 28086750 PMCID: PMC5237213 DOI: 10.1186/s12862-016-0857-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/17/2016] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diversity. Several well-known examples of balancing selection have been reported from humans, mice, plants, and parasites. However, only very few systematic studies have been carried out to detect genes under balancing selection. We performed a genome scan in Drosophila melanogaster to find signatures of balancing selection in a derived (European) and an ancestral (African) population. We screened a total of 34 genomes searching for regions of high genetic diversity and an excess of SNPs with intermediate frequency. RESULTS In total, we found 183 candidate genes: 141 in the European population and 45 in the African one, with only three genes shared between both populations. Most differences between both populations were observed on the X chromosome, though this might be partly due to false positives. Functionally, we find an overrepresentation of genes involved in neuronal development and circadian rhythm. Furthermore, some of the top genes we identified are involved in innate immunity. CONCLUSION Our results revealed evidence of genes under balancing selection in European and African populations. More candidate genes have been found in the European population. They are involved in several different functions.
Collapse
Affiliation(s)
- Myriam Croze
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
| | - Andreas Wollstein
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Vedran Božičević
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Daniel Živković
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Center of Food and Life Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Natural History Museum Berlin, 10115, Berlin, Germany
| | - Stephan Hutter
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| |
Collapse
|
18
|
Mika KM, Lynch VJ. An Ancient Fecundability-Associated Polymorphism Switches a Repressor into an Enhancer of Endometrial TAP2 Expression. Am J Hum Genet 2016; 99:1059-1071. [PMID: 27745831 DOI: 10.1016/j.ajhg.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/02/2016] [Indexed: 12/25/2022] Open
Abstract
Variation in female reproductive traits, such as fertility, fecundity, and fecundability, is heritable in humans, but identifying and functionally characterizing genetic variants associated with these traits has been challenging. Here, we explore the functional significance and evolutionary history of a T/C polymorphism of SNP rs2071473, which we have previously shown is an eQTL for TAP2 and significantly associated with fecundability (time to pregnancy). We replicated the association between the rs2071473 genotype and TAP2 expression by using GTEx data and demonstrated that TAP2 is expressed by decidual stromal cells at the maternal-fetal interface. Next, we showed that rs2071473 is located within a progesterone-responsive cis-regulatory element that functions as a repressor with the T allele and an enhancer with the C allele. Remarkably, we found that this polymorphism arose before the divergence of modern and archaic humans, segregates at intermediate to high frequencies across human populations, and has genetic signatures of long-term balancing selection. This variant has also previously been identified in genome-wide association studies of immune-related disease, suggesting that both alleles are maintained as a result of antagonistic pleiotropy.
Collapse
|
19
|
Tian S, Yan H, Neuhauser C, Slager SL. An analytical workflow for accurate variant discovery in highly divergent regions. BMC Genomics 2016; 17:703. [PMID: 27590916 PMCID: PMC5010666 DOI: 10.1186/s12864-016-3045-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/25/2016] [Indexed: 02/07/2023] Open
Abstract
Background Current variant discovery methods often start with the mapping of short reads to a reference genome; yet, their performance deteriorates in genomic regions where the reads are highly divergent from the reference sequence. This is particularly problematic for the human leukocyte antigen (HLA) region on chromosome 6p21.3. This region is associated with over 100 diseases, but variant calling is hindered by the extreme divergence across different haplotypes. Results We simulated reads from chromosome 6 exonic regions over a wide range of sequence divergence and coverage depth. We systematically assessed combinations between five mappers and five callers for their performance on simulated data and exome-seq data from NA12878, a well-studied individual in which multiple public call sets have been generated. Among those combinations, the number of known SNPs differed by about 5 % in the non-HLA regions of chromosome 6 but over 20 % in the HLA region. Notably, GSNAP mapping combined with GATK UnifiedGenotyper calling identified about 20 % more known SNPs than most existing methods without a noticeable loss of specificity, with 100 % sensitivity in three highly polymorphic HLA genes examined. Much larger differences were observed among these combinations in INDEL calling from both non-HLA and HLA regions. We obtained similar results with our internal exome-seq data from a cohort of chronic lymphocytic leukemia patients. Conclusions We have established a workflow enabling variant detection, with high sensitivity and specificity, over the full spectrum of divergence seen in the human genome. Comparing to public call sets from NA12878 has highlighted the overall superiority of GATK UnifiedGenotyper, followed by GATK HaplotypeCaller and SAMtools, in SNP calling, and of GATK HaplotypeCaller and Platypus in INDEL calling, particularly in regions of high sequence divergence such as the HLA region. GSNAP and Novoalign are the ideal mappers in combination with the above callers. We expect that the proposed workflow should be applicable to variant discovery in other highly divergent regions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3045-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shulan Tian
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Huihuang Yan
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Claudia Neuhauser
- Informatics Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Susan L Slager
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA.
| |
Collapse
|
20
|
Lenz TL, Spirin V, Jordan DM, Sunyaev SR. Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection. Mol Biol Evol 2016; 33:2555-64. [PMID: 27436009 PMCID: PMC5026253 DOI: 10.1093/molbev/msw127] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Deleterious mutations are expected to evolve under negative selection and are usually purged from the population. However, deleterious alleles segregate in the human population and some disease-associated variants are maintained at considerable frequencies. Here, we test the hypothesis that balancing selection may counteract purifying selection in neighboring regions and thus maintain deleterious variants at higher frequency than expected from their detrimental fitness effect. We first show in realistic simulations that balancing selection reduces the density of polymorphic sites surrounding a locus under balancing selection, but at the same time markedly increases the population frequency of the remaining variants, including even substantially deleterious alleles. To test the predictions of our simulations empirically, we then use whole-exome sequencing data from 6,500 human individuals and focus on the most established example for balancing selection in the human genome, the major histocompatibility complex (MHC). Our analysis shows an elevated frequency of putatively deleterious coding variants in nonhuman leukocyte antigen (non-HLA) genes localized in the MHC region. The mean frequency of these variants declined with physical distance from the classical HLA genes, indicating dependency on genetic linkage. These results reveal an indirect cost of the genetic diversity maintained by balancing selection, which has hitherto been perceived as mostly advantageous, and have implications both for the evolution of recombination and also for the epidemiology of various MHC-associated diseases.
