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Lu Y, Li M, Gao Z, Ma H, Chong Y, Hong J, Wu J, Wu D, Xi D, Deng W. Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics. Int J Mol Sci 2025; 26:372. [PMID: 39796227 PMCID: PMC11719799 DOI: 10.3390/ijms26010372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Revised: 12/26/2024] [Accepted: 01/02/2025] [Indexed: 01/13/2025] Open
Abstract
With the rapid advancement of high-throughput sequencing technologies, whole genome sequencing (WGS) has emerged as a crucial tool for studying genetic variation and population structure. Utilizing population genomics tools to analyze resequencing data allows for the effective integration of selection signals with population history, precise estimation of effective population size, historical population trends, and structural insights, along with the identification of specific genetic loci and variations. This paper reviews current whole genome sequencing technologies, detailing primary research methods, relevant software, and their advantages and limitations within population genomics. The goal is to examine the application and progress of resequencing technologies in this field and to consider future developments, including deep learning models and machine learning algorithms, which promise to enhance analytical methodologies and drive further advancements in population genomics.
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Affiliation(s)
- Ying Lu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
| | - Mengfei Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
| | - Zhendong Gao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
| | - Hongming Ma
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
| | - Yuqing Chong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
| | - Jieyun Hong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
| | - Jiao Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
| | - Dongwang Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
| | - Dongmei Xi
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
| | - Weidong Deng
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.L.); (M.L.); (Z.G.); (H.M.); (Y.C.); (J.H.); (J.W.); (D.W.)
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Kunming 650201, China
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Alam K, Raviraj VS, Paul M, Ghosh S, Nalvadi C, Kar PK, Saha S. Wild silk insect of Simlipal biosphere and its molecular genetic diversity for conservation. Biol Futur 2024; 75:459-475. [PMID: 39112755 DOI: 10.1007/s42977-024-00239-x] [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: 02/22/2024] [Accepted: 07/25/2024] [Indexed: 12/17/2024]
Abstract
Designated silkworms (Antheraea mylitta D.) are found in the Smilipal Biosphere Reserve (SBR) and consist of four ecological groups. This study examined the genetics of eight ethnic groups from four ecological groups (Modal, Nalia, Bogai and Jata) using RAPD and ISSR markers. The RAPD primer produced 127 bands, of which 41 out of 116 polymorphic regions had a PIC value above 0.45. ISSR markers assigned PIC data values to 57 of 127 polymorphic sites. Cluster analysis revealed genetic differences between ecological populations, with markers separating ecological populations into groups. Low testicles and high genetic diversity indicate that these individuals are at different levels. If adequate protection is not provided, the risk of extinction of ecospecies designed in SBR increases. This study shows that the combined use of RAPD + ISSR markers can improve the results of the technology in identifying different diseases in situations where genomic information is limited.
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Affiliation(s)
- Khasru Alam
- Cytogenetics & Plant Breeding Section, Department of Sericulture, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, 733134, India
| | - V S Raviraj
- Biotechnology Division, Central Sericultural Research and Training Institute, Berhampore, West Bengal, India
| | - Monalisa Paul
- Cytogenetics & Plant Breeding Section, Department of Sericulture, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, 733134, India
| | - Sumana Ghosh
- Cytogenetics & Plant Breeding Section, Department of Sericulture, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, 733134, India
| | - Chandrakant Nalvadi
- Silkworm Breeding Section, Central Sericultural Research and Training Institute, Mysore, Karnataka, India
| | - Prasanta Kumar Kar
- Basic Seed Multiplication & Training Centre, Pali, Chhattisgarh, 495449, India
| | - Soumen Saha
- Cytogenetics & Plant Breeding Section, Department of Sericulture, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, 733134, India.
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Perera OP, Saha S, Glover J, Parys KA, Allen KC, Grozeva S, Kurtz R, Reddy GVP, Johnston JS, Daly M, Swale T. A chromosome scale assembly of the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), genome. BMC Res Notes 2023; 16:125. [PMID: 37370172 DOI: 10.1186/s13104-023-06408-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
OBJECTIVE The tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae), is a pest damaging many cultivated crops in North America. Although partial transcriptome data are available for this pest, a genome assembly was not available for this species. This assembly of a high-quality chromosome-length genome of TPB is aimed to develop the genetic resources that can provide the foundation required for advancing research on this species. RESULTS The initial genome of TPB assembled with paired-end nucleotide sequences generated with Illumina technology was scaffolded with Illumina HiseqX reads generated from a proximity ligated (HiC) library to obtain a high-quality genome assembly. The final assembly contained 3963 scaffolds longer than 1 kbp to yield a genome of 599.96 Mbp. The N50 of the TPB genome assembly was 35.64 Mbp and 98.68% of the genome was assembled into 17 scaffolds larger than 1 Mbp. This megabase scaffold number is the same as the number of chromosomes observed in karyotyping of this insect. The TPB genome is known to have high repetitive DNA content, and the reduced assembled genome size compared to flowcytometric estimates of approximately 860 Mbp may be due to the collapsed assembly of highly similar regions.
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Affiliation(s)
- O P Perera
- Southern Insect Management Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA.
