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Shaikhutdinov NM, Klink GV, Garushyants SK, Kozlova OS, Cherkasov AV, Kikawada T, Okuda T, Pemba D, Shagimardanova EI, Penin AA, Deviatiiarov RM, Gazizova GR, Cornette R, Gusev OA, Bazykin GA. Population Genomics of Two Closely Related Anhydrobiotic Midges Reveals Differences in Adaptation to Extreme Desiccation. Genome Biol Evol 2023; 15:evad169. [PMID: 37708413 PMCID: PMC10558213 DOI: 10.1093/gbe/evad169] [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: 01/18/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
The sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process is protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, another closely related midge was discovered, Polypedilum pembai, which is able not only to tolerate desiccation but also to survive multiple desiccation-rehydration cycles. To investigate the evolution of anhydrobiosis in these species, we sequenced and assembled the genome of P. pembai and compared it with P. vanderplanki and also performed a population genomics analysis of several populations of P. vanderplanki and one population of P. pembai. We observe positive selection and radical changes in the genetic architecture of the PIMT locus between the two species, including its amplification in the P. pembai lineage. In particular, PIMT-4, the most highly expressed of these PIMTs, is present in six copies in the P. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity of the genomic region carrying these new genes is decreased in P. pembai, but not in the orthologous region carrying the ancestral gene in P. vanderplanki, providing evidence for a selective sweep associated with postduplication adaptation in the former. Overall, our results suggest an extensive relatively recent and likely ongoing adaptation of the mechanisms of anhydrobiosis.
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Affiliation(s)
- Nurislam M Shaikhutdinov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Galya V Klink
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Sofya K Garushyants
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Olga S Kozlova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Alexander V Cherkasov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Takahiro Kikawada
- National Agriculture and Food Research Organization (NARO), Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | | | - Dylo Pemba
- Vectorborne Diseases Laboratory, University of Malawi Chancellor College, Zomba, Malawi
| | - Elena I Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Ruslan M Deviatiiarov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Guzel R Gazizova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Richard Cornette
- National Agriculture and Food Research Organization (NARO), Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Oleg A Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
- Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia
- Intractable Disease Research Center, School of Medicine, Juntendo University, Tokyo, Japan
| | - Georgii A Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
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2
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Saif R, Mahmood T, Zia S, Henkel J, Ejaz A. Genomic selection pressure discovery using site-frequency spectrum and reduced local variability statistics in Pakistani Dera-Din-Panah goat. Trop Anim Health Prod 2023; 55:331. [PMID: 37750990 DOI: 10.1007/s11250-023-03758-2] [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: 12/21/2022] [Accepted: 09/12/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Population geneticists have long sought to comprehend various selection traces accumulated in the goat genome due to natural or human driven artificial selection through breeding practices, which led the wild animals to domestication, so understanding evolutionary process may helpful to utilize the full genetic potential of goat genome. METHODS AND RESULTS As a step forward to pinpoint the selection signals in Pakistani Dera-Din-Panah (DDP) goat, whole-genome pooled sequencing (n = 12) was performed, and 618,236,192 clean paired-end reads were mapped against ARS1 reference goat assembly. Five different selection signature statistics were applied using four site-frequency spectrum (SFS) methods (Tajima's D ([Formula: see text]), Fay and Wu's H ([Formula: see text]), Zeng's E ([Formula: see text]), [Formula: see text]) and one reduced local variability approach named pooled heterozygosity ([Formula: see text]). The under-selection regions were annotated with significant threshold values of [Formula: see text]≥4.7, [Formula: see text]≥6, [Formula: see text]≥2.5, Pool-HMM ≥ 12, and [Formula: see text]≥5 that resulted in accumulative 364 candidate gene hits. The highest genomic selection signals were observed on Chr. 4, 6, 10, 12, 15, 16, 18, 20, and 27 and harbor ADAMTS6, CWC27, RELN, MYCBP2, FGF14, STIM1, CFAP74, GNB1, CALML6, TMEM52, FAM149A, NADK, MMP23B, OPN3, FH, MFHAS1, KLKB1, RRM1, KMO, SPEF2, F11, KIT, KMO, ERI1, ATP8B4, and RHOG genes. Next, the validation of our captured genomic hits was also performed by more than one applied statistics which harbor meat production, immunity, and reproduction associated genes to strengthen our hypothesis of under-selection traits in this Pakistani goat breed. Furthermore, common candidate genes captured by more than one statistical method were subjected to gene ontology and KEGG pathway analysis to get insights of particular biological processes associated with this goat breed. CONCLUSION Current perception of genomic architecture of DDP goat provides a better understanding to improve its genetic potential and other economically important traits of medium to large body size, milk, and fiber production by updating the genomic insight driven breeding strategies to boost the livestock and agriculture-based economy of the country.
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Affiliation(s)
- Rashid Saif
- Department of Biotechnology, Qarshi University, Lahore, Pakistan.
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan.
| | - Tania Mahmood
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
| | - Saeeda Zia
- Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Lahore, Pakistan
| | - Jan Henkel
- MGZ-Medical Genetics Center, Munich, Germany
| | - Aniqa Ejaz
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
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Klymus KE, Hrabik RA, Thompson NL, Cornman RS. Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas. PeerJ 2022; 10:e13954. [PMID: 36042859 PMCID: PMC9420404 DOI: 10.7717/peerj.13954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/05/2022] [Indexed: 01/19/2023] Open
Abstract
Background The fathead minnow (Pimephales promelas) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the potential effects of genetic background on toxicological responses. On the other hand, a wealth of extant samples is stored in museum collections that in principle allow fine-scale analysis of contemporary and historical genetic variation. Methods Here we use short-read shotgun resequencing to investigate sequence variation among and within Pimephales species. At the genus level, our objectives were to resolve phylogenetic relationships and identify genes with signatures of positive diversifying selection. At the species level, our objective was to evaluate the utility of archived-sample resequencing for detecting selective sweeps within fathead minnow, applied to a population introduced to the San Juan River of the southwestern United States sometime prior to 1950. Results We recovered well-supported but discordant phylogenetic topologies for nuclear and mitochondrial sequences that we hypothesize arose from mitochondrial transfer among species. The nuclear tree supported bluntnose minnow (P. notatus) as sister to fathead minnow, with the slim minnow (P. tenellus) and bullhead minnow (P. vigilax) more closely related to each other. Using multiple methods, we identified 11 genes that have diversified under positive selection within the genus. Within the San Juan River population, we identified selective-sweep regions overlapping several sets of related genes, including both genes that encode the giant sarcomere protein titin and the two genes encoding the MTORC1 complex, a key metabolic regulator. We also observed elevated polymorphism and reduced differentation among populations (FST) in genomic regions containing certain immune-gene clusters, similar to what has been reported in other taxa. Collectively, our data clarify evolutionary relationships and selective pressures within the genus and establish museum archives as a fruitful resource for characterizing genomic variation. We anticipate that large-scale resequencing will enable the detection of genetic variants associated with environmental toxicants such as heavy metals, high salinity, estrogens, and agrichemicals, which could be exploited as efficient biomarkers of exposure in natural populations.
