1
|
Kao AB, Hund AK, Santos FP, Young JG, Bhat D, Garland J, Oomen RA, McCreery HF. Opposing Responses to Scarcity Emerge from Functionally Unique Sociality Drivers. Am Nat 2023; 202:302-321. [PMID: 37606948 DOI: 10.1086/725426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
AbstractFrom biofilms to whale pods, organisms across taxa live in groups, thereby accruing numerous diverse benefits of sociality. All social organisms, however, pay the inherent cost of increased resource competition. One expects that when resources become scarce, this cost will increase, causing group sizes to decrease. Indeed, this occurs in some species, but there are also species for which group sizes remain stable or even increase under scarcity. What accounts for these opposing responses? We present a conceptual framework, literature review, and theoretical model demonstrating that differing responses to sudden resource shifts can be explained by which sociality benefit exerts the strongest selection pressure on a particular species. We categorize resource-related benefits of sociality into six functionally distinct classes and model their effect on the survival of individuals foraging in groups under different resource conditions. We find that whether, and to what degree, the optimal group size (or correlates thereof) increases, decreases, or remains constant when resource abundance declines depends strongly on the dominant sociality mechanism. Existing data, although limited, support our model predictions. Overall, we show that across a wide diversity of taxa, differences in how group size shifts in response to resource declines can be driven by differences in the primary benefits of sociality.
Collapse
|
2
|
Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
Collapse
Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
| | | |
Collapse
|
3
|
Oomen RA, Knutsen H, Olsen EM, Jentoft S, Stenseth NC, Hutchings JA. Warming Accelerates the Onset of the Molecular Stress Response and Increases Mortality of Larval Atlantic Cod. Integr Comp Biol 2022; 62:1784-1801. [PMID: 36130874 PMCID: PMC9801969 DOI: 10.1093/icb/icac145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 01/05/2023] Open
Abstract
Temperature profoundly affects ectotherm physiology. Although differential thermal responses influence fitness, thus driving population dynamics and species distributions, our understanding of the molecular architecture underlying these responses is limited, especially during the critical larval stage. Here, using RNA-sequencing of laboratory-reared Atlantic cod (Gadus morhua) larvae of wild origin, we find changes in gene expression in thousands of transcripts consistent with a severe cellular stress response at both ambient and projected (+2°C and +4°C) temperatures. In addition, specific responses to stress, heat, and hypoxia were commonly identified in gene ontology enrichment analyses and 33 of the 44 genes comprising the minimum stress proteome of all organisms were upregulated. Earlier onset of the stress response was evident at higher temperatures; concomitant increased growth and mortality suggests a reduction in fitness. Temporal differences in gene expression levels do not correspond to differences in growing degree days, suggesting negative physiological consequences of warming beyond accelerated development. Because gene expression is costly, we infer that the upregulation of thousands of transcripts in response to warming in larval cod might act as an energetic drain. We hypothesize that the energetically costly stress response, coupled with increased growth rate at warmer temperatures, leads to faster depletion of energy reserves and increased risk of mortality in larval cod. As sea surface temperatures continue to rise over the next century, reduced fitness of Atlantic cod larvae might lead to population declines in this ecologically and socioeconomically important species. Further, our findings expand our understanding of transcriptomic responses to temperature by ectothermic vertebrate larvae beyond the critical first-feeding stage, a time when organisms begin balancing the energetic demands of growth, foraging, development, and maintenance. Linking the molecular basis of a thermal response to key fitness-related traits is fundamentally important to predicting how global warming will affect ectotherms.