Collapse
Affiliation(s)
- Tobias L Lenz
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Evolutionary Immunogenomics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Victor Spirin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Daniel M Jordan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Shamil R Sunyaev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA
| |
Collapse
|
21
|
Lee CY. A model for the clustered distribution of SNPs in the human genome. Comput Biol Chem 2016; 64:94-98. [PMID: 27318295 DOI: 10.1016/j.compbiolchem.2016.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/16/2016] [Accepted: 06/06/2016] [Indexed: 12/17/2022]
Abstract
Motivated by a non-random but clustered distribution of SNPs, we introduce a phenomenological model to account for the clustering properties of SNPs in the human genome. The phenomenological model is based on a preferential mutation to the closer proximity of existing SNPs. With the Hapmap SNP data, we empirically demonstrate that the preferential model is better for illustrating the clustered distribution of SNPs than the random model. Moreover, the model is applicable not only to autosomes but also to the X chromosome, although the X chromosome has different characteristics from autosomes. The analysis of the estimated parameters in the model can explain the pronounced population structure and the low genetic diversity of the X chromosome. In addition, correlation between the parameters reveals the population-wise difference of the mutation probability. These results support the mutational non-independence hypothesis against random mutation.
Collapse
Affiliation(s)
- Chang-Yong Lee
- The Department of Industrial and Systems Engineering, Kongju National University, Cheonan 330-717, South Korea.
| |
Collapse
|
22
|
Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era. BMC Genomics 2016; 17:408. [PMID: 27229151 PMCID: PMC4882841 DOI: 10.1186/s12864-016-2734-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 05/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. Results Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. Conclusion This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2734-y) contains supplementary material, which is available to authorized users.
Collapse
|
23
|
The LINK-A lncRNA activates normoxic HIF1α signalling in triple-negative breast cancer. Nat Cell Biol 2016; 18:213-24. [PMID: 26751287 PMCID: PMC4791069 DOI: 10.1038/ncb3295] [Citation(s) in RCA: 410] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022]
Abstract
Although long noncoding RNAs (lncRNAs) predominately reside in nuclear and exert their functions in many biological processes, their potential involvement in cytoplasmic signal transduction remains unexplored. Here, we identified a cytoplasmic lncRNA, Long-Intergenic Noncoding RNA for Kinase Activation (LINK-A), which mediates HB-EGF triggered, EGFR:GPNMB heterodimer-dependent HIF1α phosphorylation at Tyr565 and Ser797 by BRK and LRRK2 respectively. These events cause HIF1α stabilization, HIF1α-p300 interaction, and activation of HIF1α transcriptional programs under normoxic conditions. Mechanistically, LINK-A facilitates the recruitment of BRK to EGFR:GPNMB complex and BRK kinase activation. The BRK-dependent HIF1α Tyr565 phosphorylation interferes with Pro564 hydroxylation, leading to normoxic HIF1α stabilization. Both LINK-A and LINK-A-dependent signaling pathway activation correlate with TNBC, promoting breast cancer glycolysis reprogramming and tumorigenesis. Our findings illustrate the magnitude and diversity of cytoplasmic lncRNAs in signal transduction and highlight the important roles of lncRNAs in cancer.
Collapse
|
24
|
Schrider DR, Kern AD. Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain. Genome Biol Evol 2015; 7:3511-28. [PMID: 26590212 PMCID: PMC4700959 DOI: 10.1093/gbe/evv228] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely missed by searching for sequence conservation across species. Here we present an analysis based on variation data among human genomes that utilizes a supervised machine learning approach for the identification of human-specific purifying selection in the genome. Using only allele frequency information from the complete low-coverage 1000 Genomes Project data set in conjunction with a support vector machine trained from known functional and nonfunctional portions of the genome, we are able to accurately identify portions of the genome constrained by purifying selection. Our method identifies previously known human-specific gains or losses of function and uncovers many novel candidates. Candidate targets for gain and loss of function along the human lineage include numerous putative regulatory regions of genes essential for normal development of the central nervous system, including a significant enrichment of gain of function events near neurotransmitter receptor genes. These results are consistent with regulatory turnover being a key mechanism in the evolution of human-specific characteristics of brain development. Finally, we show that the majority of the genome is unconstrained by natural selection currently, in agreement with what has been estimated from phylogenetic methods but in sharp contrast to estimates based on transcriptomics or other high-throughput functional methods.
Collapse
Affiliation(s)
| | - Andrew D Kern
- Department of Genetics, Rutgers University, Piscataway Human Genetics Institute of New Jersey, Piscataway, New Jersey
| |
Collapse
|
25
|
Haasl RJ, Payseur BA. Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication. Mol Ecol 2015. [PMID: 26224644 DOI: 10.1111/mec.13339] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example F(ST), cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach.
