Special Issue: Genotyping by Sequencing
Population genomics based on low coverage sequencing: how low should we go?
Abstract
Research in molecular ecology is now often based on large numbers of DNA sequence reads. Given a time and financial budget for DNA sequencing, the question arises as to how to allocate the finite number of sequence reads among three dimensions: (i) sequencing individual nucleotide positions repeatedly and achieving high confidence in the true genotype of individuals, (ii) sampling larger numbers of individuals from a population, and (iii) sampling a larger fraction of the genome. Leaving aside the question of what fraction of the genome to sample, we analyze the trade‐off between repeatedly sequencing the same nucleotide position (coverage depth) and the number of individuals in the sample. We review simple Bayesian models for allele frequencies and utilize these in the analysis of how to obtain maximal information about population genetic parameters. The models indicate that sampling larger numbers of individuals, at the expense of coverage depth per nucleotide position, provides more information about population parameters. Dividing the sequencing effort maximally among individuals and obtaining approximately one read per locus and individual (1 × coverage) yields the most information about a population. Some analyses require genetic parameters for individuals, in which case Bayesian population models also support inference from lower coverage sequence data than are required for simple likelihood models. Low coverage sequencing is not only sufficient to support inference, but it is optimal to design studies to utilize low coverage because they will yield highly accurate and precise parameter estimates based on more individuals or sites in the genome.
Citing Literature
Number of times cited: 77
- Megan L. Fritz, Alexandra M. DeYonke, Alexie Papanicolaou, Stephen Micinski, John Westbrook and Fred Gould, Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices, Molecular Ecology, 27, 1, (167-181), (2017).
- Emma L. Carroll, Mike W. Bruford, J. Andrew DeWoody, Gregoire Leroy, Alan Strand, Lisette Waits and Jinliang Wang, Genetic and genomic monitoring with minimally invasive sampling methods, Evolutionary Applications, 11, 7, (1094-1119), (2018).
- Catherine R. M. Attard, Luciano B. Beheregaray and Luciana M. Möller, Genotyping‐by‐sequencing for estimating relatedness in nonmodel organisms: Avoiding the trap of precise bias, Molecular Ecology Resources, 18, 3, (381-390), (2018).
- Connor Seamus Stobie, Carel J. Oosthuizen, Michael J. Cunningham and Paulette Bloomer, Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing, Ecology and Evolution, 8, 4, (2326-2342), (2018).
- Sarah Schmid, Samuel Neuenschwander, Camille Pitteloud, Gerald Heckel, Mila Pajkovic, Raphaël Arlettaz and Nadir Alvarez, Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics, Ecology and Evolution, 8, 3, (1480-1495), (2017).
- J. A. Holliday, E. M. Hallerman and D. C. Haak, Genotyping and Sequencing Technologies in Population Genetics and Genomics, , 10.1007/13836_2017_5, (2018).
- Mikhail V. Matz, Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms, Trends in Genetics, 10.1016/j.tig.2017.11.002, 34, 2, (121-132), (2018).
- Seth M. Rudman, Matthew A. Barbour, Katalin Csilléry, Phillip Gienapp, Frederic Guillaume, Nelson G. Hairston Jr, Andrew P. Hendry, Jesse R. Lasky, Marina Rafajlović, Katja Räsänen, Paul S. Schmidt, Ole Seehausen, Nina O. Therkildsen, Martin M. Turcotte and Jonathan M. Levine, What genomic data can reveal about eco-evolutionary dynamics, Nature Ecology & Evolution, 10.1038/s41559-017-0385-2, 2, 1, (9-15), (2017).
- Caroline Fouet, Peter Atkinson and Colince Kamdem, Human Interventions: Driving Forces of Mosquito Evolution, Trends in Parasitology, 10.1016/j.pt.2017.10.012, 34, 2, (127-139), (2018).
- Gregory L. Owens, Marco Todesco, Emily B. M. Drummond, Sam Yeaman and Loren H. Rieseberg, A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X, Molecular Ecology Resources, 18, 1, (169-175), (2017).
- H. V. Huy, H. V. Hung, R. T. Buckney and L. F. De Filippis, Molecular Biodiversity Convergence with Biogeography and Ethnobotany of Rare and Endangered Medicinal Plants from Northern Vietnam, Plant and Human Health, Volume 1, 10.1007/978-3-319-93997-1_1, (1-52), (2018).
