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Glover AN, Sousa VC, Ridenbaugh RD, Sim SB, Geib SM, Linnen CR. Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow. Mol Ecol 2024; 33:e17509. [PMID: 39165007 DOI: 10.1111/mec.17509] [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: 05/03/2024] [Revised: 07/16/2024] [Accepted: 08/02/2024] [Indexed: 08/22/2024]
Abstract
Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non-exclusive processes in shaping genome-wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole-genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister-species pair of haplodiploid pine sawflies, Neodiprion lecontei and Neodiprion pinetum. We find genome-wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns of FST, dXY and π provide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage-specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome-wide patterns of genetic variation.
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Affiliation(s)
- Ashleigh N Glover
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Vitor C Sousa
- Department of Animal Biology, CE3C - Center for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Lisbon, Lisboa, Portugal
| | - Ryan D Ridenbaugh
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Sheina B Sim
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, Hawaii, USA
| | - Scott M Geib
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, Hawaii, USA
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2
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Smith ML, Hahn MW. Selection leads to false inferences of introgression using popular methods. Genetics 2024; 227:iyae089. [PMID: 38805070 DOI: 10.1093/genetics/iyae089] [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: 10/28/2023] [Revised: 10/28/2023] [Accepted: 05/21/2024] [Indexed: 05/29/2024] Open
Abstract
Detecting introgression between closely related populations or species is a fundamental objective in evolutionary biology. Existing methods for detecting migration and inferring migration rates from population genetic data often assume a neutral model of evolution. Growing evidence of the pervasive impact of selection on large portions of the genome across diverse taxa suggests that this assumption is unrealistic in most empirical systems. Further, ignoring selection has previously been shown to negatively impact demographic inferences (e.g. of population size histories). However, the impacts of biologically realistic selection on inferences of migration remain poorly explored. Here, we simulate data under models of background selection, selective sweeps, balancing selection, and adaptive introgression. We show that ignoring selection sometimes leads to false inferences of migration in popularly used methods that rely on the site frequency spectrum. Specifically, balancing selection and some models of background selection result in the rejection of isolation-only models in favor of isolation-with-migration models and lead to elevated estimates of migration rates. BPP, a method that analyzes sequence data directly, showed false positives for all conditions at recent divergence times, but balancing selection also led to false positives at medium-divergence times. Our results suggest that such methods may be unreliable in some empirical systems, such that new methods that are robust to selection need to be developed.
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Affiliation(s)
- Megan L Smith
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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3
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Vaughn AH, Nielsen R. Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA. Mol Biol Evol 2024; 41:msae156. [PMID: 39078618 PMCID: PMC11321360 DOI: 10.1093/molbev/msae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 07/02/2024] [Accepted: 07/10/2024] [Indexed: 07/31/2024] Open
Abstract
We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.
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Affiliation(s)
- Andrew H Vaughn
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720, USA
- Center for GeoGenetics, University of Copenhagen, Copenhagen DK-1350, Denmark
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Serradell JM, Lorenzo-Salazar JM, Flores C, Lao O, Comas D. Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations. Genome Biol 2024; 25:201. [PMID: 39080715 PMCID: PMC11290046 DOI: 10.1186/s13059-024-03341-4] [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: 09/29/2023] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND North African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa. RESULTS We conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through an Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole genomes at > 30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both point to a back-to-Africa origin of North African individuals and a close relationship with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, while GP4PG supports Arabization as the main source of Middle Eastern ancestry. The GP4PG model includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous decaying gene flow after population split. Contrary to ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa. CONCLUSIONS We have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations.
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Affiliation(s)
- Jose M Serradell
- Departament de Medicina i Ciències de la Vida, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona s/n, Santa Cruz de Tenerife, 38600, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona s/n, Santa Cruz de Tenerife, 38600, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Santa Cruz de Tenerife, 38206, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario 145, Santa Cruz de Tenerife, 38010, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, Madrid, 28029, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Calle de La Juventud S/N, Santa María de Guía, Las Palmas de Gran Canaria, 35450, Spain
| | - Oscar Lao
- Departament de Medicina i Ciències de la Vida, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain.
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain.
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5
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Marsh JI, Johri P. Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection. Mol Biol Evol 2024; 41:msae118. [PMID: 38874402 PMCID: PMC11245712 DOI: 10.1093/molbev/msae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While the theoretical biases introduced by the linked effects of selection have been well established, it is unclear whether ancestral recombination graph (ARG)-based approaches to demographic inference in typical empirical analyses are susceptible to misinference due to these effects. To address this, we developed highly realistic forward simulations of human and Drosophila melanogaster populations, including empirically estimated variability of gene density, mutation rates, recombination rates, purifying, and positive selection, across different historical demographic scenarios, to broadly assess the impact of selection on demographic inference using a genealogy-based approach. Our results indicate that the linked effects of selection minimally impact demographic inference for human populations, although it could cause misinference in populations with similar genome architecture and population parameters experiencing more frequent recurrent sweeps. We found that accurate demographic inference of D. melanogaster populations by ARG-based methods is compromised by the presence of pervasive background selection alone, leading to spurious inferences of recent population expansion, which may be further worsened by recurrent sweeps, depending on the proportion and strength of beneficial mutations. Caution and additional testing with species-specific simulations are needed when inferring population history with non-human populations using ARG-based approaches to avoid misinference due to the linked effects of selection.
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Affiliation(s)
- Jacob I Marsh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Parul Johri
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
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6
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Yang X, Su Y, Huang S, Hou Q, Wei P, Hao Y, Huang J, Xiao H, Ma Z, Xu X, Wang X, Cao S, Cao X, Zhang M, Wen X, Ma Y, Peng Y, Zhou Y, Cao K, Qiao G. Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex. HORTICULTURE RESEARCH 2024; 11:uhae109. [PMID: 38883333 PMCID: PMC11179850 DOI: 10.1093/hr/uhae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/06/2024] [Indexed: 06/18/2024]
Abstract
The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits; however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aimed to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the apricot-peach-plum-mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes 251.25 and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of ~1.17 Mb in the apricot genomes compared with peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting titratable acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stress tolerance, flower development, and fruit ripening, along with divergent selection shaping specific crop, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal collinearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.
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Affiliation(s)
- Xuanwen Yang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou 450009, China
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Xinjiang, Urumqi 830046, China
| | - Siyang Huang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Pengcheng Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou 450009, China
| | - Yani Hao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Jiaqi Huang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuejing Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mengyan Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Yuhua Ma
- Institute of Pomology Science, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 570100, China
| | - Ke Cao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou 450009, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China
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7
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Rodrigues MF, Kern AD, Ralph PL. Shared evolutionary processes shape landscapes of genomic variation in the great apes. Genetics 2024; 226:iyae006. [PMID: 38242701 PMCID: PMC10990428 DOI: 10.1093/genetics/iyae006] [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: 10/26/2023] [Revised: 10/26/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024] Open
Abstract
For at least the past 5 decades, population genetics, as a field, has worked to describe the precise balance of forces that shape patterns of variation in genomes. The problem is challenging because modeling the interactions between evolutionary processes is difficult, and different processes can impact genetic variation in similar ways. In this paper, we describe how diversity and divergence between closely related species change with time, using correlations between landscapes of genetic variation as a tool to understand the interplay between evolutionary processes. We find strong correlations between landscapes of diversity and divergence in a well-sampled set of great ape genomes, and explore how various processes such as incomplete lineage sorting, mutation rate variation, GC-biased gene conversion and selection contribute to these correlations. Through highly realistic, chromosome-scale, forward-in-time simulations, we show that the landscapes of diversity and divergence in the great apes are too well correlated to be explained via strictly neutral processes alone. Our best fitting simulation includes both deleterious and beneficial mutations in functional portions of the genome, in which 9% of fixations within those regions is driven by positive selection. This study provides a framework for modeling genetic variation in closely related species, an approach which can shed light on the complex balance of forces that have shaped genetic variation.