| | - Surya Saha
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY, 14853, USA
| | - James Glover
- Southern Insect Management Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Katherine A Parys
- Pollinator Health in Southern Crop Ecosystems Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - K Clint Allen
- Southern Insect Management Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Snejana Grozeva
- Institute of Zoology, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel, Sofia, 1000, Bulgaria
| | - Ryan Kurtz
- , Cotton, Incorporated, Cary, NC, 27513, USA
| | - Gadi V P Reddy
- Southern Insect Management Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Mark Daly
- Dovetail Genomics, LLC, 100 Enterprise Way, Suite A101, Scotts Valley, CA, 95066, USA
| | - Thomas Swale
- Dovetail Genomics, LLC, 100 Enterprise Way, Suite A101, Scotts Valley, CA, 95066, USA
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Lee SR, Son DC. Genetic diversity pattern reveals the primary determinant of burcucumber ( Sicyos angulatus L.) invasion in Korea. FRONTIERS IN PLANT SCIENCE 2022; 13:997521. [PMID: 36457533 PMCID: PMC9706109 DOI: 10.3389/fpls.2022.997521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Biological invasion is a complex process associated with propagule pressure, dispersal ability, environmental constraints, and human interventions, which leave genetic signatures. The population genetics of an invasive species thus provides invaluable insights into the patterns of invasion. Burcucumber, one of the most detrimental weeds for soybean production in US, has recently colonized Korea and rapidly spread posing a great threat to the natural ecosystem. We aim to infer the determinants of the rapid burcucumber invasion by examining the genetic diversity, demography, and spread pattern with advanced genomic tools. We employed 2,696 genome-wide single-nucleotide polymorphisms to assess the level of diversity and the spatial pattern associated with the landscape factors and to infer the demographic changes of 24 populations (364 genotypes) across four major river basins with the east coastal streams in South Korea. Through the approximate Bayesian computation, we inferred the likely invasion scenario of burcucumber in Korea. The landscape genetics approach adopting the circuit theory and MaxEnt model was applied to determine the landscape contributors. Our data suggested that most populations have experienced population bottlenecks, which led to lowered within-population genetic diversity and inflated population divergences. Burcucumber colonization in Korea has strongly been affected by demographic bottlenecks and multiple introductions, whereas environmental factors were not the primary determinant of the invasion. Our work highlighted the significance of preventing secondary introductions, particularly for aggressive weedy plants such as the burcucumber.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, South Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, South Korea
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Abstract
The ways in which genetic variation is distributed within and among populations is a key determinant of the evolutionary features of a species. However, most comprehensive studies of these features have been restricted to studies of subdivision in settings known to have been driven by local adaptation, leaving our understanding of the natural dispersion of allelic variation less than ideal. Here, we present a geographic population-genomic analysis of 10 populations of the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics. These populations exhibit a pattern of moderate isolation-by-distance, with an average migration rate of 0.6 individuals per generation, and average effective population sizes of ∼650,000 individuals. Most populations contain numerous private alleles, and genomic scans highlight the presence of islands of excessively high population subdivision for more common alleles. A large fraction of such islands of population divergence likely reflect historical neutral changes, including rare stochastic migration and hybridization events. The data do point to local adaptive divergence, although the precise nature of the relevant variation is diffuse and cannot be associated with particular loci, despite the very large sample sizes involved in this study. In contrast, an analysis of between-species divergence highlights positive selection operating on a large set of genes with functions nearly nonoverlapping with those involved in local adaptation, in particular ribosome structure, mitochondrial bioenergetics, light reception and response, detoxification, and gene regulation. These results set the stage for using D. pulex as a model for understanding the relationship between molecular and cellular evolution in the context of natural environments.
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Affiliation(s)
- Takahiro Maruki
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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Di Lecce I, Sudyka J, Westneat DF, Szulkin M. Preserving avian blood and DNA sampled in the wild: A survey of personal experiences. Ecol Evol 2022; 12:e9232. [PMID: 36052299 PMCID: PMC9424668 DOI: 10.1002/ece3.9232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Collecting and storing biological material from wild animals in a way that does not deteriorate DNA quality for subsequent analyses is instrumental for research in ecology and evolution. Our aims were to gather reports on the effectiveness of methods commonly used by researchers for the field collection and long-term storage of blood samples and DNA extracts from wild birds. Personal experiences were collected with an online survey targeted specifically at researchers sampling wild birds. Many researchers experienced problems with blood sample storage but not with DNA extract storage. Storage issues generated problems with obtaining adequate DNA quality and sufficient DNA quantity for the targeted molecular analyses but were not related to season of blood sampling, access to equipment, transporting samples, temperature, and method of blood storage. Final DNA quality and quantity were also not affected by storage time before DNA extraction or the methods used to extract DNA. We discuss practical aspects of field collection and storage and provide some general recommendations, with a list of pros and cons of different preservation methods of avian blood samples and DNA extracts.
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Affiliation(s)
- Irene Di Lecce
- Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Joanna Sudyka
- Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | | | - Marta Szulkin
- Centre of New TechnologiesUniversity of WarsawWarsawPoland
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Mohamed WMA, Moustafa MAM, Thu MJ, Kakisaka K, Chatanga E, Ogata S, Hayashi N, Taya Y, Ohari Y, Naguib D, Qiu Y, Matsuno K, Bawm S, Htun LL, Barker SC, Katakura K, Ito K, Nonaka N, Nakao R. Comparative mitogenomics elucidates the population genetic structure of Amblyomma testudinarium in Japan and a closely related Amblyomma species in Myanmar. Evol Appl 2022; 15:1062-1078. [PMID: 35899249 PMCID: PMC9309438 DOI: 10.1111/eva.13426] [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: 02/13/2022] [Revised: 04/27/2022] [Accepted: 05/29/2022] [Indexed: 12/05/2022] Open
Abstract
Ticks are the second most important vector capable of transmitting diseases affecting the health of both humans and animals. Amblyomma testudinarium Koch 1844 (Acari: Ixodidae), is a hard tick species having a wide geographic distribution in Asia. In this study, we analyzed the composition of A. testudinarium whole mitogenomes from various geographical regions in Japan and investigated the population structure, demographic patterns, and phylogeographic relationship with other ixodid species. In addition, we characterized a potentially novel tick species closely related to A. testudinarium from Myanmar. Phylogeographic inference and evolutionary dynamics based on the 15 mitochondrial coding genes supported that A. testudinarium population in Japan is resolved into a star-like haplogroup and suggested a distinct population structure of A. testudinarium from Amami island in Kyushu region. Correlation analysis using Mantel test statistics showed that no significant correlation was observed between the genetic and geographic distances calculated between the A. testudinarium population from different localities in Japan. Finally, demographic analyses, including mismatch analysis and Tajima's D test, suggested a possibility of recent population expansion occurred within Japanese haplogroup after a bottleneck event. Although A. testudinarium has been considered widespread and common in East and Southeast Asia, the current study suggested that potentially several cryptic Amblyomma spp. closely related to A. testudinarium are present in Asia.
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Affiliation(s)
- Wessam Mohamed Ahmed Mohamed
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
- Division of Bioinformatics, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
| | - Mohamed Abdallah Mohamed Moustafa
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
- Department of Animal Medicine, Faculty of Veterinary MedicineSouth Valley UniversityQenaEgypt
| | - May June Thu
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
- Department of Food and Drug AdministrationMinistry of HealthNay Pyi TawMyanmar
| | - Keita Kakisaka
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Elisha Chatanga
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
- Department of Veterinary Pathobiology, Faculty of Veterinary MedicineLilongwe University of Agriculture and Natural ResourcesLilongweMalawi
| | - Shohei Ogata
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Naoki Hayashi
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Yurie Taya
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Yuma Ohari
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Doaa Naguib
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
- Department of Hygiene and Zoonoses, Faculty of Veterinary MedicineMansoura UniversityMansouraEgypt
| | - Yongjin Qiu
- Division of International Research Promotion, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
| | - Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
- International Collaboration Unit, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
- One Health Research CenterHokkaido UniversitySapporoJapan
| | - Saw Bawm
- Department of International Relations and Information TechnologyUniversity of Veterinary ScienceNay Pyi TawMyanmar
- Department of Pharmacology and ParasitologyUniversity of Veterinary ScienceNay Pyi TawMyanmar
| | - Lat Lat Htun
- Department of Pharmacology and ParasitologyUniversity of Veterinary ScienceNay Pyi TawMyanmar
| | - Stephen C. Barker
- Department of Parasitology, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - Ken Katakura
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kimihito Ito
- Division of Bioinformatics, International Institute for Zoonosis ControlHokkaido UniversitySapporoJapan
| | - Nariaki Nonaka
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
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Benestan LM, Rougemont Q, Senay C, Normandeau E, Parent E, Rideout R, Bernatchez L, Lambert Y, Audet C, Parent GJ. Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus). Evol Appl 2021; 14:588-606. [PMID: 33664797 PMCID: PMC7896722 DOI: 10.1111/eva.13143] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.
