201
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202
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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: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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203
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Graham AM, Lavretsky P, Muñoz-Fuentes V, Green AJ, Wilson RE, McCracken KG. Migration-Selection Balance Drives Genetic Differentiation in Genes Associated with High-Altitude Function in the Speckled Teal (Anas flavirostris) in the Andes. Genome Biol Evol 2018; 10:14-32. [PMID: 29211852 PMCID: PMC5757641 DOI: 10.1093/gbe/evx253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2017] [Indexed: 12/30/2022] Open
Abstract
Local adaptation frequently occurs across populations as a result of migration-selection balance between divergent selective pressures and gene flow associated with life in heterogeneous landscapes. Studying the effects of selection and gene flow on the adaptation process can be achieved in systems that have recently colonized extreme environments. This study utilizes an endemic South American duck species, the speckled teal (Anas flavirostris), which has both high- and low-altitude populations. High-altitude speckled teal (A. f. oxyptera) are locally adapted to the Andean environment and mostly allopatric from low-altitude birds (A. f. flavirostris); however, there is occasional gene flow across altitudinal gradients. In this study, we used next-generation sequencing to explore genetic patterns associated with high-altitude adaptation in speckled teal populations, as well as the extent to which the balance between selection and migration have affected genetic architecture. We identified a set of loci with allele frequencies strongly correlated with altitude, including those involved in the insulin-like signaling pathway, bone morphogenesis, oxidative phosphorylation, responders to hypoxia-induced DNA damage, and feedback loops to the hypoxia-inducible factor pathway. These same outlier loci were found to have depressed gene flow estimates, as well as being highly concentrated on the Z-chromosome. Our results suggest a multifactorial response to life at high altitudes through an array of interconnected pathways that are likely under positive selection and whose genetic components seem to be providing an effective genomic barrier to interbreeding, potentially functioning as an avenue for population divergence and speciation.
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Affiliation(s)
| | | | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Andy J Green
- Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Robert E Wilson
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska, Fairbanks
| | - Kevin G McCracken
- Department of Biology, University of Miami
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska, Fairbanks
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine
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204
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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: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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205
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Razgour O, Taggart JB, Manel S, Juste J, Ibáñez C, Rebelo H, Alberdi A, Jones G, Park K. An integrated framework to identify wildlife populations under threat from climate change. Mol Ecol Resour 2018; 18:18-31. [PMID: 28649779 PMCID: PMC6849758 DOI: 10.1111/1755-0998.12694] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/14/2017] [Accepted: 06/16/2017] [Indexed: 11/29/2022]
Abstract
Climate change is a major threat to global biodiversity that will produce a range of new selection pressures. Understanding species responses to climate change requires an interdisciplinary perspective, combining ecological, molecular and environmental approaches. We propose an applied integrated framework to identify populations under threat from climate change based on their extent of exposure, inherent sensitivity due to adaptive and neutral genetic variation and range shift potential. We consider intraspecific vulnerability and population-level responses, an important but often neglected conservation research priority. We demonstrate how this framework can be applied to vertebrates with limited dispersal abilities using empirical data for the bat Plecotus austriacus. We use ecological niche modelling and environmental dissimilarity analysis to locate areas at high risk of exposure to future changes. Combining outlier tests with genotype-environment association analysis, we identify potential climate-adaptive SNPs in our genomic data set and differences in the frequency of adaptive and neutral variation between populations. We assess landscape connectivity and show that changing environmental suitability may limit the future movement of individuals, thus affecting both the ability of populations to shift their distribution to climatically suitable areas and the probability of evolutionary rescue through the spread of adaptive genetic variation among populations. Therefore, a better understanding of movement ecology and landscape connectivity is needed for predicting population persistence under climate change. Our study highlights the importance of incorporating genomic data to determine sensitivity, adaptive potential and range shift potential, instead of relying solely on exposure to guide species vulnerability assessments and conservation planning.