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Affiliation(s)
- Murillo F Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Andrew D Kern
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
- Department of Mathematics, University of Oregon, Eugene, OR 97403, USA
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8
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Matheson J, Masel J. Background Selection From Unlinked Sites Causes Nonindependent Evolution of Deleterious Mutations. Genome Biol Evol 2024; 16:evae050. [PMID: 38482769 PMCID: PMC10972689 DOI: 10.1093/gbe/evae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
Background selection describes the reduction in neutral diversity caused by selection against deleterious alleles at other loci. It is typically assumed that the purging of deleterious alleles affects linked neutral variants, and indeed simulations typically only treat a genomic window. However, background selection at unlinked loci also depresses neutral diversity. In agreement with previous analytical approximations, in our simulations of a human-like genome with a realistically high genome-wide deleterious mutation rate, the effects of unlinked background selection exceed those of linked background selection. Background selection reduces neutral genetic diversity by a factor that is independent of census population size. Outside of genic regions, the strength of background selection increases with the mean selection coefficient, contradicting the linked theory but in agreement with the unlinked theory. Neutral diversity within genic regions is fairly independent of the strength of selection. Deleterious genetic load among haploid individuals is underdispersed, indicating nonindependent evolution of deleterious mutations. Empirical evidence for underdispersion was previously interpreted as evidence for global epistasis, but we recover it from a non-epistatic model.
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Affiliation(s)
- Joseph Matheson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Ecology, Behavior, and Evolution, University of California San Diego, San Diego, CA 92093, USA
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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9
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Zurita AMI, Kyriazis CC, Lohmueller KE. The impact of non-neutral synonymous mutations when inferring selection on non-synonymous mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579314. [PMID: 38370782 PMCID: PMC10871344 DOI: 10.1101/2024.02.07.579314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The distribution of fitness effects (DFE) describes the proportions of new mutations that have different effects on reproductive fitness. Accurate measurements of the DFE are important because the DFE is a fundamental parameter in evolutionary genetics and has implications for our understanding of other phenomena like complex disease or inbreeding depression. Current computational methods to infer the DFE for nonsynonymous mutations from natural variation first estimate demographic parameters from synonymous variants to control for the effects of demography and background selection. Then, conditional on these parameters, the DFE is then inferred for nonsynonymous mutations. This approach relies on the assumption that synonymous variants are neutrally evolving. However, some evidence points toward synonymous mutations having measurable effects on fitness. To test whether selection on synonymous mutations affects inference of the DFE of nonsynonymous mutations, we simulated several possible models of selection on synonymous mutations using SLiM and attempted to recover the DFE of nonsynonymous mutations using Fit∂a∂i, a common method for DFE inference. Our results show that the presence of selection on synonymous variants leads to incorrect inferences of recent population growth. Furthermore, under certain parameter combinations, inferences of the DFE can have an inflated proportion of highly deleterious nonsynonymous mutations. However, this bias can be eliminated if the correct demographic parameters are used for DFE inference instead of the biased ones inferred from synonymous variants. Our work demonstrates how unmodeled selection on synonymous mutations may affect downstream inferences of the DFE.
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Affiliation(s)
- Aina Martinez I Zurita
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Kirk E Lohmueller
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
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10
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Soni V, Pfeifer SP, Jensen JD. The Effects of Mutation and Recombination Rate Heterogeneity on the Inference of Demography and the Distribution of Fitness Effects. Genome Biol Evol 2024; 16:evae004. [PMID: 38207127 PMCID: PMC10834165 DOI: 10.1093/gbe/evae004] [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: 08/31/2023] [Revised: 12/12/2023] [Accepted: 01/07/2024] [Indexed: 01/13/2024] Open
Abstract
Disentangling the effects of demography and selection has remained a focal point of population genetic analysis. Knowledge about mutation and recombination is essential in this endeavor; however, despite clear evidence that both mutation and recombination rates vary across genomes, it is common practice to model both rates as fixed. In this study, we quantify how this unaccounted for rate heterogeneity may impact inference using common approaches for inferring selection (DFE-alpha, Grapes, and polyDFE) and/or demography (fastsimcoal2 and δaδi). We demonstrate that, if not properly modeled, this heterogeneity can increase uncertainty in the estimation of demographic and selective parameters and in some scenarios may result in mis-leading inference. These results highlight the importance of quantifying the fundamental evolutionary parameters of mutation and recombination before utilizing population genomic data to quantify the effects of genetic drift (i.e. as modulated by demographic history) and selection; or, at the least, that the effects of uncertainty in these parameters can and should be directly modeled in downstream inference.
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Affiliation(s)
- Vivak Soni
- School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ, USA
| | - Susanne P Pfeifer
- School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ, USA
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11
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de Jong MJ, van Oosterhout C, Hoelzel AR, Janke A. Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid? Biol Rev Camb Philos Soc 2024; 99:23-55. [PMID: 37621151 DOI: 10.1111/brv.13010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
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Affiliation(s)
- Menno J de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
| | - Cock van Oosterhout
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse 9, Frankfurt am Main, 60438, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, 60325, Germany
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12
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Thom G, Moreira LR, Batista R, Gehara M, Aleixo A, Smith BT. Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds. Genome Biol Evol 2024; 16:evae002. [PMID: 38236173 PMCID: PMC10823491 DOI: 10.1093/gbe/evae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lucas Rocha Moreira
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Romina Batista
- Programa de Coleções Biológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
- School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Department of Environmental Genomics, Instituto Tecnológico Vale, Belém, Brazil
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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13
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Marchi N, Kapopoulou A, Excoffier L. Demogenomic inference from spatially and temporally heterogeneous samples. Mol Ecol Resour 2024; 24:e13877. [PMID: 37819677 DOI: 10.1111/1755-0998.13877] [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: 04/24/2023] [Revised: 09/15/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Modern and ancient genomes are not necessarily drawn from homogeneous populations, as they may have been collected from different places and at different times. This heterogeneous sampling can be an issue for demographic inferences and results in biased demographic parameters and incorrect model choice if not properly considered. When explicitly accounted for, it can result in very complex models and high data dimensionality that are difficult to analyse. In this paper, we formally study the impact of such spatial and temporal sampling heterogeneity on demographic inference, and we introduce a way to circumvent this problem. To deal with structured samples without increasing the dimensionality of the site frequency spectrum (SFS), we introduce a new structured approach to the existing program fastsimcoal2. We assess the efficiency and relevance of this methodological update with simulated and modern human genomic data. We particularly focus on spatial and temporal heterogeneities to evidence the interest of this new SFS-based approach, which can be especially useful when handling scattered and ancient DNA samples, as in conservation genetics or archaeogenetics.