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Affiliation(s)
- Katy E. Klymus
- U.S. Geological Survey, Columbia Ecological Research Center, Columbia, MO, USA
| | | | - Nathan L. Thompson
- U.S. Geological Survey, Columbia Ecological Research Center, Columbia, MO, USA
| | - Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
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Kidner J, Theodorou P, Engler JO, Taubert M, Husemann M. A brief history and popularity of methods and tools used to estimate micro-evolutionary forces. Ecol Evol 2021; 11:13723-13743. [PMID: 34707813 PMCID: PMC8525119 DOI: 10.1002/ece3.8076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/12/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
Population genetics is a field of research that predates the current generations of sequencing technology. Those approaches, that were established before massively parallel sequencing methods, have been adapted to these new marker systems (in some cases involving the development of new methods) that allow genome-wide estimates of the four major micro-evolutionary forces-mutation, gene flow, genetic drift, and selection. Nevertheless, classic population genetic markers are still commonly used and a plethora of analysis methods and programs is available for these and high-throughput sequencing (HTS) data. These methods employ various and diverse theoretical and statistical frameworks, to varying degrees of success, to estimate similar evolutionary parameters making it difficult to get a concise overview across the available approaches. Presently, reviews on this topic generally focus on a particular class of methods to estimate one or two evolutionary parameters. Here, we provide a brief history of methods and a comprehensive list of available programs for estimating micro-evolutionary forces. We furthermore analyzed their usage within the research community based on popularity (citation bias) and discuss the implications of this bias for the software community. We found that a few programs received the majority of citations, with program success being independent of both the parameters estimated and the computing platform. The only deviation from a model of exponential growth in the number of citations was found for the presence of a graphical user interface (GUI). Interestingly, no relationship was found for the impact factor of the journals, when the tools were published, suggesting accessibility might be more important than visibility.
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Affiliation(s)
- Jonathan Kidner
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Panagiotis Theodorou
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Jan O Engler
- Terrestrial Ecology Unit Department of Biology Ghent University Ghent Belgium
| | - Martin Taubert
- Aquatic Geomicrobiology Institute for Biodiversity Friedrich Schiller University Jena Jena Germany
| | - Martin Husemann
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
- Centrum für Naturkunde University of Hamburg Hamburg Germany
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5
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Miranda I, Giska I, Farelo L, Pimenta J, Zimova M, Bryk J, Dalén L, Mills LS, Zub K, Melo-Ferreira J. Museomics dissects the genetic basis for adaptive seasonal colouration in the least weasel. Mol Biol Evol 2021; 38:4388-4402. [PMID: 34157721 PMCID: PMC8476133 DOI: 10.1093/molbev/msab177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Dissecting the link between genetic variation and adaptive phenotypes provides outstanding opportunities to understand fundamental evolutionary processes. Here, we use a museomics approach to investigate the genetic basis and evolution of winter coat colouration morphs in least weasels (Mustela nivalis), a repeated adaptation for camouflage in mammals with seasonal pelage colour moults across regions with varying winter snow. Whole-genome sequence data was obtained from biological collections and mapped onto a newly assembled reference genome for the species. Sampling represented two replicate transition zones between nivalis and vulgaris colouration morphs in Europe, which typically develop white or brown winter coats, respectively. Population analyses showed that the morph distribution across transition zones is not a by-product of historical structure. Association scans linked a 200 kb genomic region to colouration morph, which was validated by genotyping museum specimens from inter-morph experimental crosses. Genotyping the wild populations narrowed down the association to pigmentation gene MC1R and pinpointed a candidate amino acid change co-segregating with colouration morph. This polymorphism replaces an ancestral leucine residue by lysine at the start of the first extracellular loop of the protein in the vulgaris morph. A selective sweep signature overlapped the association region in vulgaris, suggesting that past adaptation favoured winter-brown morphs and can anchor future adaptive responses to decreasing winter snow. Using biological collections as valuable resources to study natural adaptations, our study showed a new evolutionary route generating winter colour variation in mammals and that seasonal camouflage can be modulated by changes at single key genes.
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Affiliation(s)
- Inês Miranda
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, 4169-007, Portugal
| | - Iwona Giska
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal
| | - João Pimenta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal
| | - Marketa Zimova
- School for Environment and Sustainability, University of Michigan, Dana Natural Resources Building, 440 Church St, Ann Arbor, MI, 49109, USA
| | - Jarosław Bryk
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-10691, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm, SE-10405, Sweden
| | - L Scott Mills
- Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA.,Office of Research and Creative Scholarship, University of Montana, Missoula, MT, 59812, USA
| | - Karol Zub
- Mammal Research Institute, Polish Academy of Sciences, Stoczek 1, Białowieża 17-230, Poland
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, 4169-007, Portugal
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Oh KP, Shiels AB, Shiels L, Blondel DV, Campbell KJ, Saah JR, Lloyd AL, Thomas PQ, Gould F, Abdo Z, Godwin JR, Piaggio AJ. Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive. Evol Appl 2021; 14:1421-1435. [PMID: 34025776 PMCID: PMC8127709 DOI: 10.1111/eva.13210] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/22/2022] Open
Abstract
Introduced rodent populations pose significant threats worldwide, with particularly severe impacts on islands. Advancements in genome editing have motivated interest in synthetic gene drives that could potentially provide efficient and localized suppression of invasive rodent populations. Application of such technologies will require rigorous population genomic surveys to evaluate population connectivity, taxonomic identification, and to inform design of gene drive localization mechanisms. One proposed approach leverages the predicted shifts in genetic variation that accompany island colonization, wherein founder effects, genetic drift, and island-specific selection are expected to result in locally fixed alleles (LFA) that are variable in neighboring nontarget populations. Engineering of guide RNAs that target LFA may thus yield gene drives that spread within invasive island populations, but would have limited impacts on nontarget populations in the event of an escape. Here we used pooled whole-genome sequencing of invasive mouse (Mus musculus) populations on four islands along with paired putative source populations to test genetic predictions of island colonization and characterize locally fixed Cas9 genomic targets. Patterns of variation across the genome reflected marked reductions in allelic diversity in island populations and moderate to high degrees of differentiation from nearby source populations despite relatively recent colonization. Locally fixed Cas9 sites in female fertility genes were observed in all island populations, including a small number with multiplexing potential. In practice, rigorous sampling of presumptive LFA will be essential to fully assess risk of resistance alleles. These results should serve to guide development of improved, spatially limited gene drive design in future applications.
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Affiliation(s)
- Kevin P. Oh
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Aaron B. Shiels
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
| | - Laura Shiels
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
| | - Dimitri V. Blondel
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Karl J. Campbell
- Island ConservationPuerto AyoraEcuador
- School of Agriculture and Food SciencesThe University of QueenslandGattonQueenslandAustralia
| | - J. Royden Saah
- Island ConservationPuerto AyoraEcuador
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Alun L. Lloyd
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Biomathematics Graduate Program and Department of MathematicsNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Paul Q. Thomas
- The Robinson Research Institute and School of MedicineThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Fred Gould
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Zaid Abdo
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - John R. Godwin
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Antoinette J. Piaggio
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
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Andres KJ, Sethi SA, Lodge DM, Andrés J. Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples. Mol Ecol 2021; 30:685-697. [PMID: 33433059 PMCID: PMC7898893 DOI: 10.1111/mec.15765] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022]
Abstract
Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population-level allele frequencies and estimates of the number of genetic contributors in an eDNA sample. Using a panel of microsatellite loci developed for the round goby (Neogobius melanostomus), we tested the similarity between eDNA-based and individual tissue-based estimates of allele frequencies from experimental mesocosms and in a field-based trial. Subsequently, we used a likelihood-based DNA mixture framework to estimate the number of unique genetic contributors in eDNA samples and in simulated mixtures of alleles. In both mesocosm and field samples, allele frequencies from eDNA were highly correlated with allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples. DNA mixture analyses were able to estimate the number of genetic contributors from mesocosm eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low-frequency alleles. With this study we document the application of eDNA and multiple amplicon-based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in eDNA samples. With proper validation, this approach has the potential to advance noninvasive survey methods to characterize populations and detect population-level genetic diversity.