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Affiliation(s)
- Orly Razgour
- Biological SciencesUniversity of SouthamptonSouthamptonUK
- School of Biological SciencesUniversity of BristolBristolUK
- Biological & Environmental SciencesUniversity of StirlingStirlingUK
| | | | - Stephanie Manel
- EPHEPSL Research UniversityCNRSUMSupAgroINDINRAUMR 5175 CEFEMontpellierFrance
| | | | | | - Hugo Rebelo
- School of Biological SciencesUniversity of BristolBristolUK
- Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto (CIBIO/UP)VairãoPortugal
| | - Antton Alberdi
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
| | - Gareth Jones
- School of Biological SciencesUniversity of BristolBristolUK
| | - Kirsty Park
- Biological & Environmental SciencesUniversity of StirlingStirlingUK
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206
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Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering. Sci Rep 2017; 7:17598. [PMID: 29242627 PMCID: PMC5730610 DOI: 10.1038/s41598-017-16810-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/15/2017] [Indexed: 12/17/2022] Open
Abstract
The widespread adoption of RAD-Seq data in phylogeography means genealogical relationships previously evaluated using relatively few genetic markers can now be addressed with thousands of loci. One challenge, however, is that RAD-Seq generates complete genotypes for only a small subset of loci or individuals. Simulations indicate that loci with missing data can produce biased estimates of key population genetic parameters, although the influence of such biases in empirical studies is not well understood. Here we compare microsatellite data (8 loci) and RAD-Seq data (six datasets ranging from 239 to 25,198 loci) from red mangroves (Rhizophora mangle) in Florida to evaluate how different levels of data filtering influence phylogeographic inferences. For all datasets, we calculated population genetic statistics and evaluated population structure, and for RAD-Seq datasets, we additionally examined population structure using coalescence. We found higher FST using microsatellites, but that RAD-Seq-based estimates approached those based on microsatellites as more loci with more missing data were included. Analyses of RAD-Seq datasets resolved the classic Gulf-Atlantic coastal phylogeographic break, which was not significant in the microsatellite analyses. Applying multiple levels of filtering to RAD-Seq datasets can provide a more complete picture of potential biases in the data and elucidate subtle phylogeographic patterns.
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207
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Fritz ML, DeYonke AM, Papanicolaou A, Micinski S, Westbrook J, Gould F. Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices. Mol Ecol 2017; 27:167-181. [PMID: 29134741 DOI: 10.1111/mec.14430] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 09/30/2017] [Accepted: 10/05/2017] [Indexed: 01/04/2023]
Abstract
Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages, and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve (i) shifts in host plant selection mechanisms to avoid cotton, (ii) changes in detoxification mechanisms required for cotton-feeding vs. feeding on other hosts or (iii) loss of resistance to previously used management practices including insecticides. Here, we begin to address whether such changes occurred in H. virescens populations between 1997 and 2012, as Bt-cotton cultivation spread through the agricultural landscape. For our study, we produced an H. virescens genome assembly and used this in concert with a ddRAD-seq-enabled genome scan to identify loci with significant allele frequency changes over the 15-year period. Genetic changes at a previously described H. virescens insecticide target of selection were detectable in our genome scan and increased our confidence in this methodology. Additional loci were also detected as being under selection, and we quantified the selection strength required to elicit observed allele frequency changes at each locus. Potential contributions of genes near loci under selection to adaptive phenotypes in the H. virescens cotton system are discussed.
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Affiliation(s)
- Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, USA.,Department of Entomology, North Carolina State University, Raleigh, NC, USA
| | | | | | - Stephen Micinski
- Red River Research Station, Louisiana State University AgCenter, Bossier City, LA, USA
| | - John Westbrook
- USDA Agricultural Research Service, College Station, TX, USA
| | - Fred Gould
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
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208
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Donaldson ME, Rico Y, Hueffer K, Rando HM, Kukekova AV, Kyle CJ. Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure. Ecol Evol 2017; 8:572-583. [PMID: 29321894 PMCID: PMC5756825 DOI: 10.1002/ece3.3583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 12/30/2022] Open
Abstract
Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High‐throughput sequencing (HTS) technologies, such as genotype‐by‐sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization‐based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to “capture” specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300‐kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on‐target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer‐read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune‐related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.