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Affiliation(s)
- Nina Marchi
- CMPG, Institute for Ecology and Evolution, University of Berne, Berne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Adamandia Kapopoulou
- CMPG, Institute for Ecology and Evolution, University of Berne, Berne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Laurent Excoffier
- CMPG, Institute for Ecology and Evolution, University of Berne, Berne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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14
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Schrider DR. Allelic gene conversion softens selective sweeps. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570141. [PMID: 38106127 PMCID: PMC10723294 DOI: 10.1101/2023.12.05.570141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The prominence of positive selection, in which beneficial mutations are favored by natural selection and rapidly increase in frequency, is a subject of intense debate. Positive selection can result in selective sweeps, in which the haplotype(s) bearing the adaptive allele "sweep" through the population, thereby removing much of the genetic diversity from the region surrounding the target of selection. Two models of selective sweeps have been proposed: classical sweeps, or "hard sweeps", in which a single copy of the adaptive allele sweeps to fixation, and "soft sweeps", in which multiple distinct copies of the adaptive allele leave descendants after the sweep. Soft sweeps can be the outcome of recurrent mutation to the adaptive allele, or the presence of standing genetic variation consisting of multiple copies of the adaptive allele prior to the onset of selection. Importantly, soft sweeps will be common when populations can rapidly adapt to novel selective pressures, either because of a high mutation rate or because adaptive alleles are already present. The prevalence of soft sweeps is especially controversial, and it has been noted that selection on standing variation or recurrent mutations may not always produce soft sweeps. Here, we show that the inverse is true: selection on single-origin de novo mutations may often result in an outcome that is indistinguishable from a soft sweep. This is made possible by allelic gene conversion, which "softens" hard sweeps by copying the adaptive allele onto multiple genetic backgrounds, a process we refer to as a "pseudo-soft" sweep. We carried out a simulation study examining the impact of gene conversion on sweeps from a single de novo variant in models of human, Drosophila, and Arabidopsis populations. The fraction of simulations in which gene conversion had produced multiple haplotypes with the adaptive allele upon fixation was appreciable. Indeed, under realistic demographic histories and gene conversion rates, even if selection always acts on a single-origin mutation, sweeps involving multiple haplotypes are more likely than hard sweeps in large populations, especially when selection is not extremely strong. Thus, even when the mutation rate is low or there is no standing variation, hard sweeps are expected to be the exception rather than the rule in large populations. These results also imply that the presence of signatures of soft sweeps does not necessarily mean that adaptation has been especially rapid or is not mutation limited.
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Affiliation(s)
- Daniel R Schrider
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
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15
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Haltom J, Trovao NS, Guarnieri J, Vincent P, Singh U, Tsoy S, O'Leary CA, Bram Y, Widjaja GA, Cen Z, Meller R, Baylin SB, Moss WN, Nikolau BJ, Enguita FJ, Wallace DC, Beheshti A, Schwartz R, Wurtele ES. SARS-CoV-2 Orphan Gene ORF10 Contributes to More Severe COVID-19 Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.27.23298847. [PMID: 38076862 PMCID: PMC10705665 DOI: 10.1101/2023.11.27.23298847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The orphan gene of SARS-CoV-2, ORF10, is the least studied gene in the virus responsible for the COVID-19 pandemic. Recent experimentation indicated ORF10 expression moderates innate immunity in vitro. However, whether ORF10 affects COVID-19 in humans remained unknown. We determine that the ORF10 sequence is identical to the Wuhan-Hu-1 ancestral haplotype in 95% of genomes across five variants of concern (VOC). Four ORF10 variants are associated with less virulent clinical outcomes in the human host: three of these affect ORF10 protein structure, one affects ORF10 RNA structural dynamics. RNA-Seq data from 2070 samples from diverse human cells and tissues reveals ORF10 accumulation is conditionally discordant from that of other SARS-CoV-2 transcripts. Expression of ORF10 in A549 and HEK293 cells perturbs immune-related gene expression networks, alters expression of the majority of mitochondrially-encoded genes of oxidative respiration, and leads to large shifts in levels of 14 newly-identified transcripts. We conclude ORF10 contributes to more severe COVID-19 clinical outcomes in the human host.
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Affiliation(s)
- Jeffrey Haltom
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Nidia S Trovao
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Pan Vincent
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
| | - Sergey Tsoy
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Collin A O'Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Gabrielle A Widjaja
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zimu Cen
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Meller
- Morehouse School of Medicine, Atlanta, GA , 30310-1495, USA
| | - Stephen B Baylin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231
- Van Andel Research Institute, Grand Rapids, MI 49503
| | - Walter N Moss
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Basil J Nikolau
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Blue Marble Space Institute of Science, Seattle, WA, 98104 USA
| | - Robert Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
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16
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Soni V, Pfeifer SP, Jensen JD. The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566703. [PMID: 38014252 PMCID: PMC10680612 DOI: 10.1101/2023.11.11.566703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Disentangling the effects of demography and selection has remained a focal point of population genetic analysis. Knowledge about mutation and recombination is essential in this endeavour; however, despite clear evidence that both mutation and recombination rates vary across genomes, it is common practice to model both rates as fixed. In this study, we quantify how this unaccounted for rate heterogeneity may impact inference using common approaches for inferring selection (DFE-alpha, Grapes, and polyDFE) and/or demography (fastsimcoal2 and δaδi). We demonstrate that, if not properly modelled, this heterogeneity can increase uncertainty in the estimation of demographic and selective parameters and in some scenarios may result in mis-leading inference. These results highlight the importance of quantifying the fundamental evolutionary parameters of mutation and recombination prior to utilizing population genomic data to quantify the effects of genetic drift (i.e., as modulated by demographic history) and selection; or, at the least, that the effects of uncertainty in these parameters can and should be directly modelled in downstream inference.
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Affiliation(s)
- Vivak Soni
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine
| | - Susanne P. Pfeifer
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine
| | - Jeffrey D. Jensen
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine
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17
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Quilodrán CS, Rio J, Tsoupas A, Currat M. Past human expansions shaped the spatial pattern of Neanderthal ancestry. SCIENCE ADVANCES 2023; 9:eadg9817. [PMID: 37851812 PMCID: PMC10584333 DOI: 10.1126/sciadv.adg9817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023]
Abstract
The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.
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Affiliation(s)
| | - Jérémy Rio
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Alexandros Tsoupas
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
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18
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Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes. PLoS Genet 2023; 19:e1010931. [PMID: 37676865 PMCID: PMC10508636 DOI: 10.1371/journal.pgen.1010931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 09/19/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023] Open
Abstract
f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data-that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed-but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True "outgroup ascertainment" is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the "Affymetrix Human Origins array" which has been genotyped on thousands of modern individuals from hundreds of populations, or the "1240k" in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.
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Affiliation(s)
- Pavel Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Russia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
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19
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Liao K, Carlson J, Zöllner S. The effect of mutation subtypes on the allele frequency spectrum and population genetics inference. G3 (BETHESDA, MD.) 2023; 13:jkad035. [PMID: 36759699 PMCID: PMC10085755 DOI: 10.1093/g3journal/jkad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/11/2023]
Abstract
Population genetics has adapted as technological advances in next-generation sequencing have resulted in an exponential increase of genetic data. A common approach to efficiently analyze genetic variation present in large sequencing data is through the allele frequency spectrum, defined as the distribution of allele frequencies in a sample. While the frequency spectrum serves to summarize patterns of genetic variation, it implicitly assumes mutation types (A→C vs C→T) as interchangeable. However, mutations of different types arise and spread due to spatial and temporal variation in forces such as mutation rate and biased gene conversion that result in heterogeneity in the distribution of allele frequencies across sites. In this work, we explore the impact of this simplification on multiple aspects of population genetic modeling. As a site's mutation rate is strongly affected by flanking nucleotides, we defined a mutation subtype by the base pair change and adjacent nucleotides (e.g. AAA→ATA) and systematically assessed the heterogeneity in the frequency spectrum across 96 distinct 3-mer mutation subtypes using n = 3556 whole-genome sequenced individuals of European ancestry. We observed substantial variation across the subtype-specific frequency spectra, with some of the variation being influenced by molecular factors previously identified for single base mutation types. Estimates of model parameters from demographic inference performed for each mutation subtype's AFS individually varied drastically across the 96 subtypes. In local patterns of variation, a combination of regional subtype composition and local genomic factors shaped the regional frequency spectrum across genomic regions. Our results illustrate how treating variants in large sequencing samples as interchangeable may confound population genetic frameworks and encourages us to consider the unique evolutionary mechanisms of analyzed polymorphisms.