Collapse
Affiliation(s)
- Ryan J Haasl
- Department of Biology, University of Wisconsin-Platteville, 1 University Plaza, Platteville, WI, 53818, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA
| |
Collapse
|
26
|
Fijarczyk A, Babik W. Detecting balancing selection in genomes: limits and prospects. Mol Ecol 2015; 24:3529-45. [DOI: 10.1111/mec.13226] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Wiesław Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| |
Collapse
|
27
|
Morger J, Råberg L, Hille SM, Helsen S, Štefka J, Al-Sabi MM, Kapel CMO, Mappes T, Essbauer S, Ulrich RG, Bartolommei P, Mortelliti A, Balčiauskas L, van den Brink NW, Rémy A, Bajer A, Cheprakov M, Korva M, García-Pérez AL, Biek R, Withenshaw S, Tschirren B. Distinct haplotype structure at the innate immune receptor Toll-like receptor 2 across bank vole populations and lineages in Europe. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12593] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jennifer Morger
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Lars Råberg
- Department of Biology; Lund University; Sölvegatan 35 223 62 Lund Sweden
| | - Sabine M. Hille
- Institute of Wildlife Biology and Game Management; University of Natural Resources and Life Sciences; Gregor Mendel-Strasse 33 1180 Vienna Austria
| | - Sanne Helsen
- Evolutionary Ecology Group; Department of Biology; University of Antwerp; Groenenborgerlaan 171 2020 Antwerp Belgium
| | - Jan Štefka
- Faculty of Science; Biology Centre ASCR; Institute of Parasitology and University of South Bohemia; Branišovská 31 37005 České Budějovice Czech Republic
| | - Mohammad M. Al-Sabi
- Department of Plant and Environmental Sciences; Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Christian M. O. Kapel
- Department of Plant and Environmental Sciences; Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Tapio Mappes
- Department of Biological and Environmental Science; University of Jyväskylä; PO Box 35 40014 Jyväskylä Finland
| | - Sandra Essbauer
- Department Virology and Rickettsiology; Bundeswehr Institute of Microbiology; Neuherbergstrasse 11 80937 Munich Germany
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut; Institute for Novel and Emerging Infectious Diseases; Federal Research Institute for Animal Health; Südufer 10 17493 Greifswald - Insel Riems Germany
| | - Paola Bartolommei
- Fondazione Ethoikos; Convento dell'Osservanza Radicondoli 53030 Siena Italy
| | - Alessio Mortelliti
- Department of Biology and Biotechnology ‘Charles Darwin’; University of Rome ‘La Sapienza’; Viale dell'Università 32 00185 Rome Italy
- National Environmental Research Program; Fenner School of Environment and Society; Australian Research Council Centre for Environmental Decisions; The Australian National University; Canberra ACT 0200 Australia
| | | | - Nico W. van den Brink
- Alterra, Wageningen UR; PO-Box 47 6700 AA Wageningen the Netherlands
- Sub-Department of Toxicology; Wageningen University Wageningen UR; PO-Box 8000 6700 EA Wageningen the Netherlands
| | - Alice Rémy
- Faculty of Applied Ecology and Agricultural Sciences; Hedmark University College; Anne Evenstadsvei 80 2480 Koppang Norway
| | - Anna Bajer
- Department of Parasitology; Faculty of Biology; Institute of Zoology; University of Warsaw; 1 Miecznikowa Street 02-096 Warsaw Poland
| | - Mihail Cheprakov
- Ural Branch; Institute of Plant and Animal Ecology; Russian Academy of Sciences; Str 8 Marta 202 Yekaterinburg 620144 Russia
| | - Misa Korva
- Faculty of Medicine; Institute of Microbiology and Immunology; Zaloška 4 1000 Ljubljana Slovenia
| | - Ana L. García-Pérez
- Department of Animal Health; NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario; Berreaga 1 48160 Derio Bizkaia Spain
| | - Roman Biek
- College of Medical Veterinary and Life Sciences; Boyd Orr Centre for Population and Ecosystem Health; Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Glasgow G12 8QQ UK
| | - Susan Withenshaw
- Department of Evolution, Ecology and Behaviour; Institute of Integrative Biology; University of Liverpool; Crown Street Liverpool L69 7ZB UK
| | - Barbara Tschirren
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| |
Collapse
|
28
|
Villanea FA, Safi KN, Busch JW. A General Model of Negative Frequency Dependent Selection Explains Global Patterns of Human ABO Polymorphism. PLoS One 2015; 10:e0125003. [PMID: 25946124 PMCID: PMC4422588 DOI: 10.1371/journal.pone.0125003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/19/2015] [Indexed: 11/18/2022] Open
Abstract
The ABO locus in humans is characterized by elevated heterozygosity and very similar allele frequencies among populations scattered across the globe. Using knowledge of ABO protein function, we generated a simple model of asymmetric negative frequency dependent selection and genetic drift to explain the maintenance of ABO polymorphism and its loss in human populations. In our models, regardless of the strength of selection, models with large effective population sizes result in ABO allele frequencies that closely match those observed in most continental populations. Populations must be moderately small to fall out of equilibrium and lose either the A or B allele (N(e) ≤ 50) and much smaller (N(e) ≤ 25) for the complete loss of diversity, which nearly always involved the fixation of the O allele. A pattern of low heterozygosity at the ABO locus where loss of polymorphism occurs in our model is consistent with small populations, such as Native American populations. This study provides a general evolutionary model to explain the observed global patterns of polymorphism at the ABO locus and the pattern of allele loss in small populations. Moreover, these results inform the range of population sizes associated with the recent human colonization of the Americas.
Collapse
Affiliation(s)
- Fernando A. Villanea
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington, 99164, United States of America
| | - Kristin N. Safi
- Department of Anthropology, Washington State University, PO Box 644910, Pullman, Washington, 99164, United States of America
| | - Jeremiah W. Busch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington, 99164, United States of America
| |
Collapse
|
29
|
Abstract
We describe the scientific enterprise at the intersection of evolutionary psychology and behavioral genetics-a field that could be termed Evolutionary Behavioral Genetics-and how modern genetic data is revolutionizing our ability to test questions in this field. We first explain how genetically informative data and designs can be used to investigate questions about the evolution of human behavior, and describe some of the findings arising from these approaches. Second, we explain how evolutionary theory can be applied to the investigation of behavioral genetic variation. We give examples of how new data and methods provide insight into the genetic architecture of behavioral variation and what this tells us about the evolutionary processes that acted on the underlying causal genetic variants.