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Affiliation(s)
- Michael E Donaldson
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada
| | - Yessica Rico
- CONACYT Instituto de Ecología A.C.Centro Regional del Bajio Pátzcuaro Michoacán Mexico
| | - Karsten Hueffer
- Department of Veterinary Medicine University of Alaska Fairbanks Fairbanks AK USA
| | - Halie M Rando
- Department of Animal Sciences College of ACES University of Illinois at Urbana-Champaign Urbana IL USA
| | - Anna V Kukekova
- Department of Animal Sciences College of ACES University of Illinois at Urbana-Champaign Urbana IL USA
| | - Christopher J Kyle
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada.,Forensic Science Department Trent University Peterborough ON Canada
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209
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Flanagan SP, Jones AG. Substantial differences in bias between single‐digest and double‐digest RAD‐seq libraries: A case study. Mol Ecol Resour 2017; 18:264-280. [DOI: 10.1111/1755-0998.12734] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/29/2017] [Accepted: 10/06/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Sarah P. Flanagan
- Biology Department Texas A&M University College Station TX USA
- National Institute for Mathematical and Biological Synthesis University of Tennessee Knoxville TN USA
| | - Adam G. Jones
- Biology Department Texas A&M University College Station TX USA
- Department of Biological Sciences University of Idaho Moscow ID USA
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210
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Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms. Trends Genet 2017; 34:121-132. [PMID: 29198378 DOI: 10.1016/j.tig.2017.11.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/30/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023]
Abstract
The application of genomic approaches to 'obscure model organisms' (OMOs), meaning species with no prior genomic resources, enables increasingly sophisticated studies of the genomic basis of evolution, acclimatization, and adaptation in real ecological contexts. I consider here ecological questions that can be addressed using OMOs, and indicate optimal sequencing and data-handling solutions for each case. With this I hope to promote the diversity of OMO-based projects that would capitalize on the peculiarities of the natural history of OMOs and could feasibly be completed within the scope of a single PhD thesis.
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211
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Leblois R, Gautier M, Rohfritsch A, Foucaud J, Burban C, Galan M, Loiseau A, Sauné L, Branco M, Gharbi K, Vitalis R, Kerdelhué C. Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa. Mol Ecol 2017; 27:264-278. [DOI: 10.1111/mec.14411] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 10/17/2017] [Accepted: 10/25/2017] [Indexed: 01/01/2023]
Affiliation(s)
- R. Leblois
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
- Institut de Biologie Computationnelle (IBC); Université de Montpellier; Montpellier France
| | - M. Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
- Institut de Biologie Computationnelle (IBC); Université de Montpellier; Montpellier France
| | - A. Rohfritsch
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - J. Foucaud
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - C. Burban
- INRA, UMR1202 BIOGECO (INRA - Université de Bordeaux); Cestas Cedex France
| | - M. Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - A. Loiseau
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - L. Sauné
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - M. Branco
- Centro de Estudos Florestais (CEF); Instituto Superior de Agronomia (ISA); University of Lisbon; Lisbon Portugal
| | - K. Gharbi
- Edinburgh Genomics; School of Biological Sciences; University of Edinburgh; Edinburgh UK
| | - R. Vitalis
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
- Institut de Biologie Computationnelle (IBC); Université de Montpellier; Montpellier France
| | - C. Kerdelhué
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
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212
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Rudman SM, Barbour MA, Csilléry K, Gienapp P, Guillaume F, Hairston Jr NG, Hendry AP, Lasky JR, Rafajlović M, Räsänen K, Schmidt PS, Seehausen O, Therkildsen NO, Turcotte MM, Levine JM. What genomic data can reveal about eco-evolutionary dynamics. Nat Ecol Evol 2017; 2:9-15. [DOI: 10.1038/s41559-017-0385-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 10/16/2017] [Indexed: 01/17/2023]
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213
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Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/13836_2017_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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214