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Affiliation(s)
- Kara J Andres
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Suresh A Sethi
- U.S. Geological Survey, New York Cooperative Fish and Wildlife Unit, Cornell University, Ithaca, NY, USA
| | - David M Lodge
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY, USA
| | - Jose Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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Everhart S, Gambhir N, Stam R. Population Genomics of Filamentous Plant Pathogens-A Brief Overview of Research Questions, Approaches, and Pitfalls. PHYTOPATHOLOGY 2021; 111:12-22. [PMID: 33337245 DOI: 10.1094/phyto-11-20-0527-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With ever-decreasing sequencing costs, research on the population biology of plant pathogens is transitioning from population genetics-using dozens of genetic markers or polymorphism data of several genes-to population genomics-using several hundred to tens of thousands of markers or whole-genome sequence data. The field of population genomics is characterized by rapid theoretical and methodological advances and by numerous steps and pitfalls in its technical and analytical workflow. In this article, we aim to provide a brief overview of topics relevant to the study of population genomics of filamentous plant pathogens and direct readers to more extensive reviews for in-depth understanding. We briefly discuss different types of population genomics-inspired research questions and give insights into the sampling strategies that can be used to answer such questions. We then consider different sequencing strategies, the various options available for data processing, and some of the currently available tools for population genomic data analysis. We conclude by highlighting some of the hurdles along the population genomic workflow, providing cautionary warnings relative to assumptions and technical challenges, and presenting our own future perspectives of the field of population genomics for filamentous plant pathogens.
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Affiliation(s)
- Sydney Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Nikita Gambhir
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Remco Stam
- Phytopathology, School of Life Sciences Weihenstephan, Technical University Munich, Germany
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9
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Pinzari CA, Kang L, Michalak P, Jermiin LS, Price DK, Bonaccorso FJ. Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations. Genome Biol Evol 2020; 12:1504-1514. [PMID: 32853363 PMCID: PMC7543519 DOI: 10.1093/gbe/evaa137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We examine the genetic history and population status of Hawaiian hoary bats (Lasiurus semotus), the most isolated bats on Earth, and their relationship to northern hoary bats (Lasiurus cinereus), through whole-genome analysis of single-nucleotide polymorphisms mapped to a de novo-assembled reference genome. Profiles of genomic diversity and divergence indicate that Hawaiian hoary bats are distinct from northern hoary bats, and form a monophyletic group, indicating a single ancestral colonization event 1.34 Ma, followed by substantial divergence between islands beginning 0.51 Ma. Phylogenetic analysis indicates Maui is central to the radiation across the archipelago, with the southward expansion to Hawai'i and westward to O'ahu and Kaua'i. Because this endangered species is of conservation concern, a clearer understanding of the population genetic structure of this bat in the Hawaiian Islands is of timely importance.
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Affiliation(s)
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia
- Institute of Evolution, University of Haifa, Israel
| | - Lars S Jermiin
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
- School of Biology & Environmental Science, University College Dublin, Ireland
- Earth Institute, University College Dublin, Ireland
| | - Donald K Price
- School of Life Sciences, University of Nevada, Las Vegas
| | - Frank J Bonaccorso
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai‘i National Park, HI
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10
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Kapun M, Barrón MG, Staubach F, Obbard DJ, Wiberg RAW, Vieira J, Goubert C, Rota-Stabelli O, Kankare M, Bogaerts-Márquez M, Haudry A, Waidele L, Kozeretska I, Pasyukova EG, Loeschcke V, Pascual M, Vieira CP, Serga S, Montchamp-Moreau C, Abbott J, Gibert P, Porcelli D, Posnien N, Sánchez-Gracia A, Grath S, Sucena É, Bergland AO, Guerreiro MPG, Onder BS, Argyridou E, Guio L, Schou MF, Deplancke B, Vieira C, Ritchie MG, Zwaan BJ, Tauber E, Orengo DJ, Puerma E, Aguadé M, Schmidt P, Parsch J, Betancourt AJ, Flatt T, González J. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Mol Biol Evol 2020; 37:2661-2678. [PMID: 32413142 PMCID: PMC7475034 DOI: 10.1093/molbev/msaa120] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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Affiliation(s)
- Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
- Division of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Maite G Barrón
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - R Axel W Wiberg
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Clément Goubert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige, Italy
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - María Bogaerts-Márquez
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Annabelle Haudry
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Lena Waidele
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center of Ministry of Education and Science of Ukraine, Kyiv, Ukraine
| | - Elena G Pasyukova
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genome Variation, Institute of Molecular Genetics of RAS, Moscow, Russia
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Svitlana Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Patricia Gibert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Damiano Porcelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Animal and Plant Sciences, Sheffield, United Kingdom
| | - Nico Posnien
- The European Drosophila Population Genomics Consortium (DrosEU)
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Universität Göttingen, Göttingen, Germany
| | - Alejandro Sánchez-Gracia
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Élio Sucena
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Alan O Bergland
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Maria Pilar Garcia Guerreiro
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Lain Guio
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Bart Deplancke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Bio-engineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Cristina Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
| | - Bas J Zwaan
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Eran Tauber
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paul Schmidt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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11
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Morris KM, Hindle MM, Boitard S, Burt DW, Danner AF, Eory L, Forrest HL, Gourichon D, Gros J, Hillier LW, Jaffredo T, Khoury H, Lansford R, Leterrier C, Loudon A, Mason AS, Meddle SL, Minvielle F, Minx P, Pitel F, Seiler JP, Shimmura T, Tomlinson C, Vignal A, Webster RG, Yoshimura T, Warren WC, Smith J. The quail genome: insights into social behaviour, seasonal biology and infectious disease response. BMC Biol 2020; 18:14. [PMID: 32050986 PMCID: PMC7017630 DOI: 10.1186/s12915-020-0743-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. RESULTS We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated after H5N1 infection, and this may be key to the susceptibility of quail to H5N1. CONCLUSIONS We have produced a high-quality genome of the quail which will facilitate further studies into diverse research questions using the quail as a model avian species.