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Affiliation(s)
- Kevin Liao
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jedidiah Carlson
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
- Department of Population Health, University of Texas at Austin, Austin, TX 78712, USA
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
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20
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Terbot JW, Johri P, Liphardt SW, Soni V, Pfeifer SP, Cooper BS, Good JM, Jensen JD. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. PLoS Pathog 2023; 19:e1011265. [PMID: 37018331 PMCID: PMC10075409 DOI: 10.1371/journal.ppat.1011265] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a global health crisis. In response, genomic surveillance efforts have proliferated in the hopes of tracking and anticipating the evolution of this virus, resulting in millions of patient isolates now being available in public databases. Yet, while there is a tremendous focus on identifying newly emerging adaptive viral variants, this quantification is far from trivial. Specifically, multiple co-occurring and interacting evolutionary processes are constantly in operation and must be jointly considered and modeled in order to perform accurate inference. We here outline critical individual components of such an evolutionary baseline model-mutation rates, recombination rates, the distribution of fitness effects, infection dynamics, and compartmentalization-and describe the current state of knowledge pertaining to the related parameters of each in SARS-CoV-2. We close with a series of recommendations for future clinical sampling, model construction, and statistical analysis.
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Affiliation(s)
- John W Terbot
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Parul Johri
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Schuyler W Liphardt
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Vivak Soni
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Susanne P Pfeifer
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Brandon S Cooper
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey M Good
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey D Jensen
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
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21
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Freund F, Kerdoncuff E, Matuszewski S, Lapierre M, Hildebrandt M, Jensen JD, Ferretti L, Lambert A, Sackton TB, Achaz G. Interpreting the pervasive observation of U-shaped Site Frequency Spectra. PLoS Genet 2023; 19:e1010677. [PMID: 36952570 PMCID: PMC10072462 DOI: 10.1371/journal.pgen.1010677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 04/04/2023] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.
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Affiliation(s)
- Fabian Freund
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Elise Kerdoncuff
- Department of Genetics, University of California, Berkeley, California, United States of America
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Marguerite Lapierre
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Jeffrey D Jensen
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Amaury Lambert
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, Paris, France
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | - Timothy B Sackton
- Éco-anthropologie, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
| | - Guillaume Achaz
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
- SMILE group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Paris, France
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22
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Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. Modeling of African population history using f -statistics can be highly biased and is not addressed by previously suggested SNP ascertainment schemes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525077. [PMID: 36711923 PMCID: PMC9882349 DOI: 10.1101/2023.01.22.525077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
f -statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. These statistics can provide strong evidence for either admixture or cladality, which can be robust to substantial rates of errors or missing data. f -statistics are guaranteed to be unbiased under "SNP ascertainment" (analyzing non-randomly chosen subsets of single nucleotide polymorphisms) only if it relies on a population that is an outgroup for all groups analyzed. However, ascertainment on a true outgroup that is not co-analyzed with other populations is often impractical and uncommon in the literature. In this study focused on practical rather than theoretical aspects of SNP ascertainment, we show that many non-outgroup ascertainment schemes lead to false rejection of true demographic histories, as well as to failure to reject incorrect models. But the bias introduced by common ascertainments such as the 1240K panel is mostly limited to situations when more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans) or non-human outgroups are co-modelled, for example, f 4 -statistics involving one non-African group, two African groups, and one archaic group. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, cannot fix all these problems since for some classes of f -statistics it is not a clean outgroup ascertainment, and in other cases it demonstrates relatively low power to reject incorrect demographic models since it provides a relatively small number of variants common in anatomically modern humans. And due to the paucity of high-coverage archaic genomes, archaic individuals used for ascertainment often act as sole representatives of the respective groups in an analysis, and we show that this approach is highly problematic. By carrying out large numbers of simulations of diverse demographic histories, we find that bias in inferences based on f -statistics introduced by non-outgroup ascertainment can be minimized if the derived allele frequency spectrum in the population used for ascertainment approaches the spectrum that existed at the root of all groups being co-analyzed. Ascertaining on sites with variants common in a diverse group of African individuals provides a good approximation to such a set of SNPs, addressing the great majority of biases and also retaining high statistical power for studying population history. Such a "pan-African" ascertainment, although not completely problem-free, allows unbiased exploration of demographic models for the widest set of archaic and modern human populations, as compared to the other ascertainment schemes we explored.
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Affiliation(s)
- Pavel Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Russia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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23
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Mooney JA, Marsden CD, Yohannes A, Wayne RK, Lohmueller KE. Long-term Small Population Size, Deleterious Variation, and Altitude Adaptation in the Ethiopian Wolf, a Severely Endangered Canid. Mol Biol Evol 2023; 40:msac277. [PMID: 36585842 PMCID: PMC9847632 DOI: 10.1093/molbev/msac277] [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: 08/18/2022] [Revised: 11/07/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023] Open
Abstract
Ethiopian wolves, a canid species endemic to the Ethiopian Highlands, have been steadily declining in numbers for decades. Currently, out of 35 extant species, it is now one of the world's most endangered canids. Most conservation efforts have focused on preventing disease, monitoring movements and behavior, and assessing the geographic ranges of sub-populations. Here, we add an essential layer by determining the Ethiopian wolf's demographic and evolutionary history using high-coverage (∼40×) whole-genome sequencing from 10 Ethiopian wolves from the Bale Mountains. We observe exceptionally low diversity and enrichment of weakly deleterious variants in the Ethiopian wolves in comparison with two North American gray wolf populations and four dog breeds. These patterns are consequences of long-term small population size, rather than recent inbreeding. We infer the demographic history of the Ethiopian wolf and find it to be concordant with historic records and previous genetic analyses, suggesting Ethiopian wolves experienced a series of both ancient and recent bottlenecks, resulting in a census population size of fewer than 500 individuals and an estimated effective population size of approximately 100 individuals. Additionally, long-term small population size may have limited the accumulation of strongly deleterious recessive mutations. Finally, as the Ethiopian wolves have inhabited high-altitude areas for thousands of years, we searched for evidence of high-altitude adaptation, finding evidence of positive selection at a transcription factor in a hypoxia-response pathway [CREB-binding protein (CREBBP)]. Our findings are pertinent to continuing conservation efforts and understanding how demography influences the persistence of deleterious variation in small populations.
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Affiliation(s)
- Jazlyn A Mooney
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Clare D Marsden
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Abigail Yohannes
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Robert K Wayne
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Kirk E Lohmueller
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
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24
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Árnason E, Koskela J, Halldórsdóttir K, Eldon B. Sweepstakes reproductive success via pervasive and recurrent selective sweeps. eLife 2023; 12:80781. [PMID: 36806325 PMCID: PMC9940914 DOI: 10.7554/elife.80781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/28/2022] [Indexed: 02/22/2023] Open
Abstract
Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here, we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modelling no sweepstakes) and the Xi-Beta coalescent (modelling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.