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Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis‐Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan DM, Ingram BA, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P. Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity. Mol Ecol 2017; 26:6253-6269. [DOI: 10.1111/mec.14368] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Katherine A. Harrisson
- School of Biological Sciences Monash University Clayton Vic. Australia
- Department of Ecology Environment and Evolution School of Life Sciences La Trobe University Bundoora Vic. Australia
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Stephen J. Amish
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission Hagerman Fish Culture Experiment Station Hagerman IDUSA
| | | | - Meaghan L. Rourke
- Department of Primary Industries DPI Fisheries Narrandera NSW Australia
| | - Jarod Lyon
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Zeb Tonkin
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Dean M. Gilligan
- Department of Primary Industries DPI Fisheries, Batemans Bay Fisheries Office Batemans Bay NSW Australia
| | | | - Mark Lintermans
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
| | - Han Ming Gan
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Christopher M. Austin
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Gordon Luikart
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Paul Sunnucks
- School of Biological Sciences Monash University Clayton Vic. Australia
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215
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Campbell NR, Kamphaus C, Murdoch K, Narum SR. Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia River. Ecol Evol 2017; 7:10350-10360. [PMID: 29238560 PMCID: PMC5723619 DOI: 10.1002/ece3.3492] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/31/2017] [Accepted: 09/01/2017] [Indexed: 11/08/2022] Open
Abstract
Coho salmon were extirpated in the mid‐20th century from the interior reaches of the Columbia River but were reintroduced with relatively abundant source stocks from the lower Columbia River near the Pacific coast. Reintroduction of Coho salmon to the interior Columbia River (Wenatchee River) using lower river stocks placed selective pressures on the new colonizers due to substantial differences with their original habitat such as migration distance and navigation of six additional hydropower dams. We used restriction site‐associated DNA sequencing (RAD‐seq) to genotype 5,392 SNPs in reintroduced Coho salmon in the Wenatchee River over four generations to test for signals of temporal structure and adaptive variation. Temporal genetic structure among the three broodlines of reintroduced fish was evident among the initial return years (2000, 2001, and 2002) and their descendants, which indicated levels of reproductive isolation among broodlines. Signals of adaptive variation were detected from multiple outlier tests and identified candidate genes for further study. This study illustrated that genetic variation and structure of reintroduced populations are likely to reflect source stocks for multiple generations but may shift over time once established in nature.
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Affiliation(s)
| | | | | | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission Hagerman ID USA
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216
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Meirmans PG, Godbout J, Lamothe M, Thompson SL, Isabel N. History rather than hybridization determines population structure and adaptation inPopulus balsamifera. J Evol Biol 2017; 30:2044-2058. [DOI: 10.1111/jeb.13174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 08/10/2017] [Accepted: 08/23/2017] [Indexed: 01/12/2023]
Affiliation(s)
- P. G. Meirmans
- Institute for Biodiversity and Ecosystem Dynamics; University of Amsterdam; Amsterdam The Netherlands
| | - J. Godbout
- Laurentian Forestry Centre; Canadian Forest Service, Natural Resources Canada; Québec QC Canada
| | - M. Lamothe
- Laurentian Forestry Centre; Canadian Forest Service, Natural Resources Canada; Québec QC Canada
| | - S. L. Thompson
- Laurentian Forestry Centre; Canadian Forest Service, Natural Resources Canada; Québec QC Canada
| | - N. Isabel
- Laurentian Forestry Centre; Canadian Forest Service, Natural Resources Canada; Québec QC Canada
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217
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Liu MY, Worden P, Monahan LG, DeMaere MZ, Burke CM, Djordjevic SP, Charles IG, Darling AE. Evaluation of ddRADseq for reduced representation metagenome sequencing. PeerJ 2017; 5:e3837. [PMID: 28948110 PMCID: PMC5609526 DOI: 10.7717/peerj.3837] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 08/31/2017] [Indexed: 11/23/2022] Open
Abstract
Background Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. Methods This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool samples and generating sequence data. Results The ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool samples. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected. Discussion Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.