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Affiliation(s)
- Katrina M Morris
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Matthew M Hindle
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Simon Boitard
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet Tolosan, France
| | - David W Burt
- The John Hay Building, Queensland Biosciences Precinct, 306 Carmody Road, The University of Queensland, QLD, St Lucia, 4072, Australia
| | - Angela F Danner
- Virology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Lel Eory
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Heather L Forrest
- Virology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - David Gourichon
- PEAT Pôle d'Expérimentation Avicole de Tours, Centre de recherche Val de Loire, INRAE, 1295, Nouzilly, UE, France
| | - Jerome Gros
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 25 rue du Docteur Roux, 75724, Cedex 15, Paris, France
- CNRS URA3738, 25 rue du Dr Roux, 75015, Paris, France
| | - LaDeana W Hillier
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Blvd, St Louis, MO, 63108, USA
| | - Thierry Jaffredo
- CNRS UMR7622, Inserm U 1156, Laboratoire de Biologie du Développement, Sorbonne Université, IBPS, 75005, Paris, France
| | - Hanane Khoury
- CNRS UMR7622, Inserm U 1156, Laboratoire de Biologie du Développement, Sorbonne Université, IBPS, 75005, Paris, France
| | - Rusty Lansford
- Department of Radiology and Developmental Neuroscience Program, Saban Research Institute, Children's Hospital Los Angeles and Keck School of Medicine of the University of Southern California, Los Angeles, CA, 90027, USA
| | - Christine Leterrier
- UMR85 Physiologie de la Reproduction et des Comportements, INRAE, CNRS, Université François Rabelais, IFCE, INRAE, Val de Loire, 37380, Nouzilly, Centre, France
| | - Andrew Loudon
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, 3.001, A.V. Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Andrew S Mason
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Simone L Meddle
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Francis Minvielle
- GABI, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Blvd, St Louis, MO, 63108, USA
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet Tolosan, France
| | - J Patrick Seiler
- Virology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Tsuyoshi Shimmura
- Department of Biological Production, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo, 183-8538, Japan
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Blvd, St Louis, MO, 63108, USA
| | - Alain Vignal
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet Tolosan, France
| | - Robert G Webster
- Virology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Takashi Yoshimura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, 1201 Rollins Street, Columbia, MO, 65211, USA
| | - Jacqueline Smith
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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12
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Sigsgaard EE, Jensen MR, Winkelmann IE, Møller PR, Hansen MM, Thomsen PF. Population-level inferences from environmental DNA-Current status and future perspectives. Evol Appl 2020; 13:245-262. [PMID: 31993074 PMCID: PMC6976968 DOI: 10.1111/eva.12882] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms. This approach offers several potential advantages compared with conventional tissue-based methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances. However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.
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Affiliation(s)
| | | | | | - Peter Rask Møller
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
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13
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Khan S, Zhao X, Hou Y, Yuan C, Li Y, Luo X, Liu J, Feng X. Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations of Haemonchus contortus. J Biosci 2019; 44:97. [PMID: 31502575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The parasitic nematode Haemonchus contortus is one of the world's most important parasites of small ruminants that causes significant economic losses to the livestock sector. The population structure and selection in its various strains are poorly understood. No study so far compared its different populations using genome-wide data. Here, we focused on different geographic populations of H. contours from China (Tibet, TB; Hubei, HB; Inner Mongolia, IM; Sichuan, SC), UK and Australia (AS), using genome-wide population-genomic approaches, to explore genetic diversity, population structure and selection. We first performed next-generation high-throughput 2b RAD pool sequencing using Illumina technology, and identified single-nucleotide polymorphisms (SNPs) in all the strains. We identified 75,187 SNPs for TB, 82,271 for HB, 82,420 for IM, 79,803 for SC, 83,504 for AS and 78,747 for UK strain. The SNPs revealed low-nucleotide diversity (pi= 0.0092-0.0133) within each strain, and a significant differentiation level (average Fst = 0.34264) among them. Chinese populations TB and SC, along with the UK strain, were more divergent populations. Chinese populations IM and HB showed affinities to the Australian strain. We then analysed signature of selection and detected 44 (UK) and 03 (AS) private selective sweeps containing 49 and 05 genes, respectively. Finally, we performed the functional annotation of selective sweeps and proposed biological significance to signature of selection. Our data suggest that 2b-RAD pool sequencing can be used to assess the signature of selection in H. contortus.
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Affiliation(s)
- Sawar Khan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, People's Republic of China
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14
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Khan S, Zhao X, Hou Y, Yuan C, Li Y, Luo X, Liu J, Feng X. Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations of Haemonchus contortus. J Biosci 2019. [DOI: 10.1007/s12038-019-9917-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Genomic divergence and adaptive convergence in Drosophila simulans from Evolution Canyon, Israel. Proc Natl Acad Sci U S A 2019; 116:11839-11844. [PMID: 31127048 PMCID: PMC6576144 DOI: 10.1073/pnas.1720938116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Biodiversity refugia formed by unique features of the Mediterranean arid landscape, such as the dramatic ecological contrast of "Evolution Canyon," provide a natural laboratory in which local adaptations to divergent microclimate conditions can be investigated. Significant insights have been provided by studies of Drosophila melanogaster diversifying along the thermal gradient in Evolution Canyon, but a comparative framework to survey adaptive convergence across sister species at the site has been lacking. To fill this void, we present an analysis of genomic polymorphism and evolutionary divergence of Drosophila simulans, a close relative of Drosophila melanogaster with which it co-occurs on both slopes of the canyon. Our results show even deeper interslope divergence in D. simulans than in D. melanogaster, with extensive signatures of selective sweeps present in flies from both slopes but enhanced in the population from the hotter and drier south-facing slope. Interslope divergence was enriched for genes related to electrochemical balance and transmembrane transport, likely in response to increased selection for dehydration resistance on the hotter slope. Both species shared genomic regions that underwent major selective sweeps, but the overall level of adaptive convergence was low, demonstrating no shortage of alternative genomic solutions to cope with the challenges of the microclimate contrast. Mobile elements were a major source of genetic polymorphism and divergence, affecting all parts of the genome, including coding sequences of mating behavior-related genes.
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16
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Vignal A, Boitard S, Thébault N, Dayo GK, Yapi-Gnaore V, Youssao Abdou Karim I, Berthouly-Salazar C, Pálinkás-Bodzsár N, Guémené D, Thibaud-Nissen F, Warren WC, Tixier-Boichard M, Rognon X. A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Mol Ecol Resour 2019; 19:997-1014. [PMID: 30945415 PMCID: PMC6579635 DOI: 10.1111/1755-0998.13017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 01/25/2023]
Abstract
The helmeted guinea fowl Numida meleagris belongs to the order Galliformes. Its natural range includes a large part of sub‐Saharan Africa, from Senegal to Eritrea and from Chad to South Africa. Archaeozoological and artistic evidence suggest domestication of this species may have occurred about 2,000 years BP in Mali and Sudan primarily as a food resource, although villagers also benefit from its capacity to give loud alarm calls in case of danger, of its ability to consume parasites such as ticks and to hunt snakes, thus suggesting its domestication may have resulted from a commensal association process. Today, it is still farmed in Africa, mainly as a traditional village poultry, and is also bred more intensively in other countries, mainly France and Italy. The lack of available molecular genetic markers has limited the genetic studies conducted to date on guinea fowl. We present here a first‐generation whole‐genome sequence draft assembly used as a reference for a study by a Pool‐seq approach of wild and domestic populations from Europe and Africa. We show that the domestic populations share a higher genetic similarity between each other than they do to wild populations living in the same geographical area. Several genomic regions showing selection signatures putatively related to domestication or importation to Europe were detected, containing candidate genes, most notably EDNRB2, possibly explaining losses in plumage coloration phenotypes in domesticated populations.