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Affiliation(s)
- Einar Árnason
- Institute of Life- and environmental Sciences, University of IcelandReykjavikIceland,Department of Organismal and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Jere Koskela
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Katrín Halldórsdóttir
- Institute of Life- and environmental Sciences, University of IcelandReykjavikIceland
| | - Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Science, Museum für NaturkundeBerlinGermany
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25
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Assis JEDE, Souza JRBDE, Fitzhugh K, Christoffersen ML. A new species of Euclymene (Maldanidae, Annelida) from Brazil, with new combinations, and phylogenetic implications for Euclymeninae. AN ACAD BRAS CIENC 2022; 94:e20210283. [PMID: 36541974 DOI: 10.1590/0001-3765202220210283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/27/2021] [Indexed: 12/23/2022] Open
Abstract
Maldanids are tube-building polychaetes, known as bamboo-worms; inhabit diverse marine regions throughout the world. The subfamily Euclymeninae was proposed to include forms with anal and cephalic plates, a funnel-shaped pygidium, and a terminal anus. Euclymene, the type genus of Euclymeninae, has about 18 valid species. Euclymene vidali sp. nov. is defined and members of the species described from Northeastern Brazil. Members of this species have 23 chaetigers, and one pre-pygidial achaetous segment; nuchal grooves extend through three quarters of the cephalic plate, and there is one acicular spine with a denticulate tip. Euclymene africana, and E. watsoni, are here recognized, respectively, as Isocirrus africana comb. nov., and I. watsoni comb. nov. Three monotypic genera are invalid: Macroclymenella, Eupraxillella, and Pseudoclyemene; their species should be recognized as Clymenella stewartensis com. nov., Praxillella antarctica com. nov., and Praxillela quadrilobata com. nov., respectively. An identification key and a comparative table for all species of Euclymene are provided. A comparative table for all genera of Euclymeninae is also furnished. The paraphyletic status of Euclymene and Euclymeninae is discussed. The taxon Maldanoplaca is not code compliant and should only be regarded as an informal name.
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Affiliation(s)
- José Eriberto DE Assis
- Prefeitura Municipal de Bayeux, Departamento de Educação Básica, Rua Santa Tereza, 600, 58306-070 Bayeux, PB, Brazil
| | - José Roberto Botelho DE Souza
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Zoologia, Av. Prof. Morais Rego, 1235, 50670-901 Recife, PE, Brazil
| | - Kirk Fitzhugh
- Natural History Museum of Los Angeles County, 900 Exposition Blvd, 90007 Los Angeles, California, USA
| | - Martin Lindsey Christoffersen
- Universidade Federal da Paraíba, Centro de Ciências Exatas e da Natureza, Departamento de Sistemática e Ecologia, Cidade Universitária, 58059-900 João Pessoa, PB, Brazil
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26
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Charlesworth B, Jensen JD. Some complexities in interpreting apparent effects of hitchhiking: A commentary on Gompert et al. (2022). Mol Ecol 2022; 31:4440-4443. [PMID: 35778972 PMCID: PMC9536517 DOI: 10.1111/mec.16573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/24/2022] [Accepted: 06/06/2022] [Indexed: 12/25/2022]
Abstract
We write to address recent claims by regarding the potentially important and underappreciated phenomena of "indirect selection," the observation that neutral regions may be affected by natural selection. We argue both that this phenomenon-generally known as genetic hitchhiking-is neither new nor poorly studied, and that the patterns described by the authors have multiple alternative explanations.
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Affiliation(s)
- Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological
Sciences, University of Edinburgh, Edinburgh, UK
| | - Jeffrey D. Jensen
- School of Life Sciences, Arizona State University, Tempe,
Arizona, USA
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27
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Gompert Z, Feder JL, Nosil P. The short-term, genome-wide effects of indirect selection deserve study: A response to Charlesworth and Jensen (2022). Mol Ecol 2022; 31:4444-4450. [PMID: 35909250 DOI: 10.1111/mec.16614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
Abstract
We recently published a paper quantifying the genome-wide consequences of natural selection, including the effects of indirect selection due to the correlation of genetic regions (neutral or selected) with directly selected regions (Gompert et al., 2022). In their critique of our paper, Charlesworth and Jensen (2022) make two main points: (i) indirect selection is equivalent to hitchhiking and thus well documented (i.e., our results are not novel) and (ii) that we do not demonstrate the source of linkage disequilibrium (LD) between SNPs and the Mel-Stripe locus in the Timema cristinae experiment we analyse. As we discuss in detail below, neither of these are substantial criticisms of our work.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah, USA.,Ecology Center, Utah State University, Logan, Utah, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patrik Nosil
- CEFE, University Montpellier, CNRS, EPHE, IRD, University Paul Valéry Montpellier 3, Montpellier, France
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28
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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.
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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:
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29
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The genomic origins of the world's first farmers. Cell 2022; 185:1842-1859.e18. [PMID: 35561686 PMCID: PMC9166250 DOI: 10.1016/j.cell.2022.04.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/04/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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30
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Johri P, Aquadro CF, Beaumont M, Charlesworth B, Excoffier L, Eyre-Walker A, Keightley PD, Lynch M, McVean G, Payseur BA, Pfeifer SP, Stephan W, Jensen JD. Recommendations for improving statistical inference in population genomics. PLoS Biol 2022; 20:e3001669. [PMID: 35639797 PMCID: PMC9154105 DOI: 10.1371/journal.pbio.3001669] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The field of population genomics has grown rapidly in response to the recent advent of affordable, large-scale sequencing technologies. As opposed to the situation during the majority of the 20th century, in which the development of theoretical and statistical population genetic insights outpaced the generation of data to which they could be applied, genomic data are now being produced at a far greater rate than they can be meaningfully analyzed and interpreted. With this wealth of data has come a tendency to focus on fitting specific (and often rather idiosyncratic) models to data, at the expense of a careful exploration of the range of possible underlying evolutionary processes. For example, the approach of directly investigating models of adaptive evolution in each newly sequenced population or species often neglects the fact that a thorough characterization of ubiquitous nonadaptive processes is a prerequisite for accurate inference. We here describe the perils of these tendencies, present our consensus views on current best practices in population genomic data analysis, and highlight areas of statistical inference and theory that are in need of further attention. Thereby, we argue for the importance of defining a biologically relevant baseline model tuned to the details of each new analysis, of skepticism and scrutiny in interpreting model fitting results, and of carefully defining addressable hypotheses and underlying uncertainties.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Charles F. Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Berne, Berne, Switzerland
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Peter D. Keightley
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susanne P. Pfeifer
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | | | - Jeffrey D. Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
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31
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Wu J, Yonezawa T, Kishino H. Molecular Evolutionary Rate Predicts Intraspecific Genetic Polymorphism and Species-Specific Selection. Genes (Basel) 2022; 13:genes13040708. [PMID: 35456514 PMCID: PMC9031814 DOI: 10.3390/genes13040708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 12/04/2022] Open
Abstract
It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, and dog/wolf genomes, we found that intraspecific genetic diversity can be predicted by long-term molecular evolutionary rates rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Moreover, we developed a method to detect fluctuations of species-specific selection on genes based on the deviations of intraspecific genetic diversity predicted from long-term rates. We showed that the evolution of epithelial cells, rather than connective tissue, mainly contributed to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps caused by infectious diseases are the most representative examples of adaptive evolution.
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Affiliation(s)
- Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara 259-1193, Japan
- Correspondence: (J.W.); (H.K.)
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Atsugi 243-0034, Japan;
| | - Hirohisa Kishino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo Ward, Tokyo 113-8657, Japan
- The Research Institute of Evolutionary Biology, Tokyo 138-0098, Japan
- AI/Data Science Social Implementation Laboratory, Chuo University, Tokyo 112-8551, Japan
- Correspondence: (J.W.); (H.K.)
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32
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Liang YY, Chen XY, Zhou BF, Mitchell-Olds T, Wang B. Globally Relaxed Selection and Local Adaptation in Boechera stricta. Genome Biol Evol 2022; 14:evac043. [PMID: 35349686 PMCID: PMC9011030 DOI: 10.1093/gbe/evac043] [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] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
The strength of selection varies among populations and across the genome, but the determinants of efficacy of selection remain unclear. In this study, we used whole-genome sequencing data from 467 Boechera stricta accessions to quantify the strength of selection and characterize the pattern of local adaptation. We found low genetic diversity on 0-fold degenerate sites and conserved non-coding sites, indicating functional constraints on these regions. The estimated distribution of fitness effects and the proportion of fixed substitutions suggest relaxed negative and positive selection in B. stricta. Among the four population groups, the NOR and WES groups have smaller effective population size (Ne), higher proportions of effectively neutral sites, and lower rates of adaptive evolution compared with UTA and COL groups, reflecting the effect of Ne on the efficacy of natural selection. We also found weaker selection on GC-biased sites compared with GC-conservative (unbiased) sites, suggested that GC-biased gene conversion has affected the strength of selection in B. stricta. We found mixed evidence for the role of the recombination rate on the efficacy of selection. The positive and negative selection was stronger in high-recombination regions compared with low-recombination regions in COL but not in other groups. By scanning the genome, we found different subsets of selected genes suggesting differential adaptation among B. stricta groups. These results show that differences in effective population size, nucleotide composition, and recombination rate are important determinants of the efficacy of selection. This study enriches our understanding of the roles of natural selection and local adaptation in shaping genomic variation.