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Affiliation(s)
- Michael Y Liu
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Paul Worden
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Leigh G Monahan
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Matthew Z DeMaere
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Catherine M Burke
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Steven P Djordjevic
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Ian G Charles
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Aaron E Darling
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
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218
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Egger B, Roesti M, Böhne A, Roth O, Salzburger W. Demography and genome divergence of lake and stream populations of an East African cichlid fish. Mol Ecol 2017; 26:5016-5030. [DOI: 10.1111/mec.14248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Bernd Egger
- Zoological Institute; University of Basel; Basel Switzerland
| | - Marius Roesti
- Zoological Institute; University of Basel; Basel Switzerland
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - Astrid Böhne
- Zoological Institute; University of Basel; Basel Switzerland
| | - Olivia Roth
- Evolutionary Ecology of Marine Fishes; Helmholtz Zentrum für Ozeanforschung Kiel (GEOMAR); Kiel Germany
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219
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Fuentes-Pardo AP, Ruzzante DE. Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations. Mol Ecol 2017; 26:5369-5406. [PMID: 28746784 DOI: 10.1111/mec.14264] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
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Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N. Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study. Mol Phylogenet Evol 2017. [DOI: 10.1016/j.ympev.2017.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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221
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Samuk K, Owens GL, Delmore KE, Miller SE, Rennison DJ, Schluter D. Gene flow and selection interact to promote adaptive divergence in regions of low recombination. Mol Ecol 2017; 26:4378-4390. [DOI: 10.1111/mec.14226] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/02/2017] [Accepted: 06/13/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Kieran Samuk
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - Gregory L. Owens
- Department of Botany; University of British Columbia; Vancouver BC Canada
| | | | - Sara E. Miller
- Department of Neurobiology and Behavior; Cornell University; Ithaca NY USA
| | - Diana J. Rennison
- Institut fur Okologie und Evolution; Universitat Bern; Bern Switzerland
| | - Dolph Schluter
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
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222
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RADseq provides evidence for parallel ecotypic divergence in the autotetraploid Cochlearia officinalis in Northern Norway. Sci Rep 2017; 7:5573. [PMID: 28717144 PMCID: PMC5514025 DOI: 10.1038/s41598-017-05794-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/02/2017] [Indexed: 11/08/2022] Open
Abstract
Speciation encompasses a continuum over time from freely interbreeding populations to reproductively isolated species. Along this process, ecotypes - the result of local adaptation - may be on the road to new species. We investigated whether three autotetraploid Cochlearia officinalis ecotypes, adapted to different habitats (beach, estuary, spring), are genetically differentiated and result from parallel ecotypic divergence in two distinct geographical regions. We obtained genetic data from thousands of single nucleotide polymorphisms (SNPs) from restriction-site associated DNA sequencing (RADseq) and from six microsatellite markers for 12 populations to assess genetic divergence at ecotypic, geographic and population level. The genetic patterns support differentiation among ecotypes as suggested by morphology and ecology. The data fit a scenario where the ancestral beach ecotype has recurrently and polytopically given rise to the estuary and spring ecotypes. Several ecologically-relevant loci with consistent non-random segregating patterns are identified across the recurrent origins, in particular around genes related to salt stress. Despite being ecologically distinct, the Cochlearia ecotypes still represent an early stage in the process of speciation, as reproductive isolation has not (yet) developed. A sequenced annotated genome is needed to specifically target candidate genes underlying local adaptation.
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223
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Melville J, Haines ML, Boysen K, Hodkinson L, Kilian A, Smith Date KL, Potvin DA, Parris KM. Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates. ROYAL SOCIETY OPEN SCIENCE 2017; 4:161061. [PMID: 28791133 PMCID: PMC5541528 DOI: 10.1098/rsos.161061] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/14/2017] [Indexed: 05/04/2023]
Abstract
Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for phylogeographic and evolutionary genetics research. We detail the applicability of a restriction enzyme-mediated genome complexity reduction approach with subsequent NGS (DArTseq) in vertebrate study systems at different evolutionary and geographical scales. We present two case studies using SNP data from the DArTseq molecular marker platform. First, we used DArTseq in a large phylogeographic study of the agamid lizard Ctenophorus caudicinctus, including 91 individuals and spanning the geographical range of this species across arid Australia. A low-density DArTseq assay resulted in 28 960 SNPs, with low density referring to a comparably reduced set of identified and sequenced markers as a cost-effective approach. Second, we applied this approach to an evolutionary genetics study of a classic frog hybrid zone (Litoria ewingii-Litoria paraewingi) across 93 individuals, which resulted in 48 117 and 67 060 SNPs for a low- and high-density assay, respectively. We provide a docker-based workflow to facilitate data preparation and analysis, then analyse SNP data using multiple methods including Bayesian model-based clustering and conditional likelihood approaches. Based on comparison of results from the DArTseq platform and traditional molecular approaches, we conclude that DArTseq can be used successfully in vertebrates and will be of particular interest to researchers working at the interface between population genetics and phylogenetics, exploring species boundaries, gene exchange and hybridization.