Collapse
Affiliation(s)
| | - Halvor Knutsen
- Center for Coastal Research (CCR), Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway,Institute of Marine Research, Nye Flødevigveien 20, 4817 His, Norway
| | - Esben M Olsen
- Center for Coastal Research (CCR), Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway,Institute of Marine Research, Nye Flødevigveien 20, 4817 His, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway,Center for Coastal Research (CCR), Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway
| | - Jeffrey A Hutchings
- Center for Coastal Research (CCR), Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway,Institute of Marine Research, Nye Flødevigveien 20, 4817 His, Norway,Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
| |
Collapse
|
4
|
Oomen RA, Hutchings JA. Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. J Anim Ecol 2022; 91:1073-1087. [PMID: 35445402 PMCID: PMC9325537 DOI: 10.1111/1365-2656.13707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common‐garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity. Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change. Here, we describe the utility of integrating genomics with common‐garden‐gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential. An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco‐evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high‐dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts. We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco‐evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common‐garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible.
Collapse
Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway
| | - Jeffrey A Hutchings
- Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway.,Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
| |
Collapse
|
5
|
Rasmussen JH, Moyano M, Fuiman LA, Oomen RA. FishSizer: Software solution for efficiently measuring larval fish size. Ecol Evol 2022; 12:e8672. [PMID: 35342596 PMCID: PMC8928902 DOI: 10.1002/ece3.8672] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 11/07/2022] Open
Affiliation(s)
- Jeppe Have Rasmussen
- Center for Coastal Research University of Agder Kristiansand Norway
- Center for Artificial Intelligence Research University of Agder Kristiansand Norway
| | - Marta Moyano
- Center for Coastal Research University of Agder Kristiansand Norway
| | - Lee A. Fuiman
- Marine Science Institute University of Texas at Austin Port Aransas Texas USA
| | - Rebekah A. Oomen
- Center for Coastal Research University of Agder Kristiansand Norway
- Center for Artificial Intelligence Research University of Agder Kristiansand Norway
- Center for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
| |
Collapse
|
6
|
Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M. The era of reference genomes in conservation genomics. Trends Ecol Evol 2022; 37:197-202. [PMID: 35086739 DOI: 10.1016/j.tree.2021.11.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 02/08/2023]
Abstract
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
Collapse
Affiliation(s)
- Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; University of Koblenz-Landau, Institute for Environmental Sciences, Fortstrasse 7, 76829 Landau, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Iliana Bista
- University of Cambridge, Department of Genetics, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, CB10 1SA, Hinxton, UK
| | | | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino (FI) 50019, Italy
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - José A Godoy
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain
| | - Jacob Höglund
- Dept. of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Sweden
| | | | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Belgium
| | - Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences University of Groningen Nijenborgh, 9747, AG, Groningen, the Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5, 220 Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Belgium
| | | | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Dept. of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Germany
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark, Build 3, Universitetsparken 15, Copenhagen 2100, Denmark; China National Genebank, BGI-Shenzhen, Jinsha Road, Dapeng District, Shenzhen 518083, China
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
| | | |
Collapse
|
7
|
Wolf JF, MacKay L, Haworth SE, Cossette M, Dedato MN, Young KB, Elliott CI, Oomen RA. Preprinting is positively associated with early career researcher status in ecology and evolution. Ecol Evol 2021; 11:13624-13632. [PMID: 34707804 PMCID: PMC8525114 DOI: 10.1002/ece3.8106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/08/2021] [Accepted: 08/24/2021] [Indexed: 01/29/2023] Open
Abstract
The usage of preprint servers in ecology and evolution is increasing, allowing research to be rapidly disseminated and available through open access at no cost. Early Career Researchers (ECRs) often have limited experience with the peer review process, which can be challenging when trying to build publication records and demonstrate research ability for funding opportunities, scholarships, grants, or faculty positions. ECRs face different challenges relative to researchers with permanent positions and established research programs. These challenges might also vary according to institution size and country, which are factors associated with the availability of funding for open access journals. We predicted that the career stage and institution size impact the relative usage of preprint servers among researchers in ecology and evolution. Using data collected from 500 articles (100 from each of two open access journals, two closed access journals, and a preprint server), we showed that ECRs generated more preprints relative to non-ECRs, for both first and last authors. We speculate that this pattern is reflective of the advantages of quick and open access research that is disproportionately beneficial to ECRs. There is also a marginal association between first author, institution size, and preprint usage, whereby the number of preprints tends to increase with institution size for ECRs. The United States and United Kingdom contributed the greatest number of preprints by ECRs, whereas non-Western countries contributed relatively fewer preprints. This empirical evidence that preprint usage varies with the career stage, institution size, and country helps to identify barriers surrounding large-scale adoption of preprinting in ecology and evolution.