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Affiliation(s)
- Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences,
Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences,
Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences,
Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | | | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences,
Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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33
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Saitou M, Masuda N, Gokcumen O. Similarity-Based Analysis of Allele Frequency Distribution among Multiple Populations Identifies Adaptive Genomic Structural Variants. Mol Biol Evol 2022; 39:msab313. [PMID: 34718708 PMCID: PMC8896759 DOI: 10.1093/molbev/msab313] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to: 1) population differentiation of rapidly evolving multiallelic variants, 2) incomplete sweeps, and 3) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
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Affiliation(s)
- Marie Saitou
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Naoki Masuda
- Department of Mathematics, University at Buffalo, State University of New York, Buffalo, NY, USA
- Computational and Data-Enabled Science and Engineering Program, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
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34
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Machado AP, Topaloudis A, Cumer T, Lavanchy E, Bontzorlos V, Ceccherelli R, Charter M, Kassinis N, Lymberakis P, Manzia F, Ducrest A, Dupasquier M, Guex N, Roulin A, Goudet J. Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean. Mol Ecol 2022; 31:1375-1388. [PMID: 34894026 PMCID: PMC9305133 DOI: 10.1111/mec.16324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/01/2021] [Accepted: 11/17/2021] [Indexed: 01/25/2023]
Abstract
The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. As a result, apparently identical islands may harbour populations with contrasting histories. Here, we use whole genome sequences of 65 barn owls to investigate the patterns of inbreeding and genetic diversity of insular populations in the eastern Mediterranean Sea. We focus on Crete and Cyprus, islands with similar size, climate and distance to mainland, that provide natural replicates for a comparative analysis of the impacts of microevolutionary processes on isolated populations. We show that barn owl populations from each island have a separate origin, Crete being genetically more similar to other Greek islands and mainland Greece, and Cyprus more similar to the Levant. Further, our data show that their respective demographic histories following colonisation were also distinct. On the one hand, Crete harbours a small population and maintains very low levels of gene flow with neighbouring populations. This has resulted in low genetic diversity, strong genetic drift, increased relatedness in the population and remote inbreeding. Cyprus, on the other hand, appears to maintain enough gene flow with the mainland to avoid such an outcome. Our study provides a comparative population genomic analysis of the effects of neutral processes on a classical island-mainland model system. It provides empirical evidence for the role of stochastic processes in determining the fate of diverging isolated populations.
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Affiliation(s)
- Ana Paula Machado
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | | | - Tristan Cumer
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Eléonore Lavanchy
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Vasileios Bontzorlos
- Green FundKifisia, AthensGreece
- "TYTO" – Organization for the Management and Conservation of Biodiversity in Agricultural EcosystemsLarisaGreece
| | | | - Motti Charter
- Shamir Research InstituteUniversity of HaifaKatzrinIsrael
- Department of Geography and Environmental SciencesUniversity of HaifaHaifaIsrael
| | | | | | | | - Anne‐Lyse Ducrest
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | | | - Nicolas Guex
- Bioinformatics Competence CentreUniversity of LausanneLausanneSwitzerland
| | - Alexandre Roulin
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Jérôme Goudet
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
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35
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Moinet A, Schlichta F, Peischl S, Excoffier L. Strong neutral sweeps occurring during a population contraction. Genetics 2022; 220:6529544. [PMID: 35171980 PMCID: PMC8982045 DOI: 10.1093/genetics/iyac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/22/2022] [Indexed: 11/14/2022] Open
Abstract
A strong reduction in diversity around a specific locus is often interpreted as a recent rapid fixation of a positively selected allele, a phenomenon called a selective sweep. Rapid fixation of neutral variants can however lead to a similar reduction in local diversity, especially when the population experiences changes in population size, e.g. bottlenecks or range expansions. The fact that demographic processes can lead to signals of nucleotide diversity very similar to signals of selective sweeps is at the core of an ongoing discussion about the roles of demography and natural selection in shaping patterns of neutral variation. Here, we quantitatively investigate the shape of such neutral valleys of diversity under a simple model of a single population size change, and we compare it to signals of a selective sweep. We analytically describe the expected shape of such "neutral sweeps" and show that selective sweep valleys of diversity are, for the same fixation time, wider than neutral valleys. On the other hand, it is always possible to parametrize our model to find a neutral valley that has the same width as a given selected valley. Our findings provide further insight into how simple demographic models can create valleys of genetic diversity similar to those attributed to positive selection.
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Affiliation(s)
- Antoine Moinet
- Interfaculty Bioinformatics Unit, University of Bern, Bern 3012, Switzerland,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland,Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Flávia Schlichta
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland,Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Stephan Peischl
- Interfaculty Bioinformatics Unit, University of Bern, Bern 3012, Switzerland,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland,Corresponding author.
| | - Laurent Excoffier
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland,Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
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36
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Palazzo AF, Kejiou NS. Non-Darwinian Molecular Biology. Front Genet 2022; 13:831068. [PMID: 35251134 PMCID: PMC8888898 DOI: 10.3389/fgene.2022.831068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper “Non-Darwinian Evolution”, where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura’s new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.
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37
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Johri P, Stephan W, Jensen JD. Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers. PLoS Genet 2022; 18:e1010022. [PMID: 35202407 PMCID: PMC8870509 DOI: 10.1371/journal.pgen.1010022] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The ability to accurately identify and quantify genetic signatures associated with soft selective sweeps based on patterns of nucleotide variation has remained controversial. We here provide counter viewpoints to recent publications in PLOS Genetics that have argued not only for the statistical identifiability of soft selective sweeps, but also for their pervasive evolutionary role in both Drosophila and HIV populations. We present evidence that these claims owe to a lack of consideration of competing evolutionary models, unjustified interpretations of empirical outliers, as well as to new definitions of the processes themselves. Our results highlight the dangers of fitting evolutionary models based on hypothesized and episodic processes without properly first considering common processes and, more generally, of the tendency in certain research areas to view pervasive positive selection as a foregone conclusion.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | | | - Jeffrey D. Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
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38
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Boitard S, Arredondo A, Chikhi L, Mazet O. Heterogeneity in effective size across the genome: effects on the inverse instantaneous coalescence rate (IICR) and implications for demographic inference under linked selection. Genetics 2022; 220:6512058. [PMID: 35100421 PMCID: PMC8893248 DOI: 10.1093/genetics/iyac008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/01/2022] [Indexed: 01/22/2023] Open
Abstract
The relative contribution of selection and neutrality in shaping species genetic diversity is one of the most central and controversial questions in evolutionary theory. Genomic data provide growing evidence that linked selection, i.e. the modification of genetic diversity at neutral sites through linkage with selected sites, might be pervasive over the genome. Several studies proposed that linked selection could be modeled as first approximation by a local reduction (e.g. purifying selection, selective sweeps) or increase (e.g. balancing selection) of effective population size (Ne). At the genome-wide scale, this leads to variations of Ne from one region to another, reflecting the heterogeneity of selective constraints and recombination rates between regions. We investigate here the consequences of such genomic variations of Ne on the genome-wide distribution of coalescence times. The underlying motivation concerns the impact of linked selection on demographic inference, because the distribution of coalescence times is at the heart of several important demographic inference approaches. Using the concept of inverse instantaneous coalescence rate, we demonstrate that in a panmictic population, linked selection always results in a spurious apparent decrease of Ne along time. Balancing selection has a particularly large effect, even when it concerns a very small part of the genome. We also study more general models including genuine population size changes, population structure or transient selection and find that the effect of linked selection can be significantly reduced by that of population structure. The models and conclusions presented here are also relevant to the study of other biological processes generating apparent variations of Ne along the genome.