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Affiliation(s)
- Jane Melville
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
- Author for correspondence: Jane Melville e-mail:
| | - Margaret L. Haines
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
| | - Katja Boysen
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
| | - Luke Hodkinson
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory 2617, Australia
| | | | | | - Kirsten M. Parris
- School of Ecosystem and Forest Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
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224
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Wit J, Gilleard JS. Resequencing Helminth Genomes for Population and Genetic Studies. Trends Parasitol 2017; 33:388-399. [DOI: 10.1016/j.pt.2017.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 10/20/2022]
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225
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Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Responsible RAD: Striving for best practices in population genomic studies of adaptation. Mol Ecol Resour 2017; 17:366-369. [PMID: 28382730 PMCID: PMC11066774 DOI: 10.1111/1755-0998.12677] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/01/2017] [Accepted: 04/02/2017] [Indexed: 01/03/2023]
Abstract
Two recent articles were written in response to our paper "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation." While we agree with some of the comments made by the authors of these two response papers, we still believe caution should be employed in RADseq studies that aim to detect loci that contribute to adaptation. In this rebuttal, we evaluate the key points made in these papers, attempt to identify a middle ground and make suggestions for responsibly conducting future studies to understand the genomewide mechanisms of adaptation.
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Affiliation(s)
- David B. Lowry
- Department of Plant Biology, Michigan State University, East Lansing MI 48824, USA
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - Sean Hoban
- The Morton Arboretum, Lisle, IL, USA
- National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USA
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Katie E. Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA 01908, USA
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35406, USA
| | - Michael F. Antolin
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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226
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Schield DR, Adams RH, Card DC, Perry BW, Pasquesi GM, Jezkova T, Portik DM, Andrew AL, Spencer CL, Sanchez EE, Fujita MK, Mackessy SP, Castoe TA. Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Ecol Evol 2017; 7:3951-3966. [PMID: 28616190 PMCID: PMC5468163 DOI: 10.1002/ece3.2996] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater‐than‐expected overlap between genes linked to lineage‐specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome‐scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.
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Affiliation(s)
- Drew R Schield
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Richard H Adams
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Daren C Card
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Blair W Perry
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Giulia M Pasquesi
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
| | - Daniel M Portik
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Audra L Andrew
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Carol L Spencer
- Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Elda E Sanchez
- National Natural Toxins Research Center and Department of Chemistry Texas A&M University Kingsville Kingsville TX USA
| | - Matthew K Fujita
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Stephen P Mackessy
- School of Biological Sciences University of Northern Colorado Greeley CO USA
| | - Todd A Castoe
- Department of Biology The University of Texas at Arlington Arlington TX USA
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227
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Catchen JM, Hohenlohe PA, Bernatchez L, Funk WC, Andrews KR, Allendorf FW. Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations. Mol Ecol Resour 2017; 17:362-365. [DOI: 10.1111/1755-0998.12669] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/09/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Julian M. Catchen
- Department of Animal Biology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Paul A. Hohenlohe
- Department of Biological Sciences; Institute for Bioinformatics and Evolutionary Studies; University of Idaho; 875 Perimeter Drive Moscow ID 83844 USA
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC G1V 0A6 Canada
| | - W. Chris Funk
- Department of Biology; Graduate Degree Program in Ecology; Colorado State University; Fort Collins CO 80523 USA
| | - Kimberly R. Andrews
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Fred W. Allendorf
- Division of Biological Sciences; University of Montana; Missoula MT 59812 USA
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228