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Affiliation(s)
- Alain Vignal
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Simon Boitard
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Noémie Thébault
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet Tolosan, France
| | | | | | | | | | | | | | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri
| | | | - Xavier Rognon
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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17
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Fournier-Level A, Good RT, Wilcox SA, Rane RV, Schiffer M, Chen W, Battlay P, Perry T, Batterham P, Hoffmann AA, Robin C. The spread of resistance to imidacloprid is restricted by thermotolerance in natural populations of Drosophila melanogaster. Nat Ecol Evol 2019; 3:647-656. [DOI: 10.1038/s41559-019-0837-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 02/05/2019] [Indexed: 11/09/2022]
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18
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Kahnt B, Theodorou P, Soro A, Hollens-Kuhr H, Kuhlmann M, Pauw A, Paxton RJ. Small and genetically highly structured populations in a long-legged bee, Rediviva longimanus, as inferred by pooled RAD-seq. BMC Evol Biol 2018; 18:196. [PMID: 30567486 PMCID: PMC6300007 DOI: 10.1186/s12862-018-1313-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/28/2018] [Indexed: 11/10/2022] Open
Abstract
Adaptation to local host plants may impact a pollinator's population genetic structure by reducing gene flow and driving population genetic differentiation, representing an early stage of ecological speciation. South African Rediviva longimanus bees exhibit elongated forelegs, a bizarre adaptation for collecting oil from floral spurs of their Diascia hosts. Furthermore, R. longimanus foreleg length (FLL) differs significantly among populations, which has been hypothesised to result from selection imposed by inter-population variation in Diascia floral spur length. Here, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to investigate the population genetic structure of R. longimanus and to test if phenotypic differences in FLL translate into increased genetic differentiation (i) between R. longimanus populations and (ii) between phenotypes across populations. We also inferred the effects of demographic processes on population genetic structure and tested for genetic markers underpinning local adaptation. RESULTS: Populations showed marked genetic differentiation (average FST = 0.165), though differentiation was not statistically associated with differences between populations in FLL. All populations exhibited very low genetic diversity and were inferred to have gone through recent bottleneck events, suggesting extremely low effective population sizes. Genetic differentiation between samples pooled by leg length (short versus long) rather than by population of origin was even higher (FST = 0.260) than between populations, suggesting reduced interbreeding between long and short-legged individuals. Signatures of selection were detected in 1119 (3.8%) of a total of 29,721 SNP markers, CONCLUSIONS: Populations of R. longimanus appear to be small, bottlenecked and isolated. Though we could not detect the effect of local adaptation (FLL in response to floral spurs of host plants) on population genetic differentiation, short and long legged bees appeared to be partially differentiated, suggesting incipient ecological speciation. To test this hypothesis, greater resolution through the use of individual-based whole-genome analyses is now needed to quantify the degree of reproductive isolation between long and short legged bees between and even within populations.
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Affiliation(s)
- Belinda Kahnt
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
| | - Panagiotis Theodorou
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Antonella Soro
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Hilke Hollens-Kuhr
- Institute of Landscape Ecology, Westfälische Wilhelms-Universität Münster, Heisenbergstraße 2, 48149, Münster, Germany
| | - Michael Kuhlmann
- Zoological Museum, Kiel University, Hegewischstr. 3, 24105, Kiel, Germany
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Anton Pauw
- Department of Botany and Zoology, Stellenbosch University, Matieland, 7602, South Africa
| | - Robert J Paxton
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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19
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Michalak P, Kang L, Schou MF, Garner HR, Loeschcke V. Genomic signatures of experimental adaptive radiation in Drosophila. Mol Ecol 2018; 28:600-614. [PMID: 30375065 DOI: 10.1111/mec.14917] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/03/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022]
Abstract
Abiotic environmental factors play a fundamental role in determining the distribution, abundance and adaptive diversification of species. Empowered by new technologies enabling rapid and increasingly accurate examination of genomic variation in populations, researchers may gain new insights into the genomic background of adaptive radiation and stress resistance. We investigated genomic variation across generations of large-scale experimental selection regimes originating from a single founder population of Drosophila melanogaster, diverging in response to ecologically relevant environmental stressors: heat shock, heat knock down, cold shock, desiccation and starvation. When compared to the founder population, and to parallel unselected controls, there were more than 100,000 single nucleotide polymorphisms (SNPs) displaying consistent allelic changes in response to selective pressures across generations. These SNPs were found in both coding and noncoding sequences, with the highest density in promoter regions, and involved a broad range of functionalities, including molecular chaperoning by heat-shock proteins. The SNP patterns were highly stressor-specific despite considerable variation among line replicates within each selection regime, as reflected by a principal component analysis, and co-occurred with selective sweep regions. Only ~15% of SNPs with putatively adaptive changes were shared by at least two selective regimes, while less than 1% of SNPs diverged in opposite directions. Divergent stressors driving evolution in the experimental system of adaptive radiation left distinct genomic signatures, most pronounced in starvation and heat-shock selection regimes.
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Affiliation(s)
- Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia.,One Health Research Center, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia.,Institute of Evolution, University of Haifa, Haifa, Israel
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia
| | - Mads F Schou
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Harold R Garner
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia.,The Gibbs Cancer Center and Research Institute, Spartanburg, SC, USA
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20
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Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus. Nat Commun 2018; 9:4855. [PMID: 30451848 PMCID: PMC6242981 DOI: 10.1038/s41467-018-07374-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/25/2018] [Indexed: 01/08/2023] Open
Abstract
Pyrenestes finches are unique among birds in showing a non-sex-determined polymorphism in bill size and are considered a textbook example of disruptive selection. Morphs breed randomly with respect to bill size, and differ in diet and feeding performance relative to seed hardness. Previous breeding experiments are consistent with the polymorphism being controlled by a single genetic factor. Here, we use genome-wide pooled sequencing to explore the underlying genetic basis of bill morphology and identify a single candidate region. Targeted resequencing reveals extensive linkage disequilibrium across a 300 Kb region containing the insulin-like growth factor 1 (IGF1) gene, with a single 5-million-year-old haplotype associating with phenotypic dominance of the large-billed morph. We find no genetic similarities controlling bill size in the well-studied Darwin’s finches (Geospiza). Our results show how a single genetic factor may control bill size and provide a foundation for future studies to examine this phenomenon within and among avian species. Pyrenestes finches have a bill size polymorphism thought to be maintained by disruptive selection. Here, the authors identify a single candidate region, including insulin-like growth factor 1, differentiating small and large bill size morphs and a wider region differentiating the mega-billed morph.
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21
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Keehnen NL, Hill J, Nylin S, Wheat CW. Microevolutionary selection dynamics acting on immune genes of the green-veined white butterfly,Pieris napi. Mol Ecol 2018; 27:2807-2822. [DOI: 10.1111/mec.14722] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 04/08/2018] [Accepted: 04/23/2018] [Indexed: 12/15/2022]
Affiliation(s)
| | - Jason Hill
- Department of Zoology; Stockholm University; Stockholm Sweden
| | - Sören Nylin
- Department of Zoology; Stockholm University; Stockholm Sweden
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22
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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23
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Shi ZY, Yang CQ, Hao MD, Wang XY, Ward RD, Zhang AB. FuzzyID2: A software package for large data set species identification via barcoding and metabarcoding using hidden Markov models and fuzzy set methods. Mol Ecol Resour 2017; 18:666-675. [DOI: 10.1111/1755-0998.12738] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 10/20/2017] [Accepted: 11/12/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Zhi-yong Shi
- College of Life Sciences; Capital Normal University; Beijing China
| | - Cai-qing Yang
- College of Life Sciences; Capital Normal University; Beijing China
| | - Meng-di Hao
- College of Life Sciences; Capital Normal University; Beijing China
| | - Xiao-yang Wang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming Yunnan China
- Kunming College of Life Sciences; University of Chinese Academy of Sciences; Kunming Yunnan China
| | - Robert D. Ward
- CSIRO National Research Collections Australia; Hobart TAS Australia
| | - Ai-bing Zhang
- College of Life Sciences; Capital Normal University; Beijing China
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24
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Yablonovitch AL, Fu J, Li K, Mahato S, Kang L, Rashkovetsky E, Korol AB, Tang H, Michalak P, Zelhof AC, Nevo E, Li JB. Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates. Nat Commun 2017; 8:1570. [PMID: 29146998 PMCID: PMC5691062 DOI: 10.1038/s41467-017-01658-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/05/2017] [Indexed: 12/30/2022] Open
Abstract
Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution. In particular, relatively little is known about how transcriptional processes are fine-tuned to adjust to different environmental conditions. Here we study Drosophila melanogaster from 'Evolution Canyon' in Israel, which consists of two opposing slopes with divergent microclimates. We identify several hundred differentially expressed genes and dozens of differentially edited sites between flies from each slope, correlate these changes with genetic differences, and use CRISPR mutagenesis to validate that an intronic SNP in prominin regulates its editing levels. We also demonstrate that while temperature affects editing levels at more sites than genetic differences, genetically regulated sites tend to be less affected by temperature. This work shows the extent to which gene expression and RNA editing differ between flies from different microclimates, and provides insights into the regulation responsible for these differences.