- Kin Onn Chan, Alana M. Alexander, L. Lee Grismer, Yong‐Chao Su, Jesse L. Grismer, Evan S. H. Quah and Rafe M. Brown, Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs, Molecular Ecology, 26, 20, (5435-5450), (2017).
- Angela P. Fuentes‐Pardo and Daniel E. Ruzzante, Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations, Molecular Ecology, 26, 20, (5369-5406), (2017).
- Nina Overgaard Therkildsen and Stephen R. Palumbi, Practical low‐coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species, Molecular Ecology Resources, 17, 2, (194-208), (2016).
- Andrew L. Pais, Ross W. Whetten and Qiu‐Yun (Jenny) Xiang, Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing, Ecology and Evolution, 7, 1, (441-465), (2016).
- Zachariah Gompert and Karen E. Mock, Detection of individual ploidy levels with genotyping‐by‐sequencing (GBS) analysis, Molecular Ecology Resources, 17, 6, (1156-1167), (2017).
- Erin O. Campbell, Corey S. Davis, Julian R. Dupuis, Kevin Muirhead and Felix A. H. Sperling, Cross‐platform compatibility of de novo‐aligned SNPs in a nonmodel butterfly genus, Molecular Ecology Resources, 17, 6, (e84-e93), (2017).
- Elizabeth A. Cooper and J. Albert C. Uy, Genomic evidence for convergent evolution of a key trait underlying divergence in island birds, Molecular Ecology, 26, 14, (3760-3774), (2017).
- Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Asao Fujiyama and Jun Kitano, Different contributions of local‐ and distant‐regulatory changes to transcriptome divergence between stickleback ecotypes, Evolution, 71, 3, (565-581), (2017).
- Richard T Corlett, A Bigger Toolbox: Biotechnology in Biodiversity Conservation, Trends in Biotechnology, 10.1016/j.tibtech.2016.06.009, 35, 1, (55-65), (2017).
- Xueqin Wang, Xiaying Ye, Lei Zhao, Dezhu Li, Zhenhua Guo and Huifu Zhuang, Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae), Scientific Reports, 7, 1, (2017).
- Kim L. Vertacnik and Catherine R. Linnen, Evolutionary genetics of host shifts in herbivorous insects: insights from the age of genomics, Annals of the New York Academy of Sciences, 1389, 1, (186-212), (2017).
- Rüdiger Riesch, Moritz Muschick, Dorothea Lindtke, Romain Villoutreix, Aaron A. Comeault, Timothy E. Farkas, Kay Lucek, Elizabeth Hellen, Víctor Soria-Carrasco, Stuart R. Dennis, Clarissa F. de Carvalho, Rebecca J. Safran, Cristina P. Sandoval, Jeff Feder, Regine Gries, Bernard J. Crespi, Gerhard Gries, Zach Gompert and Patrik Nosil, Transitions between phases of genomic differentiation during stick-insect speciation, Nature Ecology & Evolution, 1, 4, (0082), (2017).
- Janneke Wit and John S. Gilleard, Resequencing Helminth Genomes for Population and Genetic Studies, Trends in Parasitology, 33, 5, (388), (2017).
- Gregorio Sánchez-Montes, Arturo H. Ariño, José L. Vizmanos, Jinliang Wang and Íñigo Martínez-Solano, Effects of Sample Size and Full Sibs on Genetic Diversity Characterization: A Case Study of Three Syntopic Iberian Pond-Breeding Amphibians, Journal of Heredity, 108, 5, (535), (2017).
- Amanda Roe, Julian Dupuis and Felix Sperling, Molecular Dimensions of Insect Taxonomy in the Genomics Era, Insect Biodiversity, (547-573), (2017).
- Krystyna Nadachowska‐Brzyska, Reto Burri, Linnéa Smeds and Hans Ellegren, PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐white Ficedula flycatchers, Molecular Ecology, 25, 5, (1058-1072), (2016).
- Paul D. Blischak, Laura S. Kubatko and Andrea D. Wolfe, Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids, Molecular Ecology Resources, 16, 3, (742-754), (2015).