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Affiliation(s)
- Laura M. Benestan
- CEFEUniv Montpellier, CNRS, EPHE‐PSL UniversityIRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Caroline Senay
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Eric Parent
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Rick Rideout
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreN.L.St. John’sCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Yvan Lambert
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Céline Audet
- Institut des sciences de la mer de RimouskiUniversité du Québec à RimouskiRimouskiQCCanada
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Cortinovis G, Frascarelli G, Di Vittori V, Papa R. Current State and Perspectives in Population Genomics of the Common Bean. PLANTS (BASEL, SWITZERLAND) 2020; 9:E330. [PMID: 32150958 PMCID: PMC7154925 DOI: 10.3390/plants9030330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 11/17/2022]
Abstract
* Correspondence: r [...].
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Affiliation(s)
| | | | | | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.C.); (G.F.); (V.D.V.)
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10
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Alves‐Pereira A, Clement CR, Picanço‐Rodrigues D, Veasey EA, Dequigiovanni G, Ramos SLF, Pinheiro JB, de Souza AP, Zucchi MI. A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia. Evol Appl 2020; 13:342-361. [PMID: 31993081 PMCID: PMC6976959 DOI: 10.1111/eva.12873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/14/2019] [Indexed: 12/19/2022] Open
Abstract
Amazonia is a major world centre of plant domestication, but the genetics of domestication remains unclear for most Amazonian crops. Manioc (Manihot esculenta) is the most important staple food crop that originated in this region. Although manioc is relatively well-studied, little is known about the diversification of bitter and sweet landraces and how they were dispersed across Amazonia. We evaluated single nucleotide polymorphisms (SNPs) in wild and cultivated manioc to identify outlier SNPs putatively under selection and to assess the neutral genetic structure of landraces to make inferences about the evolution of the crop in Amazonia. Some outlier SNPs were in putative manioc genes possibly related to plant architecture, transcriptional regulation and responses to stress. The neutral SNPs revealed contrasting genetic structuring for bitter and sweet landraces. The outlier SNPs may be signatures of the genomic changes resulting from domestication, while the neutral genetic structure suggests independent dispersals for sweet and bitter manioc, possibly related to the earlier domestication and diversification of the former. Our results highlight the role of ancient peoples and current smallholders in the management and conservation of manioc genetic diversity, including putative genes and specific genetic resources with adaptive potential in the context of climate change.
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Affiliation(s)
- Alessandro Alves‐Pereira
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
| | | | | | - Elizabeth Ann Veasey
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Gabriel Dequigiovanni
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Santiago Linorio Ferreyra Ramos
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - José Baldin Pinheiro
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Anete Pereira de Souza
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
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Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F. An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity. Mol Ecol Resour 2019; 19:1497-1515. [PMID: 31359622 PMCID: PMC7115901 DOI: 10.1111/1755-0998.13070] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 06/30/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.
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Affiliation(s)
- Badr Benjelloun
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Frédéric Boyer
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Wahid Zamani
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, 46417-76489 Noor, Mazandaran, Iran
| | - Stefan Engelen
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Adriana Alberti
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Florian J. Alberto
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Mohamed BenBati
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Mustapha Ibnelbachyr
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Mouad Chentouf
- National Institute of Agronomic Research (INRA Maroc), CRRA Tangier, 90010 Tangier, Morocco
| | - Abdelmajid Bechchari
- National Institute of Agronomic Research (INRA Maroc), CRRA Oujda, 60000 Oujda, Morocco
| | - Hamid R. Rezaei
- Department of Environmental Sci, Gorgan University of Agricultural Sciences & Natural Resources, 41996-13776 Gorgan, Iran
| | - Saeid Naderi
- Environmental Sciences Department, Natural Resources Faculty, University of Guilan, 49138-15749 Guilan, Iran
| | - Alessandra Stella
- PTP Science Park, Bioinformatics Unit, Via Einstein-Loc. Cascina Codazza, 26900 Lodi, Italy
| | - Abdelkader Chikhi
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pierre Taberlet
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Pompanon
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
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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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Francischini FJB, Cordeiro EMG, de Campos JB, Alves-Pereira A, Viana JPG, Wu X, Wei W, Brown P, Joyce A, Murua G, Fogliata S, Clough SJ, Zucchi MI. Diatraea saccharalis history of colonization in the Americas. The case for human-mediated dispersal. PLoS One 2019; 14:e0220031. [PMID: 31339922 PMCID: PMC6656350 DOI: 10.1371/journal.pone.0220031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 07/08/2019] [Indexed: 11/28/2022] Open
Abstract
The sugarcane borer moth, Diatraea saccharalis, is one of the most important pests of sugarcane and maize crops in the Western Hemisphere. The pest is widespread throughout South and Central America, the Caribbean region and the southern United States. One of the most intriguing features of D. saccharalis population dynamics is the high rate of range expansion reported in recent years. To shed light on the history of colonization of D. saccharalis, we investigated the genetic structure and diversity in American populations using single nucleotide polymorphism (SNPs) markers throughout the genome and sequences of the mitochondrial gene cytochrome oxidase (COI). Our primary goal was to propose possible dispersal routes from the putative center of origin that can explain the spatial pattern of genetic diversity. Our findings showed a clear correspondence between genetic structure and the geographical distributions of this pest insect on the American continents. The clustering analyses indicated three distinct groups: one composed of Brazilian populations, a second group composed of populations from El Salvador, Mexico, Texas and Louisiana and a third group composed of the Florida population. The predicted time of divergence predates the agriculture expansion period, but the pattern of distribution of haplotype diversity suggests that human-mediated movement was most likely the factor responsible for the widespread distribution in the Americas. The study of the early history of D. saccharalis promotes a better understanding of range expansion, the history of invasion, and demographic patterns of pest populations in the Americas.