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Affiliation(s)
- Arielle L Yablonovitch
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Jeremy Fu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kexin Li
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel.,Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Simpla Mahato
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA
| | | | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA.,Biocomplexity Institute, Virginia Tech, Blacksburg, VA, 24061, USA.,Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24060, USA
| | - Andrew C Zelhof
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel.
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Biophysics Program, Stanford University, Stanford, CA, 94305, USA.
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25
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Fariello MI, Boitard S, Mercier S, Robelin D, Faraut T, Arnould C, Recoquillay J, Bouchez O, Salin G, Dehais P, Gourichon D, Leroux S, Pitel F, Leterrier C, SanCristobal M. Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach. Mol Ecol 2017; 26:3700-3714. [DOI: 10.1111/mec.14141] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 01/19/2023]
Affiliation(s)
- María Inés Fariello
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
- Facultad de Ingeniería; Universidad de la República; Montevideo Uruguay
- Institut Pasteur; Unidad de Bioinformática; Montevideo Uruguay
| | - Simon Boitard
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Sabine Mercier
- Département Mathématique-Informatique, UFR SES; Université de Toulouse II; Toulouse Cedex 09 France
- UMR5219, Institut de Mathématiques; Université de Toulouse; Toulouse France
| | - David Robelin
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Thomas Faraut
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Cécile Arnould
- Unité de Physiologie de la Reproduction et des Comportements, UMR INRA - CNRS; Université de Tours; Tours France
| | - Julien Recoquillay
- UR83 Recherches Avicoles; INRA; Tours Nouzilly France
- Hubbard; Châteaubourg; France
| | - Olivier Bouchez
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
- GeT-PlaGe Genotoul; INRA; Castanet-Tolosan France
| | - Gérald Salin
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
- GeT-PlaGe Genotoul; INRA; Castanet-Tolosan France
| | | | - David Gourichon
- UE1295 Pôle d'Expérimentation Avicole de Tours; Tours Nouzilly France
| | - Sophie Leroux
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Frédérique Pitel
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
| | - Christine Leterrier
- Unité de Physiologie de la Reproduction et des Comportements, UMR INRA - CNRS; Université de Tours; Tours France
| | - Magali SanCristobal
- INRA, INPT, INP-ENVT, UMR1388, GenPhySE; Université de Toulouse; Castanet-Tolosan France
- UMR5219, Institut de Mathématiques; Université de Toulouse; Toulouse France
- Département de Génie Mathématiques; INSA; Toulouse Cedex 4 France
- UMR 1201 Dynafor; INRA - INP Toulouse; Castanet-Tolosan France
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26
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Michalak P, Kang L, Sarup PM, Schou MF, Loeschcke V. Nucleotide diversity inflation as a genome-wide response to experimental lifespan extension in Drosophila melanogaster. BMC Genomics 2017; 18:84. [PMID: 28088192 PMCID: PMC5237518 DOI: 10.1186/s12864-017-3485-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/10/2017] [Indexed: 11/20/2022] Open
Abstract
Background Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often reach intermediate population frequencies due to balancing selection, an elusive process when sought out empirically. Alternatively, genetic diversity may increase as a result of positive frequency-dependent selection and genetic purging in bottlenecked populations. Results While experimental evolution systems with directional phenotypic selection typically result in at least local heterozygosity loss, we report that selection for increased lifespan in Drosophila melanogaster leads to an extensive genome-wide increase of nucleotide diversity in the selected lines compared to replicate control lines, pronounced in regions with no or low recombination, such as chromosome 4 and centromere neighborhoods. These changes, particularly in coding sequences, are most consistent with the operation of balancing selection and the antagonistic pleiotropy theory of aging and life history traits that tend to be intercorrelated. Genes involved in antioxidant defenses, along with multiple lncRNAs, were among those most affected by balancing selection. Despite the overwhelming genetic diversification and the paucity of selective sweep regions, two genes with functions important for central nervous system and memory, Ptp10D and Ank2, evolved under positive selection in the longevity lines. Conclusions Overall, the ‘evolve-and-resequence’ experimental approach proves successful in providing unique insights into the complex evolutionary dynamics of genomic regions responsible for longevity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3485-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pawel Michalak
- Biocomplexity Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA.
| | - Lin Kang
- Biocomplexity Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA
| | - Pernille M Sarup
- Department of Bioscience, Aarhus University, Ny Munkegade 114-116, Aarhus, DK-8000, Denmark
| | - Mads F Schou
- Department of Bioscience, Aarhus University, Ny Munkegade 114-116, Aarhus, DK-8000, Denmark
| | - Volker Loeschcke
- Department of Bioscience, Aarhus University, Ny Munkegade 114-116, Aarhus, DK-8000, Denmark.
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27
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Phillips MA, Long AD, Greenspan ZS, Greer LF, Burke MK, Villeponteau B, Matsagas KC, Rizza CL, Mueller LD, Rose MR. Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster. Sci Rep 2016; 6:39281. [PMID: 28004838 PMCID: PMC5177908 DOI: 10.1038/srep39281] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/21/2016] [Indexed: 01/07/2023] Open
Abstract
Experimental evolutionary genomics now allows biologists to test fundamental theories concerning the genetic basis of adaptation. We have conducted one of the longest laboratory evolution experiments with any sexually-reproducing metazoan, Drosophila melanogaster. We used next-generation resequencing data from this experiment to examine genome-wide patterns of genetic variation over an evolutionary time-scale that approaches 1,000 generations. We also compared measures of variation within and differentiation between our populations to simulations based on a variety of evolutionary scenarios. Our analysis yielded no clear evidence of hard selective sweeps, whereby natural selection acts to increase the frequency of a newly-arising mutation in a population until it becomes fixed. We do find evidence for selection acting on standing genetic variation, as independent replicate populations exhibit similar population-genetic dynamics, without obvious fixation of candidate alleles under selection. A hidden-Markov model test for selection also found widespread evidence for selection. We found more genetic variation genome-wide, and less differentiation between replicate populations genome-wide, than arose in any of our simulated evolutionary scenarios.