- M. O. Burford Reiskind, K. Coyle, H. V. Daniels, P. Labadie, M. H. Reiskind, N. B. Roberts, R. B. Roberts, J. Schaff and E. L. Vargo, Development of a universal double‐digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa, Molecular Ecology Resources, 16, 6, (1303-1314), (2016).
- Emily D. Fountain, Jonathan N. Pauli, Brendan N. Reid, Per J. Palsbøll and M. Zachariah Peery, Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates, Molecular Ecology Resources, 16, 4, (966-978), (2016).
- Jill K. Olofsson, Matheus Bianconi, Guillaume Besnard, Luke T. Dunning, Marjorie R. Lundgren, Helene Holota, Maria S. Vorontsova, Oriane Hidalgo, Ilia J. Leitch, Patrik Nosil, Colin P. Osborne and Pascal‐Antoine Christin, Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait, Molecular Ecology, 25, 24, (6107-6123), (2016).
- Sarah P. Flanagan, Emily Rose and Adam G. Jones, Population genomics reveals multiple drivers of population differentiation in a sex‐role‐reversed pipefish, Molecular Ecology, 25, 20, (5043-5072), (2016).
- Lauren K. Lucas, Zachariah Gompert, J. Randy Gibson, Katherine L. Bell, C. Alex Buerkle and Chris C. Nice, Pervasive gene flow across critical habitat for four narrowly endemic, sympatric taxa, Freshwater Biology, 61, 6, (933-946), (2016).
- R. J. Safran, E. S. C. Scordato, M. R. Wilkins, J. K. Hubbard, B. R. Jenkins, T. Albrecht, S. M. Flaxman, H. Karaardıç, Y. Vortman, A. Lotem, P. Nosil, P. Pap, S. Shen, S.‐F. Chan, T.L. Parchman and N. C. Kane, Genome‐wide differentiation in closely related populations: the roles of selection and geographic isolation, Molecular Ecology, 25, 16, (3865-3883), (2016).
- Bret A. Payseur and Loren H. Rieseberg, A genomic perspective on hybridization and speciation, Molecular Ecology, 25, 11, (2337-2360), (2016).
- Laura Marilyn Benestan, Anne‐Laure Ferchaud, Paul A. Hohenlohe, Brittany A. Garner, Gavin J. P. Naylor, Iliana Brigitta Baums, Michael K. Schwartz, Joanna L. Kelley and Gordon Luikart, Conservation genomics of natural and managed populations: building a conceptual and practical framework, Molecular Ecology, 25, 13, (2967-2977), (2016).
- Cécile Berthouly-Salazar, Cédric Mariac, Marie Couderc, Juliette Pouzadoux, Jean-Baptiste Floc’h and Yves Vigouroux, Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy, Frontiers in Plant Science, 7, (2016).
- Elena Matsa, John H. Ahrens and Joseph C. Wu, Human Induced Pluripotent Stem Cells as a Platform for Personalized and Precision Cardiovascular Medicine, Physiological Reviews, 96, 3, (1093), (2016).
- Zachariah Gompert, Bayesian inference of selection in a heterogeneous environment from genetic time-series data, Molecular Ecology, 25, 1, (121), (2016).
- Giovanna Carpi, Katharine S. Walter, Choukri Ben Mamoun, Peter J. Krause, Andrew Kitchen, Timothy J. Lepore, Ankit Dwivedi, Emmanuel Cornillot, Adalgisa Caccone and Maria A. Diuk-Wasser, Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States, BMC Genomics, 10.1186/s12864-016-3225-x, 17, 1, (2016).
- David P. L. Toews, Leonardo Campagna, Scott A. Taylor, Christopher N. Balakrishnan, Daniel T. Baldassarre, Petra E. Deane-Coe, Michael G. Harvey, Daniel M. Hooper, Darren E. Irwin, Caroline D. Judy, Nicholas A. Mason, John E. McCormack, Kevin G. McCracken, Carl H. Oliveros, Rebecca J. Safran, Elizabeth S. C. Scordato, Katherine Faust Stryjewski, Anna Tigano, J. Albert C. Uy and Benjamin M. Winger, Genomic approaches to understanding population divergence and speciation in birds, The Auk, 133, 1, (13), (2016).