Collapse
Affiliation(s)
- Brendan P Zietsch
- School of Psychology, University of Queensland, Brisbane, Queensland, Australia ; Genetic Epidemiology Laboratory, QIMR Berghofer, Brisbane, Queensland, Australia
| | - Teresa R de Candia
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado, United States of America ; Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Matthew C Keller
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado, United States of America ; Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, United States of America
| |
Collapse
|
30
|
Gao Z, Przeworski M, Sella G. Footprints of ancient-balanced polymorphisms in genetic variation data from closely related species. Evolution 2015; 69:431-46. [PMID: 25403856 PMCID: PMC4335603 DOI: 10.1111/evo.12567] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 10/28/2014] [Indexed: 01/17/2023]
Abstract
When long-lasting, balancing selection can lead to “trans-species” polymorphisms
that are shared by two or more species identical by descent. In such cases, the gene genealogy at
the selected site clusters by allele instead of by species, and nearby neutral sites also have
unusual genealogies because of linkage. While this scenario is expected to leave discernible
footprints in genetic variation data, the specific patterns remain poorly characterized. Motivated
by recent findings in primates, we focus on the case of a biallelic polymorphism under ancient
balancing selection and derive approximations for summaries of the polymorphism data from two
species. Specifically, we characterize the length of the segment that carries most of the
footprints, the expected number of shared neutral single nucleotide polymorphisms (SNPs), and the
patterns of allelic associations among them. We confirm the accuracy of our approximations by
coalescent simulations. We further show that for humans and chimpanzees—more generally, for
pairs of species with low genetic diversity levels—these patterns are highly unlikely to be
generated by neutral recurrent mutations. We discuss the implications for the design and
interpretation of genome scans for ancient balanced polymorphisms in primates and other taxa.
Collapse
Affiliation(s)
- Ziyue Gao
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, 60637.
| | | | | |
Collapse
|
31
|
Hedrick PW. Heterozygote Advantage: The Effect of Artificial Selection in Livestock and Pets. J Hered 2014; 106:141-54. [DOI: 10.1093/jhered/esu070] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
32
|
Continental-scale footprint of balancing and positive selection in a small rodent (Microtus arvalis). PLoS One 2014; 9:e112332. [PMID: 25383542 PMCID: PMC4226552 DOI: 10.1371/journal.pone.0112332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/06/2014] [Indexed: 01/01/2023] Open
Abstract
Genetic adaptation to different environmental conditions is expected to lead to large differences between populations at selected loci, thus providing a signature of positive selection. Whereas balancing selection can maintain polymorphisms over long evolutionary periods and even geographic scale, thus leads to low levels of divergence between populations at selected loci. However, little is known about the relative importance of these two selective forces in shaping genomic diversity, partly due to difficulties in recognizing balancing selection in species showing low levels of differentiation. Here we address this problem by studying genomic diversity in the European common vole (Microtus arvalis) presenting high levels of differentiation between populations (average FST = 0.31). We studied 3,839 Amplified Fragment Length Polymorphism (AFLP) markers genotyped in 444 individuals from 21 populations distributed across the European continent and hence over different environmental conditions. Our statistical approach to detect markers under selection is based on a Bayesian method specifically developed for AFLP markers, which treats AFLPs as a nearly codominant marker system, and therefore has increased power to detect selection. The high number of screened populations allowed us to detect the signature of balancing selection across a large geographic area. We detected 33 markers potentially under balancing selection, hence strong evidence of stabilizing selection in 21 populations across Europe. However, our analyses identified four-times more markers (138) being under positive selection, and geographical patterns suggest that some of these markers are probably associated with alpine regions, which seem to have environmental conditions that favour adaptation. We conclude that despite favourable conditions in this study for the detection of balancing selection, this evolutionary force seems to play a relatively minor role in shaping the genomic diversity of the common vole, which is more influenced by positive selection and neutral processes like drift and demographic history.
Collapse
|
33
|
Novel genomic signals of recent selection in an Ethiopian population. Eur J Hum Genet 2014; 23:1085-92. [PMID: 25370040 DOI: 10.1038/ejhg.2014.233] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 09/17/2014] [Accepted: 09/26/2014] [Indexed: 12/31/2022] Open
Abstract
The recent feasibility of genome-wide studies of adaptation in human populations has provided novel insights into biological pathways that have been affected by adaptive pressures. However, only a few African populations have been investigated using these genome-wide approaches. Here, we performed a genome-wide analysis for evidence of recent positive selection in a sample of 120 individuals of Wolaita ethnicity belonging to Omotic-speaking people who have inhabited the mid- and high-land areas of southern Ethiopia for millennia. Using the 11 HapMap populations as the comparison group, we found Wolaita-specific signals of recent positive selection in several human leukocyte antigen (HLA) loci. Notably, the selected loci overlapped with HLA regions that we previously reported to be associated with podoconiosis-a geochemical lymphedema of the lower legs common in the Wolaita area. We found selection signals in PPARA, a gene involved in energy metabolism during prolonged food deficiency. This finding is consistent with the dietary use of enset, a crop with high-carbohydrate and low-fat and -protein contents domesticated in Ethiopia subsequent to food deprivation 10 000 years ago, and with metabolic adaptation to high-altitude hypoxia. We observed novel selection signals in CDKAL1 and NEGR1, well-known diabetes and obesity susceptibility genes. Finally, the SLC24A5 gene locus known to be associated with skin pigmentation was in the top selection signals in the Wolaita, and the alleles of single-nucleotide polymorphisms rs1426654 and rs1834640 (SLC24A5) associated with light skin pigmentation in Eurasian populations were of high frequency (47.9%) in this Omotic-speaking indigenous Ethiopian population.