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Affiliation(s)
- Mark A. Phillips
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA
| | - Anthony D. Long
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA
- Genescient Inc., Fountain Valley, CA 92708, USA
| | - Zachary S. Greenspan
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA
| | - Lee F. Greer
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA
- Genescient Inc., Fountain Valley, CA 92708, USA
| | - Molly K. Burke
- Oregon State University, Department of Integrative Biology, Corvallis, OR 97331, USA
| | | | | | | | - Laurence D. Mueller
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA
- Genescient Inc., Fountain Valley, CA 92708, USA
| | - Michael R. Rose
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA
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28
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Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data. G3-GENES GENOMES GENETICS 2016; 6:3507-3515. [PMID: 27613752 PMCID: PMC5100849 DOI: 10.1534/g3.116.034488] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and widespread use of this method for many research questions, ranging from unraveling the genetic basis of complex traits, to the clonal evolution of cancer cells. Because the accuracy of Pool-Seq could be affected by many potential sources of error, several studies have determined, for example, the influence of sequencing technology, the library preparation protocol, and mapping parameters. Nevertheless, the impact of the mapping tools has not yet been evaluated. Using simulated and real Pool-Seq data, we demonstrate a substantial impact of the mapping tools, leading to characteristic false positives in genome-wide scans. The problem of false positives was particularly pronounced when data with different read lengths and insert sizes were compared. Out of 14 evaluated algorithms novoalign, bwa mem and clc4 are most suitable for mapping Pool-Seq data. Nevertheless, no single algorithm is sufficient for avoiding all false positives. We show that the intersection of the results of two mapping algorithms provides a simple, yet effective, strategy to eliminate false positives. We propose that the implementation of a consistent Pool-Seq bioinformatics pipeline, building on the recommendations of this study, can substantially increase the reliability of Pool-Seq results, in particular when libraries generated with different protocols are being compared.
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29
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Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution. Genetics 2016; 204:723-735. [PMID: 27542959 PMCID: PMC5068858 DOI: 10.1534/genetics.116.191197] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/30/2016] [Indexed: 01/22/2023] Open
Abstract
The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their Ne estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest.
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30
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Abstract
Whole-genome sequencing of wild-derived rat species can provide novel genomic resources, which may help decipher the genetics underlying complex phenotypes. As a notorious pest, reservoir of human pathogens, and colonizer, the Asian house rat, Rattus tanezumi, is successfully adapted to its habitat. However, little is known regarding genetic variation in this species. In this study, we identified over 41,000,000 single-nucleotide polymorphisms, plus insertions and deletions, through whole-genome sequencing and bioinformatics analyses. Moreover, we identified over 12,000 structural variants, including 143 chromosomal inversions. Further functional analyses revealed several fixed nonsense mutations associated with infection and immunity-related adaptations, and a number of fixed missense mutations that may be related to anticoagulant resistance. A genome-wide scan for loci under selection identified various genes related to neural activity. Our whole-genome sequencing data provide a genomic resource for future genetic studies of the Asian house rat species and have the potential to facilitate understanding of the molecular adaptations of rats to their ecological niches.
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31
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Stam R, Scheikl D, Tellier A. Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population. Genome Biol Evol 2016; 8:1501-15. [PMID: 27189991 PMCID: PMC4898808 DOI: 10.1093/gbe/evw094] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2016] [Indexed: 12/13/2022] Open
Abstract
Nod-like receptors (NLRs) are nucleotide-binding domain and leucine-rich repeats containing proteins that are important in plant resistance signaling. Many of the known pathogen resistance (R) genes in plants are NLRs and they can recognize pathogen molecules directly or indirectly. As such, divergence and copy number variants at these genes are found to be high between species. Within populations, positive and balancing selection are to be expected if plants coevolve with their pathogens. In order to understand the complexity of R-gene coevolution in wild nonmodel species, it is necessary to identify the full range of NLRs and infer their evolutionary history. Here we investigate and reveal polymorphism occurring at 220 NLR genes within one population of the partially selfing wild tomato species Solanum pennellii. We use a combination of enrichment sequencing and pooling ten individuals, to specifically sequence NLR genes in a resource and cost-effective manner. We focus on the effects which different mapping and single nucleotide polymorphism calling software and settings have on calling polymorphisms in customized pooled samples. Our results are accurately verified using Sanger sequencing of polymorphic gene fragments. Our results indicate that some NLRs, namely 13 out of 220, have maintained polymorphism within our S. pennellii population. These genes show a wide range of πN/πS ratios and differing site frequency spectra. We compare our observed rate of heterozygosity with expectations for this selfing and bottlenecked population. We conclude that our method enables us to pinpoint NLR genes which have experienced natural selection in their habitat.
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Affiliation(s)
- Remco Stam
- Section of Population Genetics, Technische Universität München, Freising, Germany
| | - Daniela Scheikl
- Section of Population Genetics, Technische Universität München, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, Technische Universität München, Freising, Germany
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32
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Asgharian H, Chang PL, Lysenkov S, Scobeyeva VA, Reisen WK, Nuzhdin SV. Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors. Proc Biol Sci 2016; 282:rspb.2015.0728. [PMID: 26085592 PMCID: PMC4590483 DOI: 10.1098/rspb.2015.0728] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5–20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.
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Affiliation(s)
- Hosseinali Asgharian
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter L Chang
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergey Lysenkov
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA Department of Evolution, Moscow State University, Moscow 119991, Russia
| | | | - William K Reisen
- Center for Vectorborne Diseases, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Sergey V Nuzhdin
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA Department of Evolution, Moscow State University, Moscow 119991, Russia St. Petersburg State Polytechnical University, Sanct Petersburg, Russia
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Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution system. BMC Genomics 2016; 17:233. [PMID: 26979755 PMCID: PMC4791783 DOI: 10.1186/s12864-016-2556-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Experimental evolution studies, coupled with whole genome resequencing and advances in bioinformatics, have become a powerful tool for exploring how populations respond to selection at the genome-wide level, complementary to genome-wide association studies (GWASs) and linkage mapping experiments as strategies to connect genotype and phenotype. In this experiment, we analyzed genomes of Drosophila melanogaster from lines evolving under long-term directional selection for increased desiccation resistance in comparison with control (no-selection) lines. RESULTS We demonstrate that adaptive responses to desiccation stress have exerted extensive footprints on the genomes, manifested through a high degree of fixation of alleles in surrounding neighborhoods of eroded heterozygosity. These patterns were highly convergent across replicates, consistent with signatures of 'soft' selective sweeps, where multiple alleles present as standing genetic variation become beneficial and sweep through the replicate populations at the same time. Albeit much less frequent, we also observed line-unique sweep regions with zero or near-zero heterozygosity, consistent with classic, or 'hard', sweeps, where novel rather than pre-existing adaptive mutations may have been driven to fixation. Genes responsible for cuticle and protein deubiquitination seemed to be central to these selective sweeps. High divergence within coding sequences between selected and control lines was also reflected by significant results of the McDonald-Kreitman and Ka/Ks tests, showing that as many as 347 genes may have been under positive selection. CONCLUSIONS Desiccation stress, a common challenge to many organisms inhabiting dry environments, proves to be a very potent selecting factor having a big impact on genome diversity.
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Fracassetti M, Griffin PC, Willi Y. Validation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyrata. PLoS One 2015; 10:e0140462. [PMID: 26461136 PMCID: PMC4604096 DOI: 10.1371/journal.pone.0140462] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 09/25/2015] [Indexed: 12/21/2022] Open
Abstract
Sequencing pooled DNA of multiple individuals from a population instead of sequencing individuals separately has become popular due to its cost-effectiveness and simple wet-lab protocol, although some criticism of this approach remains. Here we validated a protocol for pooled whole-genome re-sequencing (Pool-seq) of Arabidopsis lyrata libraries prepared with low amounts of DNA (1.6 ng per individual). The validation was based on comparing single nucleotide polymorphism (SNP) frequencies obtained by pooling with those obtained by individual-based Genotyping By Sequencing (GBS). Furthermore, we investigated the effect of sample number, sequencing depth per individual and variant caller on population SNP frequency estimates. For Pool-seq data, we compared frequency estimates from two SNP callers, VarScan and Snape; the former employs a frequentist SNP calling approach while the latter uses a Bayesian approach. Results revealed concordance correlation coefficients well above 0.8, confirming that Pool-seq is a valid method for acquiring population-level SNP frequency data. Higher accuracy was achieved by pooling more samples (25 compared to 14) and working with higher sequencing depth (4.1× per individual compared to 1.4× per individual), which increased the concordance correlation coefficient to 0.955. The Bayesian-based SNP caller produced somewhat higher concordance correlation coefficients, particularly at low sequencing depth. We recommend pooling at least 25 individuals combined with sequencing at a depth of 100× to produce satisfactory frequency estimates for common SNPs (minor allele frequency above 0.05).