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Burghardt LT, Young ND, Tiffin P. A Guide to Genome-Wide Association Mapping in Plants. ACTA ACUST UNITED AC 2017; 2:22-38. [PMID: 31725973 DOI: 10.1002/cppb.20041] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have developed into a valuable approach for identifying the genetic basis of phenotypic variation. In this article, we provide an overview of the design, analysis, and interpretation of GWAS. First, we present results from simulations that explore key elements of experimental design as well as considerations for collecting the relevant genomic and phenotypic data. Next, we outline current statistical methods and tools used for GWA analyses and discuss the inclusion of covariates to account for population structure and the interpretation of results. Given that many false positive associations will occur in any GWA analysis, we highlight strategies for prioritizing GWA candidates for further statistical and empirical validation. While focused on plants, the material we cover is also applicable to other systems. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Liana T Burghardt
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota
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229
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Oziolor EM, Bickham JW, Matson CW. Evolutionary toxicology in an omics world. Evol Appl 2017; 10:752-761. [PMID: 29151868 PMCID: PMC5680431 DOI: 10.1111/eva.12462] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
Evolutionary toxicology is a young field that has grown rapidly in the past two decades. The potential of this field comes from the ability to link chemical contamination to multigenerational and population-wide effects in various species. The advancements and rapidly decreasing costs of -omic tools are improving the power and resolution of evolutionary toxicology studies. In this manuscript, we aim to address the trajectories and perspectives for conducting evolutionary toxicology studies with -omic approaches. We discuss the complementarity of using multiple -omic tools (genomics, eDNA, transcriptomics, proteomics, and metabolomics) for utility in understanding the toxicological relevance of adaptive responses in populations. In addition, we discuss phenotypic plasticity and its relevance to transcriptomic studies in toxicology. As evolutionary toxicology grows and expands its capacity to link toxicology with population-wide end points, we emphasize the applications of such studies in answering questions about ecological and population health, as well as future applicability to regulation. Thus, we aim to emphasize the enormous potential for evolutionary toxicology in an -omics world and give perspectives on the directions of future investigations.
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Affiliation(s)
- Elias M Oziolor
- Department of Environmental Science Center for Reservoir and Aquatic Systems Research (CRASR), and the Institute for Biomedical Studies Baylor University Waco TX USA
| | - John W Bickham
- Department of Wildlife and Fisheries Science Texas A&M University College Station TX USA
| | - Cole W Matson
- Department of Environmental Science Center for Reservoir and Aquatic Systems Research (CRASR), and the Institute for Biomedical Studies Baylor University Waco TX USA
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230
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Vertacnik KL, Linnen CR. Evolutionary genetics of host shifts in herbivorous insects: insights from the age of genomics. Ann N Y Acad Sci 2017; 1389:186-212. [DOI: 10.1111/nyas.13311] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/16/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022]
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231
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McKinney GJ, Larson WA, Seeb LW, Seeb JE. RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al
. (2016). Mol Ecol Resour 2017; 17:356-361. [DOI: 10.1111/1755-0998.12649] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Garrett J. McKinney
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - Wesley A. Larson
- U.S. Geological Survey; Wisconsin Cooperative Fishery Research Unit; College of Natural Resources; University of Wisconsin-Stevens Point; 800 Reserve St. Stevens Point WI 54481 USA
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - James E. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
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232
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Garvin MR, Templin WD, Gharrett AJ, DeCovich N, Kondzela CM, Guyon JR, McPhee MV. Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael R. Garvin
- Oregon State University Ringgold Standard Institution ‐ Integrative Biology 3029 Cordley Hall, 2701 SW Campus Way Corvallis OR 97331‐4501 USA
| | - William D. Templin
- Alaska Department of Fish and Game Division of Commercial Fisheries 333 Raspberry Road Anchorage AK 99518 USA
| | - Anthony J. Gharrett
- University of Alaska Fairbanks College Fisheries and Ocean Sciences Juneau AK 99821 USA
| | - Nick DeCovich
- Alaska Department of Fish and Game Division of Commercial Fisheries 333 Raspberry Road Anchorage AK 99518 USA
| | - Christine M. Kondzela
- Auke Bay Laboratories Alaska Fisheries Science Center National Oceanic and Atmospheric Administration National Marine Fisheries Service 17109 Point Lena Loop Road Juneau AK 99801 USA
| | - Jeffrey R. Guyon
- Auke Bay Laboratories Alaska Fisheries Science Center National Oceanic and Atmospheric Administration National Marine Fisheries Service 17109 Point Lena Loop Road Juneau AK 99801 USA
| | - Megan V. McPhee
- University of Alaska Fairbanks College Fisheries and Ocean Sciences Juneau AK 99821 USA
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