Collapse
|
34
|
DeGiorgio M, Lohmueller KE, Nielsen R. A model-based approach for identifying signatures of ancient balancing selection in genetic data. PLoS Genet 2014; 10:e1004561. [PMID: 25144706 PMCID: PMC4140648 DOI: 10.1371/journal.pgen.1004561] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 06/26/2014] [Indexed: 01/19/2023] Open
Abstract
While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated methods for identifying sites under balancing selection. Here we develop two composite likelihood ratio tests for detecting balancing selection. Using simulations, we show that these methods outperform competing methods under a variety of assumptions and demographic models. We apply the new methods to whole-genome human data, and find a number of previously-identified loci with strong evidence of balancing selection, including several HLA genes. Additionally, we find evidence for many novel candidates, the strongest of which is FANK1, an imprinted gene that suppresses apoptosis, is expressed during meiosis in males, and displays marginal signs of segregation distortion. We hypothesize that balancing selection acts on this locus to stabilize the segregation distortion and negative fitness effects of the distorter allele. Thus, our methods are able to reproduce many previously-hypothesized signals of balancing selection, as well as discover novel interesting candidates. In the past, balancing selection was a topic of great theoretical interest that received much attention. However, there has been little focus toward developing methods to identify regions of the genome that are under balancing selection. In this article, we present the first set of likelihood-based methods that explicitly model the spatial distribution of polymorphism expected near a site under long-term balancing selection. Simulation results show that our methods outperform commonly-used summary statistics for identifying regions under balancing selection. Finally, we performed a scan for balancing selection in Africans and Europeans using our new methods and identified a gene called FANK1 as our top candidate outside the HLA region. We hypothesize that the maintenance of polymorphism at FANK1 is the result of segregation distortion.
Collapse
Affiliation(s)
- Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
35
|
A Monte Carlo permutation test for random mating using genome sequences. PLoS One 2013; 8:e71496. [PMID: 23940765 PMCID: PMC3734302 DOI: 10.1371/journal.pone.0071496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/05/2013] [Indexed: 11/19/2022] Open
Abstract
Testing for random mating of a population is important in population genetics, because deviations from randomness of mating may indicate inbreeding, population stratification, natural selection, or sampling bias. However, current methods use only observed numbers of genotypes and alleles, and do not take advantage of the fact that the advent of sequencing technology provides an opportunity to investigate this topic in unprecedented detail. To address this opportunity, a novel statistical test for random mating is required in population genomics studies for which large sequencing datasets are generally available. Here, we propose a Monte-Carlo-based-permutation test (MCP) as an approach to detect random mating. Computer simulations used to evaluate the performance of the permutation test indicate that its type I error is well controlled and that its statistical power is greater than that of the commonly used chi-square test (CHI). Our simulation study shows the power of our test is greater for datasets characterized by lower levels of migration between subpopulations. In addition, test power increases with increasing recombination rate, sample size, and divergence time of subpopulations. For populations exhibiting limited migration and having average levels of population divergence, the statistical power approaches 1 for sequences longer than 1Mbp and for samples of 400 individuals or more. Taken together, our results suggest that our permutation test is a valuable tool to detect random mating of populations, especially in population genomics studies.
Collapse
|
36
|
Hoffman JI, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs. PLoS One 2013; 8:e68365. [PMID: 23874599 PMCID: PMC3712990 DOI: 10.1371/journal.pone.0068365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 05/28/2013] [Indexed: 01/17/2023] Open
Abstract
High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome.
Collapse
Affiliation(s)
- Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, North Rhine-Westphalia, Germany
- * E-mail:
| | - Michael A. S. Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Rob McEwing
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| | - Jaume Forcada
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Rob Ogden
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| |
Collapse
|
37
|
Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A. Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet 2013; 45:723-9. [PMID: 23749186 DOI: 10.1038/ng.2658] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 05/08/2013] [Indexed: 11/09/2022]
Abstract
For decades, it has been hypothesized that gene regulation has had a central role in human evolution, yet much remains unknown about the genome-wide impact of regulatory mutations. Here we use whole-genome sequences and genome-wide chromatin immunoprecipitation and sequencing data to demonstrate that natural selection has profoundly influenced human transcription factor binding sites since the divergence of humans from chimpanzees 4-6 million years ago. Our analysis uses a new probabilistic method, called INSIGHT, for measuring the influence of selection on collections of short, interspersed noncoding elements. We find that, on average, transcription factor binding sites have experienced somewhat weaker selection than protein-coding genes. However, the binding sites of several transcription factors show clear evidence of adaptation. Several measures of selection are strongly correlated with predicted binding affinity. Overall, regulatory elements seem to contribute substantially to both adaptive substitutions and deleterious polymorphisms with key implications for human evolution and disease.
Collapse
Affiliation(s)
- Leonardo Arbiza
- Department of Biological Statistics & Computational Biology, Cornell University, Ithaca, NY, USA
| | | | | | | | | | | | | |
Collapse
|
38
|
Gokcumen O, Zhu Q, Mulder LCF, Iskow RC, Austermann C, Scharer CD, Raj T, Boss JM, Sunyaev S, Price A, Stranger B, Simon V, Lee C. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence. PLoS Genet 2013; 9:e1003404. [PMID: 23593015 PMCID: PMC3623772 DOI: 10.1371/journal.pgen.1003404] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 02/07/2013] [Indexed: 11/25/2022] Open
Abstract
Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations. Natural selection shapes the genome in a non-random way, as an allele that contributes more to the reproductive fitness of a species increases in frequency within the population. Under balancing selection, a particular kind of natural selection, more than one allele increases in frequency in the population, likely due to a reproductive advantage of individuals carrying both alleles. Only a handful of loci have been well documented to evolve under balancing selection, with the HBB gene (sickle cell locus) being the best studied. Here, we report a non-coding (but putatively functional) locus that has maintained two divergent alleles in the human population since before the Human–Neandertal divergence and is therefore likely to be under balancing selection. These findings also provide a clear example for ancient African substructure.