- C. D. H. Sherman, K. E. Lotterhos, M. F. Richardson, C. K. Tepolt, L. A. Rollins, S. R. Palumbi and A. D. Miller, What are we missing about marine invasions? Filling in the gaps with evolutionary genomics, Marine Biology, 10.1007/s00227-016-2961-4, 163, 10, (2016).
- Marina Querejeta, Jorge González-Esteban, Asunción Gómez, Angel Fernández-González, Pere Aymerich, Joaquim Gosálbez, Lídia Escoda, Javier Igea and Jose Castresana, Genomic diversity and geographical structure of the Pyrenean desman, Conservation Genetics, 17, 6, (1333), (2016).
- Jeffrey M. DaCosta and Michael D. Sorenson, ddRAD-seq phylogenetics based on nucleotide, indel, and presence–absence polymorphisms: Analyses of two avian genera with contrasting histories, Molecular Phylogenetics and Evolution, 94, (122), (2016).
- M. R. Wilkins, H. Karaardıç, Y. Vortman, T. L. Parchman, T. Albrecht, A. Petrželková, L. Özkan, P. L. Pap, J. K. Hubbard, A. K. Hund and R. J. Safran, Phenotypic differentiation is associated with divergent sexual selection among closely related barn swallow populations, Journal of Evolutionary Biology, 29, 12, (2410-2421), (2016).
- Deren A. R. Eaton, Elizabeth L. Spriggs, Brian Park and Michael J. Donoghue, Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants, Systematic Biology, (syw092), (2016).
- Christine A. McAllister and Allison J. Miller, Single nucleotide polymorphism discovery via genotyping by sequencing to assess population genetic structure and recurrent polyploidization in Andropogon gerardii, American Journal of Botany, 103, 7, (1314-1325), (2016).
- E. J. Dowle, M. Morgan‐Richards, F. Brescia and S. A. Trewick, Correlation between shell phenotype and local environment suggests a role for natural selection in the evolution of Placostylus snails, Molecular Ecology, 24, 16, (4205-4221), (2015).
- A. Mastretta‐Yanes, N. Arrigo, N. Alvarez, T. H. Jorgensen, D. Piñero and B. C. Emerson, Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference, Molecular Ecology Resources, 15, 1, (28-41), (2014).
- B. Nevado and M. Perez‐Enciso, Pipeliner: software to evaluate the performance of bioinformatics pipelines for next‐generation resequencing, Molecular Ecology Resources, 15, 1, (99-106), (2014).
- Zhe‐Chen Qi, Yi Yu, Xiang Liu, Andrew Pais, Thomas Ranney, Ross Whetten and Qiu‐Yun (Jenny) Xiang, Phylogenomics of polyploid Fothergilla (Hamamelidaceae) by RAD‐tag based GBS—insights into species origin and effects of software pipelines, Journal of Systematics and Evolution, 53, 5, (432-447), (2015).
- Aaron B. A. Shafer, Lucie M. Gattepaille, Robert E. A. Stewart and Jochen B. W. Wolf, Demographic inferences using short‐read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus, Molecular Ecology, 24, 2, (328-345), (2015).
- Christophe Délye, Romain Causse, Véronique Gautier, Charles Poncet and Séverine Michel, Using next‐generation sequencing to detect mutations endowing resistance to pesticides: application to acetolactate‐synthase (ALS)‐based resistance in barnyard grass, a polyploid grass weed, Pest Management Science, 71, 5, (675-685), (2014).
- Elizabeth G. Mandeville, Thomas L. Parchman, David B. McDonald and C. Alex Buerkle, Highly variable reproductive isolation among pairs of Catostomus species, Molecular Ecology, 24, 8, (1856-1872), (2015).
- Krystyna Nadachowska-Brzyska, Cai Li, Linnea Smeds, Guojie Zhang and Hans Ellegren, Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences, Current Biology, 25, 10, (1375), (2015).
- Gregor Gorjanc, Matthew A Cleveland, Ross D Houston and John M Hickey, Potential of genotyping-by-sequencing for genomic selection in livestock populations, Genetics Selection Evolution, 47, 1, (12), (2015).
- Michael A. Russello, Matthew D. Waterhouse, Paul D. Etter and Eric A. Johnson, From promise to practice: pairing non-invasive sampling with genomics in conservation, PeerJ, 3, (e1106), (2015).
