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Whitehouse LS, Ray D, Schrider DR. Tree sequences as a general-purpose tool for population genetic inference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581288. [PMID: 39185244 PMCID: PMC11343121 DOI: 10.1101/2024.02.20.581288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
As population genetics data increases in size new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient, but are not interchangeable with existing data structures used for many population genetic inference methodologies such as the use of convolutional neural networks (CNNs) applied to population genetic alignments. To better utilize these new data structures we propose and implement a graph convolutional network (GCN) to directly learn from tree sequence topology and node data, allowing for the use of neural network applications without an intermediate step of converting tree sequences to population genetic alignment format. We then compare our approach to standard CNN approaches on a set of previously defined benchmarking tasks including recombination rate estimation, positive selection detection, introgression detection, and demographic model parameter inference. We show that tree sequences can be directly learned from using a GCN approach and can be used to perform well on these common population genetics inference tasks with accuracies roughly matching or even exceeding that of a CNN-based method. As tree sequences become more widely used in population genetics research we foresee developments and optimizations of this work to provide a foundation for population genetics inference moving forward.
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Salazar-Tortosa DF, Huang YF, Enard D. Assessing the Presence of Recent Adaptation in the Human Genome With Mixture Density Regression. Genome Biol Evol 2023; 15:evad170. [PMID: 37713622 PMCID: PMC10563788 DOI: 10.1093/gbe/evad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023] Open
Abstract
How much genome differences between species reflect neutral or adaptive evolution is a central question in evolutionary genomics. In humans and other mammals, the presence of adaptive versus neutral genomic evolution has proven particularly difficult to quantify. The difficulty notably stems from the highly heterogeneous organization of mammalian genomes at multiple levels (functional sequence density, recombination, etc.) which complicates the interpretation and distinction of adaptive versus neutral evolution signals. In this study, we introduce mixture density regressions (MDRs) for the study of the determinants of recent adaptation in the human genome. MDRs provide a flexible regression model based on multiple Gaussian distributions. We use MDRs to model the association between recent selection signals and multiple genomic factors likely to affect the occurrence/detection of positive selection, if the latter was present in the first place to generate these associations. We find that an MDR model with two Gaussian distributions provides an excellent fit to the genome-wide distribution of a common sweep summary statistic (integrated haplotype score), with one of the two distributions likely enriched in positive selection. We further find several factors associated with signals of recent adaptation, including the recombination rate, the density of regulatory elements in immune cells, GC content, gene expression in immune cells, the density of mammal-wide conserved elements, and the distance to the nearest virus-interacting gene. These results support the presence of strong positive selection in recent human evolution and highlight MDRs as a powerful tool to make sense of signals of recent genomic adaptation.
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Affiliation(s)
- Diego F Salazar-Tortosa
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
- Department of Ecology, University of Granada, Granada, Spain
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, State College, Pennsylvania, PA 16801, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, State College, Pennsylvania, PA 16801, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data. Mol Biol Evol 2023; 40:msad216. [PMID: 37772983 PMCID: PMC10581699 DOI: 10.1093/molbev/msad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023] Open
Abstract
Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under nonconvex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data although preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.
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Affiliation(s)
- Md Ruhul Amin
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mahmudul Hasan
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Sandipan Paul Arnab
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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Zhao H, Souilljee M, Pavlidis P, Alachiotis N. Genome-wide scans for selective sweeps using convolutional neural networks. Bioinformatics 2023; 39:i194-i203. [PMID: 37387128 DOI: 10.1093/bioinformatics/btad265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Recent methods for selective sweep detection cast the problem as a classification task and use summary statistics as features to capture region characteristics that are indicative of a selective sweep, thereby being sensitive to confounding factors. Furthermore, they are not designed to perform whole-genome scans or to estimate the extent of the genomic region that was affected by positive selection; both are required for identifying candidate genes and the time and strength of selection. RESULTS We present ASDEC (https://github.com/pephco/ASDEC), a neural-network-based framework that can scan whole genomes for selective sweeps. ASDEC achieves similar classification performance to other convolutional neural network-based classifiers that rely on summary statistics, but it is trained 10× faster and classifies genomic regions 5× faster by inferring region characteristics from the raw sequence data directly. Deploying ASDEC for genomic scans achieved up to 15.2× higher sensitivity, 19.4× higher success rates, and 4× higher detection accuracy than state-of-the-art methods. We used ASDEC to scan human chromosome 1 of the Yoruba population (1000Genomes project), identifying nine known candidate genes.