Collapse
Affiliation(s)
- Omer Gokcumen
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Qihui Zhu
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lubbertus C. F. Mulder
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Rebecca C. Iskow
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christian Austermann
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Christopher D. Scharer
- Department of Microbiology, Emory University, Atlanta, Georgia, United States of America
| | - Towfique Raj
- Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Jeremy M. Boss
- Department of Microbiology, Emory University, Atlanta, Georgia, United States of America
| | - Shamil Sunyaev
- Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Alkes Price
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Barbara Stranger
- Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Viviana Simon
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, New York, New York, United States of America
- Division of Infectious Diseases, Department of Medicine, New York, New York, United States of America
- * E-mail: (VS); (CL)
| | - Charles Lee
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (VS); (CL)
| |
Collapse
|
39
|
Cagliani R, Guerini FR, Rubio-Acero R, Baglio F, Forni D, Agliardi C, Griffanti L, Fumagalli M, Pozzoli U, Riva S, Calabrese E, Sikora M, Casals F, Comi GP, Bresolin N, Cáceres M, Clerici M, Sironi M. Long-standing balancing selection in the THBS4 gene: influence on sex-specific brain expression and gray matter volumes in Alzheimer disease. Hum Mutat 2013; 34:743-53. [PMID: 23420636 DOI: 10.1002/humu.22301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/01/2013] [Indexed: 01/08/2023]
Abstract
The THBS4 gene encodes a glycoprotein involved in inflammatory responses and synaptogenesis. THBS4 is expressed at higher levels in the brain of humans compared with nonhuman primates, and the protein accumulates in β-amyloid plaques. We analyzed THBS4 genetic variability in humans and show that two haplotypes (hap1 and hap2) are maintained by balancing selection and modulate THBS4 expression in lymphocytes. Indeed, the balancing selection region covers a predicted transcriptional enhancer. In humans, but not in macaques and chimpanzees, THBS4 brain expression increases with age, and variants in the balancing selection region interact with sex in influencing THBS4 expression (pinteraction = 0.038), with hap1 homozygous females showing lowest expression. In Alzheimer disease (AD) patients, significant interactions between sex and THBS4 genotype were detected for peripheral gray matter (pinteraction = 0.014) and total gray matter (pinteraction = 0.012) volumes. Similarly to the gene expression results, the interaction is mainly mediated by hap1 homozygous AD females, who show reduced volumes. Thus, the balancing selection target in THBS4 is likely represented by one or more variants that regulate tissue-specific and sex-specific gene expression. The selection signature associated with THBS4 might not be related to AD pathogenesis, but rather to inflammatory responses.
Collapse
|
40
|
Cutter AD, Jovelin R, Dey A. Molecular hyperdiversity and evolution in very large populations. Mol Ecol 2013; 22:2074-95. [PMID: 23506466 PMCID: PMC4065115 DOI: 10.1111/mec.12281] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/24/2013] [Accepted: 01/29/2013] [Indexed: 02/06/2023]
Abstract
The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements.
Collapse
Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
| | | | | |
Collapse
|
41
|
Leffler EM, Gao Z, Pfeifer S, Ségurel L, Auton A, Venn O, Bowden R, Bontrop R, Wall JD, Sella G, Donnelly P, McVean G, Przeworski M. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 2013; 339:1578-82. [PMID: 23413192 PMCID: PMC3612375 DOI: 10.1126/science.1234070] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Instances in which natural selection maintains genetic variation in a population over millions of years are thought to be extremely rare. We conducted a genome-wide scan for long-lived balancing selection by looking for combinations of SNPs shared between humans and chimpanzees. In addition to the major histocompatibility complex, we identified 125 regions in which the same haplotypes are segregating in the two species, all but two of which are noncoding. In six cases, there is evidence for an ancestral polymorphism that persisted to the present in humans and chimpanzees. Regions with shared haplotypes are significantly enriched for membrane glycoproteins, and a similar trend is seen among shared coding polymorphisms. These findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets.
Collapse
Affiliation(s)
- Ellen M Leffler
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
van Dongen J, Boomsma DI. The evolutionary paradox and the missing heritability of schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:122-36. [PMID: 23355297 DOI: 10.1002/ajmg.b.32135] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 01/04/2013] [Indexed: 12/11/2022]
Abstract
Schizophrenia is one of the most detrimental common psychiatric disorders, occurring at a prevalence of approximately 1%, and characterized by increased mortality and reduced reproduction, especially in men. The heritability has been estimated around 70% and the genome-wide association meta-analyses conducted by the Psychiatric Genomics Consortium have been successful at identifying an increasing number of risk loci. Various theories have been proposed to explain why genetic variants that predispose to schizophrenia persist in the population, despite the fitness reduction in affected individuals, a question known as the evolutionary paradox. In this review, we consider evolutionary perspectives of schizophrenia and of the empirical evidence that may support these perspectives. Proposed evolutionary explanations include balancing selection, fitness trade-offs, fluctuating environments, sexual selection, mutation-selection balance and genomic conflicts. We address the expectations about the genetic architecture of schizophrenia that are predicted by different evolutionary scenarios and discuss the implications for genetic studies. Several potential sources of "missing" heritability, including gene-environment interactions, epigenetic variation, and rare genetic variation are examined from an evolutionary perspective. A better understanding of evolutionary history may provide valuable clues to the genetic architecture of schizophrenia and other psychiatric disorders, which is highly relevant to genetic studies that aim to detect genetic risk variants.
Collapse
Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands.
| | | |
Collapse
|
43
|
Ségurel L, Thompson EE, Flutre T, Lovstad J, Venkat A, Margulis SW, Moyse J, Ross S, Gamble K, Sella G, Ober C, Przeworski M. The ABO blood group is a trans-species polymorphism in primates. Proc Natl Acad Sci U S A 2012; 109:18493-8. [PMID: 23091028 PMCID: PMC3494955 DOI: 10.1073/pnas.1210603109] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with a current consensus in support of convergent evolution. We show instead that genetic variation data in humans and gibbons as well as in Old World monkeys are inconsistent with a model of convergent evolution and support the hypothesis of an ancient, multiallelic polymorphism of which some alleles are shared by descent among species. These results demonstrate that the A and B blood groups result from a trans-species polymorphism among distantly related species and has remained under balancing selection for tens of millions of years-to date, the only such example in hominoids and Old World monkeys outside of the major histocompatibility complex.