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Affiliation(s)
- Simon Boitard
- CBGP, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montferrier-sur-Lez 34988, France
- Corresponding author: Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, 755 Avenue du Campus Agropolis, CS 30016, Montferrier-sur-Lez 34988, France.
| | - Armando Arredondo
- Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Université de Toulouse,Toulouse 31062, France
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Oeiras P-2780-156, Portugal
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), CNRS, IRD, UPS, Université de Toulouse Midi-Pyrénées, Toulouse 31062, France
| | - Olivier Mazet
- Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Université de Toulouse,Toulouse 31062, France
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39
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Willi Y, Kristensen TN, Sgrò CM, Weeks AR, Ørsted M, Hoffmann AA. Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species. Proc Natl Acad Sci U S A 2022; 119:e2105076119. [PMID: 34930821 PMCID: PMC8740573 DOI: 10.1073/pnas.2105076119] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
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Affiliation(s)
- Yvonne Willi
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Torsten N Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Andrew R Weeks
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
- Cesar Australia, Brunswick, VIC 3056, Australia
| | - Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
- Department of Biology, Aarhus University, Aarhus 8000, Denmark
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia;
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40
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Cumer T, Machado AP, Dumont G, Bontzorlos V, Ceccherelli R, Charter M, Dichmann K, Kassinis N, Lourenço R, Manzia F, Martens HD, Prévost L, Rakovic M, Roque I, Siverio F, Roulin A, Goudet J. Landscape and climatic variations shaped secondary contacts amid barn owls of the Western Palearctic. Mol Biol Evol 2021; 39:6454100. [PMID: 34893883 PMCID: PMC8789042 DOI: 10.1093/molbev/msab343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.
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Affiliation(s)
- Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Dumont
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Vasileios Bontzorlos
- Green Fund, Kifisia, Athens, Greece.,"TYTO" - Organization for the Management and Conservation of Biodiversity in Agricultural Ecosystems, Larisa, Greece
| | | | - Motti Charter
- Shamir Research Institute, University of Haifa, Katzrin, Israel.,Department of Geography and Environmental Sciences, University of Haifa, Haifa, Israel
| | | | | | - Rui Lourenço
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | | | | | - Laure Prévost
- Association C.H.E.N.E, Centre d'Hébergement et d'Etude sur la Nature et l'Environnement, Allouville-Bellefosse, 76190, France
| | - Marko Rakovic
- Natural History Museum of Belgrade, Belgrade, Serbia
| | - Inês Roque
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | - Felipe Siverio
- Canary Islands' Ornithology and Natural History Group (GOHNIC), 38480 Buenavista del Norte, Tenerife, Canary Islands, Spain
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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41
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Abstract
Alleles that introgress between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments.
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Affiliation(s)
- Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Current affiliation: Yale Institute for Biospheric Studies and Yale School of the Environment, Yale University, New Haven, Connecticut 06511, USA;
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
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42
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Charlesworth B, Jensen JD. Effects of Selection at Linked Sites on Patterns of Genetic Variability. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021; 52:177-197. [PMID: 37089401 PMCID: PMC10120885 DOI: 10.1146/annurev-ecolsys-010621-044528] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.
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Affiliation(s)
- Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Jeffrey D. Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona 85281, USA
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43
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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
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44
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Gompert Z, Feder JL, Nosil P. Natural selection drives genome-wide evolution via chance genetic associations. Mol Ecol 2021; 31:467-481. [PMID: 34704650 DOI: 10.1111/mec.16247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022]
Abstract
Understanding selection's impact on the genome is a major theme in biology. Functionally neutral genetic regions can be affected indirectly by natural selection, via their statistical association with genes under direct selection. The genomic extent of such indirect selection, particularly across loci not physically linked to those under direct selection, remains poorly understood, as does the time scale at which indirect selection occurs. Here, we use field experiments and genomic data in stick insects, deer mice and stickleback fish to show that widespread statistical associations with genes known to affect fitness cause many genetic loci across the genome to be impacted indirectly by selection. This includes regions physically distant from those directly under selection. Then, focusing on the stick insect system, we show that statistical associations between SNPs and other unknown, causal variants result in additional indirect selection in general and specifically within genomic regions of physically linked loci. This widespread indirect selection necessarily makes aspects of evolution more predictable. Thus, natural selection combines with chance genetic associations to affect genome-wide evolution across linked and unlinked loci and even in modest-sized populations. This process has implications for the application of evolutionary principles in basic and applied science.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah, USA.,Ecology Center, Utah State University, Logan, Utah, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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45
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Mortimer K, Fitzhugh K, dos Brasil AC, Lana P. Who's who in Magelona: phylogenetic hypotheses under Magelonidae Cunningham & Ramage, 1888 (Annelida: Polychaeta). PeerJ 2021; 9:e11993. [PMID: 35070516 PMCID: PMC8759375 DOI: 10.7717/peerj.11993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022] Open
Abstract
Known as shovel head worms, members of Magelonidae comprise a group of polychaetes readily recognised by the uniquely shaped, dorso-ventrally flattened prostomium and paired ventro-laterally inserted papillated palps. The present study is the first published account of inferences of phylogenetic hypotheses within Magelonidae. Members of 72 species of Magelona and two species of Octomagelona were included, with outgroups including members of one species of Chaetopteridae and four of Spionidae. The phylogenetic inferences were performed to causally account for 176 characters distributed among 79 subjects, and produced 2,417,600 cladograms, each with 404 steps. A formal definition of Magelonidae is provided, represented by a composite phylogenetic hypothesis explaining seven synapomorphies: shovel-shaped prostomium, prostomial ridges, absence of nuchal organs, ventral insertion of palps and their papillation, presence of a burrowing organ, and unique body regionation. Octomagelona is synonymised with Magelona due to the latter being paraphyletic relative to the former. The consequence is that Magelonidae is monotypic, such that Magelona cannot be formally defined as associated with any phylogenetic hypotheses. As such, the latter name is an empirically empty placeholder, but because of the binomial name requirement mandated by the International Code of Zoological Nomenclature, the definition is identical to that of Magelonidae. Several key features for future descriptions are suggested: prostomial dimensions, presence/absence of prostomial horns, morphology of anterior lamellae, presence/absence of specialised chaetae, and lateral abdominal pouches. Additionally, great care must be taken to fully describe and illustrate all thoracic chaetigers in descriptions.