- D Porcelli, R K Butlin, K J Gaston, D Joly and R R Snook, The environmental genomics of metazoan thermal adaptation, Heredity, 10.1038/hdy.2014.119, 114, 5, (502-514), (2015).
- Giovanna Carpi, Katharine S. Walter, Stephen J. Bent, Anne Gatewood Hoen, Maria Diuk-Wasser and Adalgisa Caccone, Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi, BMC Genomics, 16, 1, (2015).
- Degui Zhi, Nianjun Liu and Kui Zhang, On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative reads, Methods, 79-80, (41), (2015).
- M. Konczal, P. Koteja, M. T. Stuglik, J. Radwan and W. Babik, Accuracy of allele frequency estimation using pooled RNA‐Seq, Molecular Ecology Resources, 14, 2, (381-392), (2013).
- B. Nevado, S. E. Ramos‐Onsins and M. Perez‐Enciso, Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics, Molecular Ecology, 23, 7, (1764-1779), (2014).
- Loren Rieseberg, Tim Vines, Jennifer Gow and Nolan Kane, Editorial 2014, Molecular Ecology, 23, 1, (1-15), (2013).
- Hilde Nybom, Kurt Weising and Björn Rotter, DNA fingerprinting in botany: past, present, future, Investigative Genetics, 5, 1, (1), (2014).
- Jeffrey C. Glaubitz, Terry M. Casstevens, Fei Lu, James Harriman, Robert J. Elshire, Qi Sun, Edward S. Buckler and Nicholas A. Tinker, TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline, PLoS ONE, 9, 2, (e90346), (2014).
- Dorothea Lindtke, Zachariah Gompert, Christian Lexer and C. Alex Buerkle, Unexpected ancestry ofPopulusseedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species, Molecular Ecology, 23, 17, (4316), (2014).
- Zhengfeng Zhang, Frederik R. D. van Parijs and Benze Xiao, The status of AFLP in the genomics era and a pipeline for converting AFLPs into single-locus markers, Molecular Breeding, 34, 3, (1245), (2014).
- Jeffrey M. DaCosta, Michael D. Sorenson and Christophe Antoniewski, Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol, PLoS ONE, 9, 9, (e106713), (2014).
- Martin P. Schilling, Paul G. Wolf, Aaron M. Duffy, Hardeep S. Rai, Carol A. Rowe, Bryce A. Richardson, Karen E. Mock and Pär K. Ingvarsson, Genotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches, PLoS ONE, 9, 4, (e95292), (2014).
- José Lucas-Lledó, David Vicente-Salvador, Cristina Aguado and Mario Cáceres, Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm, BMC Bioinformatics, 15, 1, (163), (2014).
- Shawn R. Narum, C. Alex Buerkle, John W. Davey, Michael R. Miller and Paul A. Hohenlohe, Genotyping‐by‐sequencing in ecological and conservation genomics, Molecular Ecology, 22, 11, (2841-2847), (2013).
- Zachariah Gompert and C. Alex Buerkle, Analyses of genetic ancestry enable key insights for molecular ecology, Molecular Ecology, 22, 21, (5278-5294), (2013).
- Julian Catchen, Paul A. Hohenlohe, Susan Bassham, Angel Amores and William A. Cresko, Stacks: an analysis tool set for population genomics, Molecular Ecology, 22, 11, (3124-3140), (2013).
- Francois Olivier Hebert, Sébastien Renaut and Louis Bernatchez, Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (oregonus clupeaformis), Molecular Ecology, 22, 19, (4896-4914), (2013).
- Jonathan B. Puritz and Katie E. Lotterhos, Expressed exome capture sequencing: A method for cost‐effective exome sequencing for all organisms, Molecular Ecology Resources, , (2018).
- Mandy Man-Ying Tin, Evan Philip Economo, Alexander Sergeyevich Mikheyev and David Caramelli, Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics, PLoS ONE, 10.1371/journal.pone.0096793, 9, 5, (e96793), (2014).
- Carolyn A. Wessinger, John K. Kelly, Peng Jiang, Mark D. Rausher and Lena C. Hileman, SNP‐skimming: A fast approach to map loci generating quantitative variation in natural populations, Molecular Ecology Resources, , (2018).