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Affiliation(s)
- Fabricio J. B. Francischini
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Erick M. G. Cordeiro
- Department of Entomology and Acarology, University of Sao Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, São Paulo, Brazil
| | - Jaqueline B. de Campos
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - João Paulo Gomes Viana
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Xing Wu
- Department of Crop Science, University of Illinois, Urbana, Illinois, United States of America
| | - Wei Wei
- Department of Crop Science, University of Illinois, Urbana, Illinois, United States of America
| | - Patrick Brown
- Department of Crop Science, University of Illinois, Urbana, Illinois, United States of America
| | - Andrea Joyce
- Department of Public Health, University of California, Merced, California, United States of America
| | - Gabriela Murua
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres, Consejo Nacional de Investigaciones Científicas y Técnicas (ITANOA-EEAOC-CONICET), Tucumán, Argentina
| | - Sofia Fogliata
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres, Consejo Nacional de Investigaciones Científicas y Técnicas (ITANOA-EEAOC-CONICET), Tucumán, Argentina
| | - Steven J. Clough
- Department of Crop Science, University of Illinois, Urbana, Illinois, United States of America
- US Department of Agriculture-Agricultural Research Service, Urbana, Illinois, United States of America
| | - Maria I. Zucchi
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Laboratory of Conservation Genetics and Genomics, Agribusiness Technological Development of São Paulo (APTA), Piracicaba, São Paulo, Brazil
- * E-mail:
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Viviani A, Bernardi R, Cavallini A, Rossi E. Genotypic Characterization of Torymus sinensis (Hymenoptera: Torymidae) After Its Introduction in Tuscany (Italy) for the Biological Control of Dryocosmus kuriphilus (Hymenoptera: Cynipidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2019; 19:5550985. [PMID: 31422419 PMCID: PMC6698180 DOI: 10.1093/jisesa/iez080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Indexed: 06/10/2023]
Abstract
Torymus sinensis Kamijo (Hymenoptera: Torymidae) is an alien parasitoid that is used in many areas of the world for biological control the Asian chestnut gall wasp, Dryocosmus kuriphilus Yasumatsu (Hymenoptera: Cynipidae). In Italy, this parasitoid was imported from Japan in 2003 and subsequently multiplied and released throughout the country. In this study, a phylogenetic investigation was carried out on insects from three different sites in northern Tuscany (Italy). Moreover, the possible hybridization between T. sinensis and some native Torymus species was evaluated. The conserved region 18S rRNA gene and the hypervariable ITS2 (Internal Transcribed Spacer 2) region of the ribosomal cistrone were selected as molecular markers. Sequencing the amplified products, after cloning, ruled out any hybridization between T. sinensis and the native Torymus species, and also confirmed the presence of two haplotypes for the Tuscan population of T. sinensis both for the region of the 18S rRNA gene as well as for the ITS2 region. These results confirm that the environmental impact of the alien parasitoid T. sinensis in the study site is acceptable, although an extensive and repeated monitoring would be desirable.
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Affiliation(s)
- Ambra Viviani
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
| | - Rodolfo Bernardi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
| | - Elisabetta Rossi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
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Improving conservation policy with genomics: a guide to integrating adaptive potential into U.S. Endangered Species Act decisions for conservation practitioners and geneticists. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1096-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Storfer A, Patton A, Fraik AK. Navigating the Interface Between Landscape Genetics and Landscape Genomics. Front Genet 2018; 9:68. [PMID: 29593776 PMCID: PMC5859105 DOI: 10.3389/fgene.2018.00068] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/15/2018] [Indexed: 11/13/2022] Open
Abstract
As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species' phylogeographic history. To this end, we summarize recent simulation studies that test the power and accuracy of genome scan methods under a variety of demographic scenarios and sampling designs. We conclude with a discussion of additional considerations for future method development, and a summary of methods that show promise for landscape genomics studies but are not yet widely used.
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Affiliation(s)
- Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Austin Patton
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, WA, United States
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Lee SR, Jo YS, Park CH, Friedman JM, Olson MS. Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States. Mol Ecol 2018; 27:636-646. [PMID: 29274176 DOI: 10.1111/mec.14468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 11/22/2017] [Accepted: 12/04/2017] [Indexed: 01/19/2023]
Abstract
Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Yeong-Seok Jo
- National Institute of Biological Resources, Seo-gu, Incheon, Korea
| | - Chan-Ho Park
- National Institute of Biological Resources, Seo-gu, Incheon, Korea
| | | | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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19
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Hohenlohe PA, Hand BK, Andrews KR, Luikart G. Population Genomics Provides Key Insights in Ecology and Evolution. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_20] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Andersen JC, Mills NJ. Comparative genetics of invasive populations of walnut aphid, Chromaphis juglandicola, and its introduced parasitoid, Trioxys pallidus, in California. Ecol Evol 2018; 8:801-811. [PMID: 29321915 PMCID: PMC5756880 DOI: 10.1002/ece3.3667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/13/2017] [Accepted: 10/27/2017] [Indexed: 01/08/2023] Open
Abstract
Coevolution may be an important component of the sustainability of importation biological control, but how frequently introduced natural enemies coevolve with their target pests is unclear. Here we explore whether comparative population genetics of the invasive walnut aphid, Chromaphis juglandicola, and its introduced parasitoid, Trioxys pallidus, provide insights into the localized breakdown of biological control services in walnut orchards in California. We found that sampled populations of C. juglandicola exhibited higher estimates of genetic differentiation (FST) than co-occurring populations of T. pallidus. In contrast, estimates of both the inbreeding coefficient (GIS) and contemporary gene flow were higher for T. pallidus than for C. juglandicola. We also found evidence of reciprocal outlier loci in some locations, but none showed significant signatures of selection. Synthesis and applications. Understanding the importance of coevolutionary interactions for the sustainability of biological control remains an important and understudied component of biological control research. Given the observed differences in gene flow and genetic differentiation among populations of T. pallidus and C. juglandicola, we suspect that temporary local disruption of biological control services may occur more frequently than expected while remaining stable at broader regional scales. Further research that combines genomewide single nucleotide polymorphism genotyping with measurements of phenotypic traits is needed to provide more conclusive evidence of whether the occurrence of outlier loci that display significant signatures of selection can be interpreted as evidence of the presence of a geographic mosaic of coevolution in this system.
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Affiliation(s)
- Jeremy C. Andersen
- Department of Environmental Science Policy and ManagementUniversity of California BerkeleyBerkeleyCAUSA
| | - Nicholas J. Mills
- Department of Environmental Science Policy and ManagementUniversity of California BerkeleyBerkeleyCAUSA
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23
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Landscape genomics analysis of Achyranthes bidentata reveal adaptive genetic variations are driven by environmental variations relating to ecological habit. POPUL ECOL 2017. [DOI: 10.1007/s10144-017-0599-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Abstract
Genotype calling plays important roles in population-genomic studies, which have been greatly accelerated by sequencing technologies. To take full advantage of the resultant information, we have developed maximum-likelihood (ML) methods for calling genotypes from high-throughput sequencing data. As the statistical uncertainties associated with sequencing data depend on depths of coverage, we have developed two types of genotype callers. One approach is appropriate for low-coverage sequencing data, and incorporates population-level information on genotype frequencies and error rates pre-estimated by an ML method. Performance evaluation using computer simulations and human data shows that the proposed framework yields less biased estimates of allele frequencies and more accurate genotype calls than current widely used methods. Another type of genotype caller applies to high-coverage sequencing data, requires no prior genotype-frequency estimates, and makes no assumption on the number of alleles at a polymorphic site. Using computer simulations, we determine the depth of coverage necessary to accurately characterize polymorphisms using this second method. We applied the proposed method to high-coverage (mean 18×) sequencing data of 83 clones from a population of Daphnia pulex. The results show that the proposed method enables conservative and reasonably powerful detection of polymorphisms with arbitrary numbers of alleles. We have extended the proposed method to the analysis of genomic data for polyploid organisms, showing that calling accurate polyploid genotypes requires much higher coverage than diploid genotypes.