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Affiliation(s)
- Marco Fracassetti
- Institute of Biology, Evolutionary Botany, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail:
| | - Philippa C. Griffin
- Institute of Biology, Evolutionary Botany, University of Neuchâtel, Neuchâtel, Switzerland
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Yvonne Willi
- Institute of Biology, Evolutionary Botany, University of Neuchâtel, Neuchâtel, Switzerland
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Sequencing pools of individuals — mining genome-wide polymorphism data without big funding. Nat Rev Genet 2014; 15:749-63. [DOI: 10.1038/nrg3803] [Citation(s) in RCA: 512] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Lynch M, Bost D, Wilson S, Maruki T, Harrison S. Population-genetic inference from pooled-sequencing data. Genome Biol Evol 2014; 6:1210-8. [PMID: 24787620 PMCID: PMC4040993 DOI: 10.1093/gbe/evu085] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although pooled-population sequencing has become a widely used approach for estimating allele frequencies, most work has proceeded in the absence of a proper statistical framework. We introduce a self-sufficient, closed-form, maximum-likelihood estimator for allele frequencies that accounts for errors associated with sequencing, and a likelihood-ratio test statistic that provides a simple means for evaluating the null hypothesis of monomorphism. Unbiased estimates of allele frequencies (where N is the number of individuals sampled) appear to be unachievable, and near-certain identification of a polymorphism requires a minor-allele frequency . A framework is provided for testing for significant differences in allele frequencies between populations, taking into account sampling at the levels of individuals within populations and sequences within pooled samples. Analyses that fail to account for the two tiers of sampling suffer from very large false-positive rates and can become increasingly misleading with increasing depths of sequence coverage. The power to detect significant allele-frequency differences between two populations is very limited unless both the number of sampled individuals and depth of sequencing coverage exceed 100.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington
| | - Darius Bost
- Department of Biology, North Carolina A&T State University
| | - Sade Wilson
- Department of Biology, North Carolina A&T State University
| | | | - Scott Harrison
- Department of Biology, North Carolina A&T State University
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Clément JAJ, Toulza E, Gautier M, Parrinello H, Roquis D, Boissier J, Rognon A, Moné H, Mouahid G, Buard J, Mitta G, Grunau C. Private selective sweeps identified from next-generation pool-sequencing reveal convergent pathways under selection in two inbred Schistosoma mansoni strains. PLoS Negl Trop Dis 2013; 7:e2591. [PMID: 24349597 PMCID: PMC3861164 DOI: 10.1371/journal.pntd.0002591] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 10/30/2013] [Indexed: 01/12/2023] Open
Abstract
Background The trematode flatworms of the genus Schistosoma, the causative agents of schistosomiasis, are among the most prevalent parasites in humans, affecting more than 200 million people worldwide. In this study, we focused on two well-characterized strains of S. mansoni, to explore signatures of selection. Both strains are highly inbred and exhibit differences in life history traits, in particular in their compatibility with the intermediate host Biomphalaria glabrata. Methodology/Principal Findings We performed high throughput sequencing of DNA from pools of individuals of each strain using Illumina technology and identified single nucleotide polymorphisms (SNP) and copy number variations (CNV). In total, 708,898 SNPs were identified and roughly 2,000 CNVs. The SNPs revealed low nucleotide diversity (π = 2×10−4) within each strain and a high differentiation level (Fst = 0.73) between them. Based on a recently developed in-silico approach, we further detected 12 and 19 private (i.e. specific non-overlapping) selective sweeps among the 121 and 151 sweeps found in total for each strain. Conclusions/Significance Functional annotation of transcripts lying in the private selective sweeps revealed specific selection for functions related to parasitic interaction (e.g. cell-cell adhesion or redox reactions). Despite high differentiation between strains, we identified evolutionary convergence of genes related to proteolysis, known as a key virulence factor and a potential target of drug and vaccine development. Our data show that pool-sequencing can be used for the detection of selective sweeps in parasite populations and enables one to identify biological functions under selection. Adaptation of parasites to their environment is governed by the principle of selection. Favourable mutations are fixed in populations while deleterious mutations are progressively eliminated. Here, we aimed to find signatures of selection in two strains of Schistosoma mansoni, the causative agent of intestinal schistosomiasis. The strains differ in specific characters, in particular in their capacity to infect intermediate host snails. The reason for this is unknown and understanding it could help control the spreading of the disease. Finding footprints of adaptation to different snail hosts would lead to the discovery of genes that are particularly important for the interaction. Since a single parasite does not contain sufficient DNA to be sequenced, we pooled several individuals, sequenced them as a whole analysed them. In the regions under selection we found genes that are indeed linked to the parasitic lifestyle. We also discovered that natural selection led to diversification of genes that are related to proteolysis, the process by which the parasite destroys host tissue. The related proteins are considered good targets for drug development and vaccination. Our results suggest that in natural populations many variants of these genes exist and that they evolve rapidly, which might hamper therapeutic approaches.
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Affiliation(s)
- Julie A. J. Clément
- Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
| | - Eve Toulza
- Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
| | - Mathieu Gautier
- INRA, UMR CBGP (INRA – IRD – Cirad – Montpellier SupAgro), Montferrier-sur-Lez, France
| | | | - David Roquis
- Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
| | - Jérôme Boissier
- Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
| | - Anne Rognon
- Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
| | - Hélène Moné
- Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
| | - Gabriel Mouahid
- Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
| | - Jérôme Buard
- CNRS, Institut de Génétique Humaine, UPR 1142, Montpellier, France
| | - Guillaume Mitta
- Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
| | - Christoph Grunau
- Univ.Perpignan Via Domitia, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Perpignan, France
- * E-mail:
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Ferretti L, Ramos-Onsins SE, Pérez-Enciso M. Population genomics from pool sequencing. Mol Ecol 2013; 22:5561-76. [DOI: 10.1111/mec.12522] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 08/03/2013] [Accepted: 09/06/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Luca Ferretti
- Center for Research in Agricultural Genomics (CRAG); UAB 08193 Bellaterra Spain
| | | | - Miguel Pérez-Enciso
- Center for Research in Agricultural Genomics (CRAG); UAB 08193 Bellaterra Spain
- Department of Animal Science and Food; Faculty of Veterinary; Universitat Autonoma de Barcelona; 08193 Bellaterra Spain
- Institut Català de Recerca i Estudis Avancats (ICREA); Passeig Lluís Companys 23 08010 Barcelona Spain
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Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA. Stacks: an analysis tool set for population genomics. Mol Ecol 2013; 22:3124-40. [PMID: 23701397 DOI: 10.1111/mec.12354] [Citation(s) in RCA: 2073] [Impact Index Per Article: 188.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 04/16/2013] [Accepted: 04/16/2013] [Indexed: 02/06/2023]
Abstract
Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
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Affiliation(s)
- Julian Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
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