Collapse
Affiliation(s)
- Jesse F. Wolf
- Department of Environmental and Life SciencesTrent UniversityPeterboroughONCanada
| | - Layla MacKay
- Department of Forensic ScienceTrent UniversityPeterboroughONCanada
| | - Sarah E. Haworth
- Department of Environmental and Life SciencesTrent UniversityPeterboroughONCanada
| | | | - Morgan N. Dedato
- Department of Environmental and Life SciencesTrent UniversityPeterboroughONCanada
| | - Kiana B. Young
- Department of Environmental and Life SciencesTrent UniversityPeterboroughONCanada
| | - Colin I. Elliott
- Department of Forensic ScienceTrent UniversityPeterboroughONCanada
| | - Rebekah A. Oomen
- Department of BiosciencesCentre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
- Department of Natural SciencesCentre for Coastal ResearchUniversity of AgderKristiansandNorway
| |
Collapse
|
8
|
Raatikainen KJ, Purhonen J, Pohjanmies T, Peura M, Nieminen E, Mustajärvi L, Helle I, Shennan‐Farpón Y, Ahti PA, Basile M, Bernardo N, Bertram MG, Bouarakia O, Brias‐Guinart A, Fijen T, Froidevaux JSP, Hemmingmoore H, Hocevar S, Kendall L, Lampinen J, Marjakangas E, Martin JM, Oomen RA, Segre H, Sidemo‐Holm W, Silva AP, Thorbjørnsen SH, Torrents‐Ticó M, Zhang D, Ziemacki J. Pathways towards a sustainable future envisioned by early‐career conservation researchers. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Kaisa J. Raatikainen
- Department of Geography and Geology, Geography Section University of Turku Turku Finland
- Department of Biological and Environmental Science & School of Resource Wisdom University of Jyvaskyla Jyväskylä Finland
| | - Jenna Purhonen
- Department of Music, Art and Cultural Studies, Department of Biological and Environmental Science & School of Resource Wisdom University of Jyvaskyla Jyväskylä Finland
| | - Tähti Pohjanmies
- Department of Biological and Environmental Science & School of Resource Wisdom University of Jyvaskyla Jyväskylä Finland
- Natural Resources Institute Finland Helsinki Finland
| | - Maiju Peura
- Department of Biological and Environmental Science & School of Resource Wisdom University of Jyvaskyla Jyväskylä Finland
| | - Eini Nieminen
- Department of Biological and Environmental Science & School of Resource Wisdom University of Jyvaskyla Jyväskylä Finland
| | - Linda Mustajärvi
- Department of Biological and Environmental Science & School of Resource Wisdom University of Jyvaskyla Jyväskylä Finland
| | - Ilona Helle
- Department of Biological and Environmental Science & School of Resource Wisdom University of Jyvaskyla Jyväskylä Finland
| | - Yara Shennan‐Farpón
- ZSL Institute of Zoology, Zoological Society of London London UK
- UCL Department of Anthropology University College London London UK
| | - Pauliina A. Ahti
- Department of Biological and Environmental Science & School of Resource Wisdom University of Jyvaskyla Jyväskylä Finland
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow UK
| | - Marco Basile
- Swiss Federal Research Institute WSL Birmensdorf Switzerland
- Swiss Ornithological Institute Sempach Switzerland
- Chair of Wildlife Ecology and Management University of Freiburg Freiburg Germany
| | | | - Michael G. Bertram
- Department of Wildlife, Fish, and Environmental Studies Swedish University of Agricultural Sciences Umeå Sweden
- School of Biological Sciences, Monash University Clayton Victoria Australia
| | - Oussama Bouarakia
- SARChI Chair on Biodiversity Value and Change University of Venda Thohoyandou South Africa
- Laboratory Biodiversity Ecology Genome, Research Center BIOBIO, Faculty of Sciences Mohammed V University in Rabat Rabat Morocco
- Institut Systématique Evolution Biodiversité, MNHN, CNRS Sorbonne Université Paris France