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Abstract
Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data.
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27
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Martinez E, Buonaccorsi V, Hyde JR, Aguilar A. Population genomics reveals high gene flow in grass rockfish (Sebastes rastrelliger). Mar Genomics 2017; 33:57-63. [PMID: 28169128 DOI: 10.1016/j.margen.2017.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 02/06/2023]
Abstract
Variation at the genomic level is important for understanding a species' demographic and phylogenetic history, in addition to identifying candidate regions that may be under selection and important to local adaptation. We used restriction-site associated DNA (RAD) sequencing to sample single nucleotide polymorphisms (SNPs) from the grass rockfish genome (Sebastes rastrelliger) to assess range-wide patterns of population structure and test for signatures of selection (i.e. outlier loci). Two different filtering criteria yielded 6572 and 10,393 SNPs that were genotyped in over 70% of 110 individuals from six sampling areas using RAD loci. Global FST across sampling sites is 0.0009-0.002 for all loci. Two methods for the detection of outlier loci failed to identify any outlier loci. Clustering analyses and discriminant analysis of principal components were not able to detect any population structure in our dataset. These results suggest high levels of gene flow for this species across its range and that this level of gene flow makes it difficult to detect outlier loci in the current dataset.
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Affiliation(s)
- Edith Martinez
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, CA, USA, 90032
| | | | - John R Hyde
- NOAA Fisheries, Southwest Fisheries Science Center, 8901 La Jolla Shores Dr., La Jolla, CA, USA, 92037
| | - Andres Aguilar
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, CA, USA, 90032.
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28
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Allendorf FW. Genetics and the conservation of natural populations: allozymes to genomes. Mol Ecol 2017; 26:420-430. [DOI: 10.1111/mec.13948] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/28/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Fred W. Allendorf
- Division of Biological Sciences University of Montana Missoula MT 59812 USA
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Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species. Int J Genomics 2016; 2016:3460416. [PMID: 28025636 PMCID: PMC5153469 DOI: 10.1155/2016/3460416] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/23/2016] [Accepted: 11/08/2016] [Indexed: 12/01/2022] Open
Abstract
In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a “sixth” mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.
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Trends in Next-Generation Sequencing and a New Era for Whole Genome Sequencing. Int Neurourol J 2016; 20:S76-83. [PMID: 27915479 PMCID: PMC5169091 DOI: 10.5213/inj.1632742.371] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 12/28/2022] Open
Abstract
This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields. De novo genome assembly and large scale DNA resequencing to understand genomic variations are popular genomic research tools for processing a tremendous amount of data at low cost. Studies on transcriptomes are now available, from previous-hybridization based microarray methods. Epigenetic studies are also available with NGS applications such as whole genome methylation sequencing and chromatin immunoprecipitation followed by sequencing. Human genetics has faced a new paradigm of research and medical genomics by sequencing technologies since the Human Genome Project. The trend of NGS technologies in human genomics has brought a new era of WGS by enabling the building of human genomes databases and providing appropriate human reference genomes, which is a necessary component of personalized medicine and precision medicine.
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Rodrigues ASB, Silva SE, Pina-Martins F, Loureiro J, Castro M, Gharbi K, Johnson KP, Dietrich CH, Borges PAV, Quartau JA, Jiggins CD, Paulo OS, Seabra SG. Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources. BMC Genet 2016; 17:144. [PMID: 27846816 PMCID: PMC5111214 DOI: 10.1186/s12863-016-0455-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 11/07/2016] [Indexed: 01/08/2023] Open
Abstract
Background Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes underlying phenotypic evolution. The meadow spittlebug, Philaenus spumarius (L.) (Hemiptera, Aphrophoridae), a widespread insect species in the Holarctic region, exhibits a striking dorsal colour/pattern balanced polymorphism. Although experimental crosses have revealed the Mendelian inheritance of this trait, its genetic basis remains unknown. In this study we aimed to identify candidate genomic regions associated with the colour balanced polymorphism in this species. Results By using restriction site-associated DNA (RAD) sequencing we were able to obtain a set of 1,837 markers across 33 individuals to test for associations with three dorsal colour phenotypes (typicus, marginellus, and trilineatus). Single and multi-association analyses identified a total of 60 SNPs associated with dorsal colour morphs. The genome size of P. spumarius was estimated by flow cytometry, revealing a 5.3 Gb genome, amongst the largest found in insects. A partial genome assembly, representing 24% of the total size, and an 81.4 Mb transcriptome, were also obtained. From the SNPs found to be associated with colour, 35% aligned to the genome and 10% to the transcriptome. Our data suggested that major loci, consisting of multi-genomic regions, may be involved in dorsal colour variation among the three dorsal colour morphs analysed. However, no homology was found between the associated loci and candidate genes known to be responsible for coloration pattern in other insect species. The associated markers showed stronger differentiation of the trilineatus colour phenotype, which has been shown previously to be more differentiated in several life-history and physiological characteristics as well. It is possible that colour variation and these traits are linked in a complex genetic architecture. Conclusions The loci detected to have an association with colour and the genomic and transcriptomic resources developed here constitute a basis for further research on the genetic basis of colour pattern in the meadow spittlebug P. spumarius. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0455-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana S B Rodrigues
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal.