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Affiliation(s)
- Kate Mortimer
- Natural Sciences, Amgueddfa Cymru–National Museum Wales, Cardiff, Wales, United Kingdom
| | - Kirk Fitzhugh
- Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Ana Claudia dos Brasil
- Departamento de Biologia Animal, Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Paulo Lana
- Centro de Estudos do Mar, Universidade Federal do Paraná, Pontal do Sul, Paraná, Brazil
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46
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Bertram J. Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila. PLoS Genet 2021; 17:e1009833. [PMID: 34591854 PMCID: PMC8509871 DOI: 10.1371/journal.pgen.1009833] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/12/2021] [Accepted: 09/22/2021] [Indexed: 12/04/2022] Open
Abstract
Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection. Yet it seems likely such episodes are the exception; the norm is more likely to involve subtle, concurrent selective changes at a large number of loci. We develop a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection in the collective divergence of allele frequencies over time. Applying our approach to temporally resolved allele frequency measurements from laboratory and wild Drosophila populations, we quantify the selective contribution to allele frequency divergence and find that selection has substantial effects on much of the genome. We further quantify the magnitude of the total selection coefficient (a measure of the combined effects of direct and linked selection) at a typical polymorphic locus, and find this to be large (of order 1%) even though most mutations are not directly under selection. We find that selective allele frequency divergence is substantially elevated at intermediate allele frequencies, which we argue is most parsimoniously explained by positive-not negative-selection. Thus, in these populations most mutations are far from evolving neutrally in the short term (tens of generations), including mutations with neutral fitness effects, and the result cannot be explained simply as an ongoing purging of deleterious mutations.
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Affiliation(s)
- Jason Bertram
- Environmental Resilience Institute, Indiana University, Bloomington, Indiana, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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47
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Armstrong EE, Khan A, Taylor RW, Gouy A, Greenbaum G, Thiéry A, Kang JT, Redondo SA, Prost S, Barsh G, Kaelin C, Phalke S, Chugani A, Gilbert M, Miquelle D, Zachariah A, Borthakur U, Reddy A, Louis E, Ryder OA, Jhala YV, Petrov D, Excoffier L, Hadly E, Ramakrishnan U. Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection. Mol Biol Evol 2021; 38:2366-2379. [PMID: 33592092 PMCID: PMC8136513 DOI: 10.1093/molbev/msab032] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, their evolutionary history and genomic variation remain poorly known, especially for Indian tigers. With 70% of the world’s wild tigers living in India, such knowledge is critical. We re-sequenced 65 individual tiger genomes representing most extant subspecies with a specific focus on tigers from India. As suggested by earlier studies, we found strong genetic differentiation between the putative tiger subspecies. Despite high total genomic diversity in India, individual tigers host longer runs of homozygosity, potentially suggesting recent inbreeding or founding events, possibly due to small and fragmented protected areas. We suggest the impacts of ongoing connectivity loss on inbreeding and persistence of Indian tigers be closely monitored. Surprisingly, demographic models suggest recent divergence (within the last 20,000 years) between subspecies and strong population bottlenecks. Amur tiger genomes revealed the strongest signals of selection related to metabolic adaptation to cold, whereas Sumatran tigers show evidence of weak selection for genes involved in body size regulation. We recommend detailed investigation of local adaptation in Amur and Sumatran tigers prior to initiating genetic rescue.
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Affiliation(s)
| | - Anubhab Khan
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Ryan W Taylor
- Department of Biology, Stanford University, Stanford, CA, USA.,End2End Genomics, LLC, Davis, CA, USA
| | - Alexandre Gouy
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gili Greenbaum
- Department of Biology, Stanford University, Stanford, CA, USA.,Department of Ecology, Evolution & Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexandre Thiéry
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jonathan T Kang
- Department of Biology, Stanford University, Stanford, CA, USA.,Genome Institute of Singapore, A*STAR, Singapore
| | | | - Stefan Prost
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Gregory Barsh
- Hudsonalpha Institute, Hunstville, AL, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | | | - Martin Gilbert
- Wildlife Conservation Society, Russia Program, New York, NY, USA.,College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Dale Miquelle
- Wildlife Conservation Society, Russia Program, New York, NY, USA
| | | | | | - Anuradha Reddy
- Laboratory for Conservation of Endangered Species, CCMB, Hyderabad, India
| | - Edward Louis
- Department of Genetics, Omaha Zoo, Omaha, NE, USA
| | - Oliver A Ryder
- San Diego Zoo, Institute for Conservation Research, Escondido, CA, USA
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Elizabeth Hadly
- Wildlife Conservation Society, Russia Program, New York, NY, USA
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48
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Yengo L, Yang J, Keller MC, Goddard ME, Wray NR, Visscher PM. Genomic partitioning of inbreeding depression in humans. Am J Hum Genet 2021; 108:1488-1501. [PMID: 34214457 DOI: 10.1016/j.ajhg.2021.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Across species, offspring of related individuals often exhibit significant reduction in fitness-related traits, known as inbreeding depression (ID), yet the genetic and molecular basis for ID remains elusive. Here, we develop a method to quantify enrichment of ID within specific genomic annotations and apply it to human data. We analyzed the phenomes and genomes of ∼350,000 unrelated participants of the UK Biobank and found, on average of over 11 traits, significant enrichment of ID within genomic regions with high recombination rates (>21-fold; p < 10-5), with conserved function across species (>19-fold; p < 10-4), and within regulatory elements such as DNase I hypersensitive sites (∼5-fold; p = 8.9 × 10-7). We also quantified enrichment of ID within trait-associated regions and found suggestive evidence that genomic regions contributing to additive genetic variance in the population are enriched for ID signal. We find strong correlations between functional enrichment of SNP-based heritability and that of ID (r = 0.8, standard error: 0.1). These findings provide empirical evidence that ID is most likely due to many partially recessive deleterious alleles in low linkage disequilibrium regions of the genome. Our study suggests that functional characterization of ID may further elucidate the genetic architectures and biological mechanisms underlying complex traits and diseases.
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49
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Garcia JA, Lohmueller KE. Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome. PLoS Genet 2021; 17:e1009676. [PMID: 34319975 PMCID: PMC8351996 DOI: 10.1371/journal.pgen.1009676] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/09/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
Evolutionary forces like Hill-Robertson interference and negative epistasis can lead to deleterious mutations being found on distinct haplotypes. However, the extent to which these forces depend on the selection and dominance coefficients of deleterious mutations and shape genome-wide patterns of linkage disequilibrium (LD) in natural populations with complex demographic histories has not been tested. In this study, we first used forward-in-time simulations to predict how negative selection impacts LD. Under models where deleterious mutations have additive effects on fitness, deleterious variants less than 10 kb apart tend to be carried on different haplotypes relative to pairs of synonymous SNPs. In contrast, for recessive mutations, there is no consistent ordering of how selection coefficients affect LD decay, due to the complex interplay of different evolutionary effects. We then examined empirical data of modern humans from the 1000 Genomes Project. LD between derived alleles at nonsynonymous SNPs is lower compared to pairs of derived synonymous variants, suggesting that nonsynonymous derived alleles tend to occur on different haplotypes more than synonymous variants. This result holds when controlling for potential confounding factors by matching SNPs for frequency in the sample (allele count), physical distance, magnitude of background selection, and genetic distance between pairs of variants. Lastly, we introduce a new statistic HR(j) which allows us to detect interference using unphased genotypes. Application of this approach to high-coverage human genome sequences confirms our finding that nonsynonymous derived alleles tend to be located on different haplotypes more often than are synonymous derived alleles. Our findings suggest that interference may play a pervasive role in shaping patterns of LD between deleterious variants in the human genome, and consequently influences genome-wide patterns of LD.
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Affiliation(s)
- Jesse A. Garcia
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
| | - Kirk E. Lohmueller
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
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50
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Excofffier L, Marchi N, Marques DA, Matthey-Doret R, Gouy A, Sousa VC. fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics 2021; 37:4882-4885. [PMID: 34164653 PMCID: PMC8665742 DOI: 10.1093/bioinformatics/btab468] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 01/25/2023] Open
Abstract
Motivation fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework. Results Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes. Availability and implementation fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.
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Affiliation(s)
- Laurent Excofffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Nina Marchi
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Alexander Marques
- Life Science Division, Natural History Museum Basel, 4051 Basel, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG swiss Federal institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Remi Matthey-Doret
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Alexandre Gouy
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Gouy Data Consulting, 1026 Denges, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
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