Collapse
Affiliation(s)
- Laure Ségurel
- Department of Human Genetics
- Howard Hughes Medical Institute, and
| | | | - Timothée Flutre
- Department of Human Genetics
- Department of Genetics and Plant Breeding, Institut National de la Recherche Agronomique, Unité de Recherche 1164, 78026 Versailles, France
| | | | | | | | - Jill Moyse
- Lincoln Park Zoo, Chicago, IL 60614; and
| | - Steve Ross
- Lincoln Park Zoo, Chicago, IL 60614; and
| | | | - Guy Sella
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | - Molly Przeworski
- Department of Human Genetics
- Howard Hughes Medical Institute, and
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
| |
Collapse
|
44
|
Roux C, Pauwels M, Ruggiero MV, Charlesworth D, Castric V, Vekemans X. Recent and ancient signature of balancing selection around the S-locus in Arabidopsis halleri and A. lyrata. Mol Biol Evol 2012; 30:435-47. [PMID: 23104079 PMCID: PMC3548311 DOI: 10.1093/molbev/mss246] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Balancing selection can maintain different alleles over long evolutionary times. Beyond this direct effect on the molecular targets of selection, balancing selection is also expected to increase neutral polymorphism in linked genome regions, in inverse proportion to their genetic map distances from the selected sites. The genes controlling plant self-incompatibility are subject to one of the strongest forms of balancing selection, and they show clear signatures of balancing selection. The genome region containing those genes (the S-locus) is generally described as nonrecombining, and the physical size of the region with low recombination has recently been established in a few species. However, the size of the region showing the indirect footprints of selection due to linkage to the S-locus is only roughly known. Here, we improved estimates of this region by surveying synonymous polymorphism and estimating recombination rates at 12 flanking region loci at known physical distances from the S-locus region boundary, in two closely related self-incompatible plants Arabidopsis halleri and A. lyrata. In addition to studying more loci than previous studies and using known physical distances, we simulated an explicit demographic scenario for the divergence between the two species, to evaluate the extent of the genomic region whose diversity departs significantly from neutral expectations. At the closest flanking loci, we detected signatures of both recent and ancient indirect effects of selection on the S-locus flanking genes, finding ancestral polymorphisms shared by both species, as well as an excess of derived mutations private to either species. However, these effects are detected only in a physically small region, suggesting that recombination in the flanking regions is sufficient to quickly break up linkage disequilibrium with the S-locus. Our approach may be useful for distinguishing cases of ancient versus recently evolved balancing selection in other systems.
Collapse
Affiliation(s)
- Camille Roux
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université de Lille, Sciences et Technologies, Villeneuve d'Ascq, France
| | | | | | | | | | | |
Collapse
|
45
|
Hedrick PW. What is the evidence for heterozygote advantage selection? Trends Ecol Evol 2012; 27:698-704. [PMID: 22975220 DOI: 10.1016/j.tree.2012.08.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/09/2012] [Accepted: 08/10/2012] [Indexed: 10/27/2022]
Abstract
Recent genomic data have found that many genes show the signal of selection. How many of these genes are undergoing heterozygote advantage selection is only beginning to be known. Initial genomic surveys have suggested that only a small proportion of loci have polymorphisms maintained by heterozygote advantage and this is consistent with the few examples generated from other approaches within given species. Unless further studies provide large numbers of loci with heterozygote advantage, it appears that loci with heterozygote advantage must be considered only a small minority of all loci in a species. This is not to say that some heterozygote advantage loci do not have important adaptive functions, but that their role in overall evolutionary change might be more of an unusual phenomenon than a major player in adaptation.
Collapse
|
46
|
Abstract
The central preoccupation of human genetics is an effort to understand the genotypic basis of human phenotypic diversity. Although recent progress in identifying the genes that, when mutated, underlie major genetic diseases has been rapid, knowledge of the genetic influences on the vast range of variable, and at least partially heritable, traits that constitute the "normal" range of human phenotypic variation lags. Spectacular advances in our knowledge of human genetic variation have laid the groundwork for a synthesis of insights from medical genetics, population genetics, molecular evolution, and the study of human origins that places basic constraints on models of human genetic individuality. Balancing selection, local adaptation, mutation-selection balance, and founder effects have all extensively shaped contemporary genetic variation. Long-term-balancing selection appears largely to reflect the consequences of host-pathogen arms races. Local adaptation has been widespread-and involved responses to a plethora of selective pressures, some identifiable but most unknown. However, it appears to be a combination of mutation-selection balance and founder effects that largely accounts for genetic individuality. If true, this inference has major implications for future research programs in human genetics.
Collapse
Affiliation(s)
- Maynard V Olson
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
47
|
Hofer T, Foll M, Excoffier L. Evolutionary forces shaping genomic islands of population differentiation in humans. BMC Genomics 2012; 13:107. [PMID: 22439654 PMCID: PMC3317871 DOI: 10.1186/1471-2164-13-107] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 03/22/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Levels of differentiation among populations depend both on demographic and selective factors: genetic drift and local adaptation increase population differentiation, which is eroded by gene flow and balancing selection. We describe here the genomic distribution and the properties of genomic regions with unusually high and low levels of population differentiation in humans to assess the influence of selective and neutral processes on human genetic structure. METHODS Individual SNPs of the Human Genome Diversity Panel (HGDP) showing significantly high or low levels of population differentiation were detected under a hierarchical-island model (HIM). A Hidden Markov Model allowed us to detect genomic regions or islands of high or low population differentiation. RESULTS Under the HIM, only 1.5% of all SNPs are significant at the 1% level, but their genomic spatial distribution is significantly non-random. We find evidence that local adaptation shaped high-differentiation islands, as they are enriched for non-synonymous SNPs and overlap with previously identified candidate regions for positive selection. Moreover there is a negative relationship between the size of islands and recombination rate, which is stronger for islands overlapping with genes. Gene ontology analysis supports the role of diet as a major selective pressure in those highly differentiated islands. Low-differentiation islands are also enriched for non-synonymous SNPs, and contain an overly high proportion of genes belonging to the 'Oncogenesis' biological process. CONCLUSIONS Even though selection seems to be acting in shaping islands of high population differentiation, neutral demographic processes might have promoted the appearance of some genomic islands since i) as much as 20% of islands are in non-genic regions ii) these non-genic islands are on average two times shorter than genic islands, suggesting a more rapid erosion by recombination, and iii) most loci are strongly differentiated between Africans and non-Africans, a result consistent with known human demographic history.