| | - Sara E Silva
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
| | - Francisco Pina-Martins
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal.,Centro de Estudos do Ambiente e do Mar (CESAM), DBA/FCUL, Lisbon, Portugal
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Mariana Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Paulo A V Borges
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências e Engenharia do Ambiente, Angra do Heroísmo, Açores, Portugal
| | - José A Quartau
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
| | - Sofia G Seabra
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
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Joost S, Negrini R, Milanesi E, Pellecchia M, Ajmone Marsan P, Consortium E. Detecting footprints of selection inOvis ariesby a spatial analysis approach. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2007.1s.171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- S. Joost
- Istituto di Zootecnica, Università Cattolica del S. Cuore, Piacenza, Italy
| | - R. Negrini
- Istituto di Zootecnica, Università Cattolica del S. Cuore, Piacenza, Italy
| | - E. Milanesi
- Istituto di Zootecnia Generale, Università di Milano, Italy
| | - M. Pellecchia
- Istituto di Zootecnica, Università Cattolica del S. Cuore, Piacenza, Italy
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Magdy M, Werner O, McDaniel SF, Goffinet B, Ros RM. Genomic scanning using AFLP to detect loci under selection in the moss Funaria hygrometrica along a climate gradient in the Sierra Nevada Mountains, Spain. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:280-288. [PMID: 26284822 DOI: 10.1111/plb.12381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/11/2015] [Indexed: 06/04/2023]
Abstract
The common cord moss Funaria hygrometrica has a worldwide distribution and thrives in a wide variety of environments. Here, we studied the genetic diversity in F. hygrometrica along an abiotic gradient in the Mediterranean high mountain of Sierra Nevada (Spain) using a genome scan method. Eighty-four samples from 17 locations from 24 to 2700 m were fingerprinted based on their amplified fragment length polymorphism (AFLP) banding pattern. Using PCA and Bayesian inference we found that the genetic diversity was structured in three or four clusters, respectively. Using a genome scan method we identified 13 outlier loci, which showed a signature of positive selection. Partial Mantel tests were performed between the Euclidean distance matrices of geographic and climatic variables, versus the pair-wise genetic distance of the AFLP dataset and AFLP-positive outliers dataset. AFLP-positive outlier data were significantly correlated with the gradient of the climatic variables, suggesting adaptive variation among populations of F. hygrometrica along the Sierra Nevada Mountains. We highlight the additional analyses necessary to identify the nature of these loci, and their biological role in the adaptation process.
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Affiliation(s)
- M Magdy
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Murcia, Spain
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - O Werner
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - S F McDaniel
- Biology Department, University of Florida, Gainesville, FL, USA
| | - B Goffinet
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - R M Ros
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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Peter J, Schacherer J. Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale. Yeast 2016; 33:73-81. [PMID: 26592376 DOI: 10.1002/yea.3142] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 11/08/2022] Open
Abstract
With the advent of high-throughput technologies for sequencing, the complete description of the genetic variation that occurs in populations, also known as population genomics, is foreseeable but far from being reached. Explaining the forces that govern patterns of genetic variation is essential to elucidate the evolutionary history of species. Genetic variation results from a wide assortment of evolutionary forces, among which mutation, selection, recombination and drift play major roles in shaping genomes. In addition, exploring the genetic variation within a population also corresponds to the first step towards dissecting the genotype-phenotype relationship. In this context, yeast species are of particular interest because they represent a unique resource for studying the evolution of intraspecific genetic diversity in a phylum spanning a broad evolutionary scale. Here, we briefly review recent progress in yeast population genomics and provide some perspective on this rapidly evolving field. In fact, we truly believe that it is of interest to supplement comparative and early population genomic studies with the deep sequencing of more extensive sets of individuals from the same species. In parallel, it would be more than valuable to uncover the intraspecific variation of a large number of unexplored species, including those that are closely and more distantly related. Altogether, these data would enable substantially more powerful genomic scans for functional dissection.
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Affiliation(s)
- Jackson Peter
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
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Magdy M, Eshak MG, Rashed MAS. Genetic structure of Mugil cephalus L. populations from the northern coast of Egypt. Vet World 2016; 9:53-9. [PMID: 27051185 PMCID: PMC4819350 DOI: 10.14202/vetworld.2016.53-59] [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: 06/19/2015] [Revised: 11/15/2015] [Accepted: 11/30/2015] [Indexed: 11/26/2022] Open
Abstract
AIM The gray mullet, Mugil cephalus, has been farmed in semi-intensive ponds with tilapia and carps in Egypt for years. The current study used the fluorescent amplified fragment length polymorphism (F-AFLP) technique to search for genetic differences between the populations of M. cephalus in the northern region of Egypt and to detect the gene flow between sampled locations and the homogeneity within M. cephalus genetic pool in Egypt. MATERIALS AND METHODS To fulfill the study objectives 60 (15/location) samples were collected from four northern coast governorates of Egypt (Alexandria "sea," Kafr El-Sheikh "farm," Damietta "farm" and Port Said "sea"). Three replicates of bulked DNA (5 samples/replicate) for each location were successfully amplified using the standard AFLP protocol using fluorescent primers. DNA polymorphism, genetic diversity, and population structure were assessed while positive outlier loci were successfully detected among the sampled locations. Based on the geographical distribution of sampling sites, the gene flow, the genetic differentiation, and correlations to sampling locations were estimated. RESULTS A total of 1890 polymorphic bands were scored for all locations, where 765, 1054, 673, and 751 polymorphic bands were scored between samples from Alexandria, Kafr El-Sheikh, Damietta and Port Said, respectively. The effective number of alleles (ne) for all bulked samples combined together was 1.42. The expected heterozygosity under Hardy-Weinberg assumption (He) for all bulked samples combined together was 0.28. Bulked samples from Damietta yielded the lowest ne (1.35) and the lowest He (0.23) when inbreeding coefficient (FIS) = 1. Bulked samples from Kafr El-Sheikh scored the highest ne (1.55) and the highest He (0.37). Bulked samples from Alexandria scored 1.40 for ne and 0.26 for He, while bulked samples from Port Said scored 1.39 for ne and 0.26 for He. The observed bulked samples formed three sub-population groups, where none is limited to a certain sampling location. A high differentiation among locations was detected, however, is not fully isolating the locations. Gene flow was 0.58. Positive outliers loci (117) were detected among the four sampled locations while weak significant correlation (r=0.15, p=0.03) was found for the distance between them. CONCLUSION Even though this species is cultivated in Egypt, the wild population is still present and by the current study a flow of its genes is still exchanged through the northern coast of Egypt. Which contribute to the cultivated populations leading to heterogeneity in its genetic pool and consequently affects the production consistency of M. cephalus in Egypt.
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Affiliation(s)
- Mahmoud Magdy
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shubra, 11241 Cairo, Egypt
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36
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Parks M, Subramanian S, Baroni C, Salvatore MC, Zhang G, Millar CD, Lambert DM. Ancient population genomics and the study of evolution. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130381. [PMID: 25487332 DOI: 10.1098/rstb.2013.0381] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.