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Affiliation(s)
- Hanqing Zhao
- Faculty of EEMCS, University of Twente, Enschede, The Netherlands
| | | | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, Greece
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Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor decomposition based feature extraction and classification to detect natural selection from genomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.527731. [PMID: 37034767 PMCID: PMC10081272 DOI: 10.1101/2023.03.27.527731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under non-convex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data while preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx , which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.
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DeGiorgio M, Szpiech ZA. A spatially aware likelihood test to detect sweeps from haplotype distributions. PLoS Genet 2022; 18:e1010134. [PMID: 35404934 PMCID: PMC9022890 DOI: 10.1371/journal.pgen.1010134] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 04/21/2022] [Accepted: 03/04/2022] [Indexed: 01/13/2023] Open
Abstract
The inference of positive selection in genomes is a problem of great interest in evolutionary genomics. By identifying putative regions of the genome that contain adaptive mutations, we are able to learn about the biology of organisms and their evolutionary history. Here we introduce a composite likelihood method that identifies recently completed or ongoing positive selection by searching for extreme distortions in the spatial distribution of the haplotype frequency spectrum along the genome relative to the genome-wide expectation taken as neutrality. Furthermore, the method simultaneously infers two parameters of the sweep: the number of sweeping haplotypes and the "width" of the sweep, which is related to the strength and timing of selection. We demonstrate that this method outperforms the leading haplotype-based selection statistics, though strong signals in low-recombination regions merit extra scrutiny. As a positive control, we apply it to two well-studied human populations from the 1000 Genomes Project and examine haplotype frequency spectrum patterns at the LCT and MHC loci. We also apply it to a data set of brown rats sampled in NYC and identify genes related to olfactory perception. To facilitate use of this method, we have implemented it in user-friendly open source software.
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Affiliation(s)
- Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Zachary A. Szpiech
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
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Harris AM, DeGiorgio M. A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data. Mol Biol Evol 2021; 37:3023-3046. [PMID: 32392293 PMCID: PMC7530616 DOI: 10.1093/molbev/msaa115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverages the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic T to probe whole-genome polymorphism data sets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the T statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the T statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including LCT, RSPH3, and ZNF211 in CEU, SYT1, RGS18, and NNT in YRI, and HLA genes in both populations. We also searched for sweep signatures in Drosophila melanogaster, finding expected candidates at Ace, Uhg1, and Pimet. Finally, we provide open-source software to compute the T statistic and the inferred number of presently sweeping haplotypes from whole-genome data.
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Affiliation(s)
- Alexandre M Harris
- Department of Biology, Pennsylvania State University, University Park, PA.,Molecular, Cellular, and Integrative Biosciences, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL
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DeGiorgio M, Assis R. Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data. Mol Biol Evol 2021; 38:1209-1224. [PMID: 33045078 PMCID: PMC7947822 DOI: 10.1093/molbev/msaa267] [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] [Indexed: 12/12/2022] Open
Abstract
Learning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. A previous method for achieving this goal, CDROM, employs gene expression distances as proxies for functional divergence and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the parameters driving duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built on a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents a major advancement in classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.
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Affiliation(s)
- Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FL 33431
| | - Raquel Assis
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FL 33431
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Lindo J, DeGiorgio M. Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics. Genes (Basel) 2021; 12:360. [PMID: 33801556 PMCID: PMC8001801 DOI: 10.3390/genes12030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/03/2022] Open
Abstract
The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas.
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Affiliation(s)
- John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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