Collapse
Affiliation(s)
- Tamara Hofer
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Matthieu Foll
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| |
Collapse
|
48
|
Frankham R. How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination. Heredity (Edinb) 2012; 108:167-78. [PMID: 21878983 PMCID: PMC3282390 DOI: 10.1038/hdy.2011.66] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Revised: 06/21/2011] [Accepted: 06/27/2011] [Indexed: 11/09/2022] Open
Abstract
Levels of genetic diversity in finite populations are crucial in conservation and evolutionary biology. Genetic diversity is required for populations to evolve and its loss is related to inbreeding in random mating populations, and thus to reduced population fitness and increased extinction risk. Neutral theory is widely used to predict levels of genetic diversity. I review levels of genetic diversity in finite populations in relation to predictions of neutral theory. Positive associations between genetic diversity and population size, as predicted by neutral theory, are observed for microsatellites, allozymes, quantitative genetic variation and usually for mitochondrial DNA (mtDNA). However, there are frequently significant deviations from neutral theory owing to indirect selection at linked loci caused by balancing selection, selective sweeps and background selection. Substantially lower genetic diversity than predicted under neutrality was found for chromosomes with low recombination rates and high linkage disequilibrium (compared with 'normally' recombining chromosomes within species and adjusted for different copy numbers and mutation rates), including W (median 100% lower) and Y (89% lower) chromosomes, dot fourth chromosomes in Drosophila (94% lower) and mtDNA (67% lower). Further, microsatellite genetic and allelic diversity were lost at 12 and 33% faster rates than expected in populations adapting to captivity, owing to widespread selective sweeps. Overall, neither neutral theory nor most versions of the genetic draft hypothesis are compatible with all empirical results.
Collapse
Affiliation(s)
- R Frankham
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.
| |
Collapse
|
49
|
Cagliani R, Guerini FR, Fumagalli M, Riva S, Agliardi C, Galimberti D, Pozzoli U, Goris A, Dubois B, Fenoglio C, Forni D, Sanna S, Zara I, Pitzalis M, Zoledziewska M, Cucca F, Marini F, Comi GP, Scarpini E, Bresolin N, Clerici M, Sironi M. A trans-specific polymorphism in ZC3HAV1 is maintained by long-standing balancing selection and may confer susceptibility to multiple sclerosis. Mol Biol Evol 2012; 29:1599-613. [PMID: 22319148 PMCID: PMC7187542 DOI: 10.1093/molbev/mss002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The human ZC3HAV1 gene encodes an antiviral protein. The longest splicing isoform of ZC3HAV1 contains a C-terminal PARP-like domain, which has evolved under positive selection in primates. We analyzed the evolutionary history of this same domain in humans and in Pan troglodytes. We identified two variants that segregate in both humans and chimpanzees; one of them (rs3735007) does not occur at a hypermutable site and accounts for a nonsynonymous substitution (Thr851Ile). The probability that the two trans-specific polymorphisms have occurred independently in the two lineages was estimated to be low (P = 0.0054), suggesting that at least one of them has arisen before speciation and has been maintained by selection. Population genetic analyses in humans indicated that the region surrounding the shared variants displays strong evidences of long-standing balancing selection. Selection signatures were also observed in a chimpanzee population sample. Inspection of 1000 Genomes data confirmed these findings but indicated that search for selection signatures using low-coverage whole-genome data may need masking of repetitive sequences. A case–control study of more than 1,000 individuals from mainland Italy indicated that the Thr851Ile SNP is significantly associated with susceptibility to multiple sclerosis (MS) (odds ratio [OR] = 1.47, 95% confidence intervals [CI]: 1.08–1.99, P = 0.011). This finding was confirmed in a larger sample of 4,416 Sardinians cases/controls (OR = 1.18, 95% CI: 1.037–1.344, P = 0.011), but not in a population from Belgium. We provide one of the first instances of human/chimpanzee trans-specific coding variant located outside the major histocompatibility complex region. The selective pressure is likely to be virus driven; in modern populations, this variant associates with susceptibility to MS, possibly via the interaction with environmental factors.
Collapse
Affiliation(s)
- R Cagliani
- Scientific Institute IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Del Giudice M. Sex ratio dynamics and fluctuating selection on personality. J Theor Biol 2011; 297:48-60. [PMID: 22185978 DOI: 10.1016/j.jtbi.2011.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 12/01/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
Abstract
Fluctuating selection has often been proposed as an explanation for the maintenance of genetic variation in personality. Here I argue that the temporal dynamics of the sex ratio can be a powerful source of fluctuating selection on personality traits, and develop this hypothesis with respect to humans. First, I review evidence that sex ratios modulate a wide range of social processes related to mating and parenting. Since most personality traits affect mating and parenting behavior, changes in the sex ratio can be expected to result in variable selection on personality. I then show that the temporal dynamics of the sex ratio are intrinsically characterized by fluctuations at various timescales. Finally, I address a number of evolutionary genetic challenges to the hypothesis. I conclude that the sex ratio hypothesis is a plausible explanation of genetic variation in human personality, and may be fruitfully applied to other species as well.
Collapse
Affiliation(s)
- Marco Del Giudice
- Biology of Social Behavior Lab-Center for Cognitive Science, Department of Psychology, University of Turin, via Po 14, 10123 Torino, Italy.
| |
Collapse
|