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Affiliation(s)
- M Parks
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - S Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - C Baroni
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - M C Salvatore
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - G Zhang
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, Republic of China Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - C D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - D M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
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37
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Abstract
Rapidly improving high-throughput sequencing technologies provide unprecedented opportunities for carrying out population-genomic studies with various organisms. To take full advantage of these methods, it is essential to correctly estimate allele and genotype frequencies, and here we present a maximum-likelihood method that accomplishes these tasks. The proposed method fully accounts for uncertainties resulting from sequencing errors and biparental chromosome sampling and yields essentially unbiased estimates with minimal sampling variances with moderately high depths of coverage regardless of a mating system and structure of the population. Moreover, we have developed statistical tests for examining the significance of polymorphisms and their genotypic deviations from Hardy-Weinberg equilibrium. We examine the performance of the proposed method by computer simulations and apply it to low-coverage human data generated by high-throughput sequencing. The results show that the proposed method improves our ability to carry out population-genomic analyses in important ways. The software package of the proposed method is freely available from https://github.com/Takahiro-Maruki/Package-GFE.
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38
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Hasselmann M, Ferretti L, Zayed A. Beyond fruit-flies: population genomic advances in non-Drosophila arthropods. Brief Funct Genomics 2015; 14:424-31. [DOI: 10.1093/bfgp/elv010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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39
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Evolution and population genomics of the Lyme borreliosis pathogen, Borrelia burgdorferi. Trends Genet 2015; 31:201-7. [PMID: 25765920 DOI: 10.1016/j.tig.2015.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 11/22/2022]
Abstract
Population genomic studies have the potential to address many unresolved questions about microbial pathogens by facilitating the identification of genes underlying ecologically important traits, such as novel virulence factors and adaptations to humans or other host species. Additionally, this framework improves estimations of population demography and evolutionary history to accurately reconstruct recent epidemics and identify the molecular and environmental factors that resulted in the outbreak. The Lyme disease bacterium, Borrelia burgdorferi, exemplifies the power and promise of the application of population genomics to microbial pathogens. We discuss here the future of evolutionary studies in B. burgdorferi, focusing on the primary evolutionary forces of horizontal gene transfer, natural selection, and migration, as investigations transition from analyses of single genes to genomes.
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40
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López ME, Neira R, Yáñez JM. Applications in the search for genomic selection signatures in fish. Front Genet 2015; 5:458. [PMID: 25642239 PMCID: PMC4294200 DOI: 10.3389/fgene.2014.00458] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/15/2014] [Indexed: 11/25/2022] Open
Abstract
Selection signatures are genomic regions harboring DNA sequences functionally involved in the genetic variation of traits subject to selection. Selection signatures have been intensively studied in recent years because of their relevance to evolutionary biology and their potential association with genes that control phenotypes of interest in wild and domestic populations. Selection signature research in fish has been confined to a smaller scale, due in part to the relatively recent domestication of fish species and limited genomic resources such as molecular markers, genetic mapping, DNA sequences, and reference genomes. However, recent genomic technology advances are paving the way for more studies that may contribute to the knowledge of genomic regions underlying phenotypes of biological and productive interest in fish.
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Affiliation(s)
- María E López
- Faculty of Agricultural Sciences, University of Chile Santiago, Chile ; Aquainnovo, Puerto Montt Chile
| | - Roberto Neira
- Faculty of Agricultural Sciences, University of Chile Santiago, Chile
| | - José M Yáñez
- Aquainnovo, Puerto Montt Chile ; Faculty of Veterinary and Animal Sciences, University of Chile Santiago, Chile
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41
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Serieys LEK, Lea A, Pollinger JP, Riley SPD, Wayne RK. Disease and freeways drive genetic change in urban bobcat populations. Evol Appl 2014; 8:75-92. [PMID: 25667604 PMCID: PMC4310583 DOI: 10.1111/eva.12226] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/20/2014] [Indexed: 01/04/2023] Open
Abstract
Urbanization profoundly impacts animal populations by causing isolation, increased susceptibility to disease, and exposure to toxicants. Genetic effects include reduced effective population size, increased population substructure, and decreased adaptive potential. We investigated the influence that urbanization and a disease epizootic had on the population genetics of bobcats (Lynx rufus) distributed across a highly fragmented urban landscape. We genotyped more than 300 bobcats, sampled from 1996 to 2012, for variation at nine neutral and seven immune gene-linked microsatellite loci. We found that two freeways are significant barriers to gene flow. Further, a 3-year disease epizootic, associated with secondary anticoagulant rodenticide exposure, caused a population bottleneck that led to significant genetic differentiation between pre- and post-disease populations that was greater than that between populations separated by major freeways for >60 years. However, balancing selection acted on immune-linked loci during the epizootic, maintaining variation at functional regions. Conservation assessments need to assay loci that are potentially under selection to better preserve the adaptive potential of populations at the urban–wildland interface. Further, interconnected regions that contain appropriate habitat for wildlife will be critical to the long-term viability of animal populations in urban landscapes.
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Affiliation(s)
- Laurel E K Serieys
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, CA, USA
| | - Amanda Lea
- Department of Biology, Duke University Durham, NC, USA
| | - John P Pollinger
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, CA, USA
| | - Seth P D Riley
- Santa Monica Mountains National Recreation Area, National Park Service Thousand Oaks, CA, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, CA, USA
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42
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Genome-wide detection of selective signatures in Simmental cattle. J Appl Genet 2014; 55:343-51. [DOI: 10.1007/s13353-014-0200-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 01/15/2014] [Accepted: 02/04/2014] [Indexed: 12/28/2022]
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43
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Ellegren H. Genome sequencing and population genomics in non-model organisms. Trends Ecol Evol 2014; 29:51-63. [DOI: 10.1016/j.tree.2013.09.008] [Citation(s) in RCA: 410] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 09/02/2013] [Accepted: 09/16/2013] [Indexed: 12/20/2022]
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Knolhoff LM, Heckel DG. Behavioral assays for studies of host plant choice and adaptation in herbivorous insects. ANNUAL REVIEW OF ENTOMOLOGY 2014; 59:263-78. [PMID: 24160429 DOI: 10.1146/annurev-ento-011613-161945] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The association of insect herbivores with their host plants is influenced by behaviors governing acceptance of those plants for feeding and oviposition. Behavioral changes accompany and may even precede host range expansion. Characterization and quantification of specific behaviors often form the basis of studies on host plant adaptation and chemical ecology. Behavioral assays of insects are usually designed to measure attraction for feeding or oviposition in relation to their host plants or specific chemistry. We review behavioral assays of insect herbivores with host plants or the volatiles they emit, with special consideration given to design, analysis, and interpretation to maximize ecological relevance. A toolkit of robust assays can help address fundamental issues at the intersection of ecology and evolution, such as the underpinnings of plant-insect interactions and the identification of genes involved in host race formation.
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Affiliation(s)
- Lisa M Knolhoff
- Genective, c/o AgReliant Genetics, Champaign, Illinois 61801;
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45
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Abstract
The recent advent of high-throughput sequencing and genotyping technologies makes it possible to produce, easily and cost effectively, large amounts of detailed data on the genotype composition of populations. Detecting locus-specific effects may help identify those genes that have been, or are currently, targeted by natural selection. How best to identify these selected regions, loci, or single nucleotides remains a challenging issue. Here, we introduce a new model-based method, called SelEstim, to distinguish putative selected polymorphisms from the background of neutral (or nearly neutral) ones and to estimate the intensity of selection at the former. The underlying population genetic model is a diffusion approximation for the distribution of allele frequency in a population subdivided into a number of demes that exchange migrants. We use a Markov chain Monte Carlo algorithm for sampling from the joint posterior distribution of the model parameters, in a hierarchical Bayesian framework. We present evidence from stochastic simulations, which demonstrates the good power of SelEstim to identify loci targeted by selection and to estimate the strength of selection acting on these loci, within each deme. We also reanalyze a subset of SNP data from the Stanford HGDP-CEPH Human Genome Diversity Cell Line Panel to illustrate the performance of SelEstim on real data. In agreement with previous studies, our analyses point to a very strong signal of positive selection upstream of the LCT gene, which encodes for the enzyme lactase-phlorizin hydrolase and is associated with adult-type hypolactasia. The geographical distribution of the strength of positive selection across the Old World matches the interpolated map of lactase persistence phenotype frequencies, with the strongest selection coefficients in Europe and in the Indus Valley.
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46
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Lachance J, Tishkoff SA. Population Genomics of Human Adaptation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013; 44:123-143. [PMID: 25383060 DOI: 10.1146/annurev-ecolsys-110512-135833] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recent advances in genotyping technologies have facilitated genome-wide scans for natural selection. Identification of targets of natural selection will shed light on processes of human adaptation and evolution and could be important for identifying variation that influences both normal human phenotypic variation as well as disease susceptibility. Here we focus on studies of natural selection in modern humans who originated ~200,000 years go in Africa and migrated across the globe ~50,000 - 100,000 years ago. Movement into new environments, as well as changes in culture and technology including plant and animal domestication, resulted in local adaptation to diverse environments. We summarize statistical approaches for detecting targets of natural selection and for distinguishing the effects of demographic history from natural selection. On a genome-wide scale, immune-related genes appear to be major targets of positive selection. Genes associated with reproduction and fertility also appear to be fast evolving. Additional examples of recent human adaptation include genes associated with lactase persistence, eccrine glands, and response to hypoxia. Lastly, we emphasize the need to supplement scans of selection with functional studies to demonstrate the physiologic impact of candidate loci.
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Affiliation(s)
- Joseph Lachance
- Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sarah A Tishkoff
- Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104 USA
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47
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Tetushkin EY. Landscape and ecological genomics. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413090111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Campo D, Lehmann K, Fjeldsted C, Souaiaia T, Kao J, Nuzhdin SV. Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection. Mol Ecol 2013; 22:5084-97. [PMID: 24102956 DOI: 10.1111/mec.12468] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 07/15/2013] [Accepted: 07/16/2013] [Indexed: 11/29/2022]
Abstract
The prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set of 35 individual whole-genome sequences from inbred lines of D. melanogaster from a west coast US population (Winters, California, USA) and compared them with a public genome data set from Raleigh (Raleigh, North Carolina, USA). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two North American D. melanogaster populations. Both populations exhibit negative values of Tajima's D across the genome, a common signature of demographic expansion. We also detected a low but significant level of genome-wide differentiation between the two populations, as well as multiple allele surfing events, which can be the result of gene drift in local subpopulations on the edge of an expansion wave. In contrast to this genome-wide pattern, we uncovered a 50-kilobase segment in chromosome arm 3L that showed all the hallmarks of a soft selective sweep in both populations. A comparison of allele frequencies within this divergent region among six populations from three continents allowed us to cluster these populations in two differentiated groups, providing evidence for the action of natural selection on a global scale.
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Affiliation(s)
- D Campo
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
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Divergent selection and local adaptation in disjunct populations of an endangered conifer, Keteleeria davidiana var. formosana (Pinaceae). PLoS One 2013; 8:e70162. [PMID: 23894608 PMCID: PMC3718774 DOI: 10.1371/journal.pone.0070162] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/16/2013] [Indexed: 12/18/2022] Open
Abstract
The present study investigated the genetic diversity, population structure, FST outliers, and extent and pattern of linkage disequilibrium in five populations of Keteleeria davidiana var. formosana, which is listed as a critically endangered species by the Council of Agriculture, Taiwan. Twelve amplified fragment length polymorphism primer pairs generated a total of 465 markers, of which 83.74% on average were polymorphic across populations, with a mean Nei’s genetic diversity of 0.233 and a low level of genetic differentiation (approximately 6%) based on the total dataset. Linkage disequilibrium and HICKORY analyses suggested recent population bottlenecks and inbreeding in K. davidiana var. formosana. Both STRUCTURE and BAPS observed extensive admixture of individual genotypes among populations based on the total dataset in various clustering scenarios, which probably resulted from incomplete lineage sorting of ancestral variation rather than a high rate of recent gene flow. Our results based on outlier analysis revealed generally high levels of genetic differentiation and suggest that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, and humidity. Identification of ecologically associated outliers among environmentally disparate populations further support divergent selection and potential local adaptation.
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DHCR7 mutations linked to higher vitamin D status allowed early human migration to northern latitudes. BMC Evol Biol 2013; 13:144. [PMID: 23837623 PMCID: PMC3708787 DOI: 10.1186/1471-2148-13-144] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/04/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Vitamin D is essential for a wide range of physiological processes including immune function and calcium homeostasis. Recent investigations have identified candidate genes which are strongly linked to concentrations of 25-hydroxyvitamin D. Since there is insufficient UVB radiation to induce year-round cutaneous synthesis of vitamin D at latitudes distant from the equator it is likely that these genes were subject to forces of natural selection. We used the fixation index (F(ST)) to measure differences in allele frequencies in 993 individuals from ten populations to identify the presence of evolutionary selection in genes in the vitamin D pathway. We then explored the length of haplotypes in chromosomes to confirm recent positive selection. RESULTS We find evidence of positive selection for DHCR7, which governs availability of 7-dehydrocholesterol for conversion to vitamin D3 by the action of sunlight on the skin. We show that extended haplotypes related to vitamin D status are highly prevalent at Northern latitudes (Europe 0.72, Northeast Asia 0.41). The common DHCR7 haplotype underwent a recent selective sweep in Northeast Asia, with relative extended haplotype homozygosity of 5.03 (99th percentile). In contrast, CYP2R1, which 25-hydroxylates vitamin D, is under balancing selection and we found no evidence of recent selection pressure on GC, which is responsible for vitamin D transport. CONCLUSIONS Our results suggest that genetic variation in DHCR7 is the major adaptation affecting vitamin D metabolism in recent evolutionary history which helped early humans to avoid severe vitamin D deficiency and enabled them to inhabit areas further from the equator.
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