| | - Aina Brias‐Guinart
- Faculty of Biological and Environmental Science & Faculty of Social Sciences, Global Change and Conservation Lab University of Helsinki, Helsinki Institute of Sustainability Science Helsinki Finland
| | - Thijs Fijen
- Plant Ecology and Nature Conservation Group Wageningen University Wageningen The Netherlands
| | - Jérémy S. P. Froidevaux
- Faculty of Natural Sciences University of Stirling, Biological and Environmental Sciences Stirling UK
- University of Bristol, School of Biological Sciences Bristol UK
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204) CNRS, MNHN, Sorbonne‐Université, Station marine Concarneau France
- Dynafor, Université de Toulouse, INRA, INPT, INP‐EI Purpan Castanet‐Tolosan France
| | - Heather Hemmingmoore
- Grimsö Wildlife Research Station, Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Sara Hocevar
- Department of Biological and Environmental Science & School of Resource Wisdom University of Jyvaskyla Jyväskylä Finland
| | - Liam Kendall
- Centre for Environmental and Climate Science Lund University Lund Sweden
- University of New England, School of Environmental and Rural Science Armidale NSW Australia
| | - Jussi Lampinen
- Department of Biology & Biodiversity Research Unit University of Turku Turku Finland
| | - Emma‐Liina Marjakangas
- Centre for Biodiversity Dynamics, Department of Biology Norwegian University of Science and Technology Trondheim Norway
- The Helsinki Lab of Ornithology, Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | - Jake M. Martin
- School of Biological Sciences, Monash University Clayton Victoria Australia
| | - Rebekah A. Oomen
- Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
- Centre for Coastal Research, Department of Natural Sciences University of Agder Kristiansand Norway
- Department of Biology Dalhousie University Halifax Nova Scotia Canada
| | - Hila Segre
- Human and Biodiversity Research Lab, Faculty of Architecture and Town Planning, Technion – Israel Institute of Technology Haifa Israel
| | | | - André P. Silva
- Department of Animal Ecology, Evolutionary Biology Centre Uppsala University Uppsala Sweden
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | | | - Miquel Torrents‐Ticó
- Faculty of Biological and Environmental Science & Faculty of Social Sciences, Global Change and Conservation Lab University of Helsinki, Helsinki Institute of Sustainability Science Helsinki Finland
| | - Di Zhang
- School of Life Sciences, Peking University Beijing China
| | - Jasmin Ziemacki
- Center for Development Research University of Bonn Bonn Germany
| |
Collapse
|
9
|
Abstract
Phenotypic variance is a function of genetic variability, environmental variation, and the ways in which genetic and environmental variation interact, i.e., VG×E. Reaction norms are a means of conceptually, graphically, and mathematically describing this total variance and are a powerful tool for decomposing it into its constituent parts (i.e., nature, nurture, and, critically, their interaction). A reaction norm is defined as the range of phenotypes expressed by a genotype along an environmental gradient. It is represented by a linear or nonlinear function which describes the value of a phenotypic trait for a particular genotype or group of genotypes in different environments. As such, it is closely related to the concept of phenotypic plasticity, which can be represented by a reaction norm with a non-zero slope (i.e., the phenotype varies with respect to the environment). While the term (which originated as Reaktionsnorm) has been in use for over one hundred years, there has been some debate about the most appropriate way to describe it mathematically. Nonetheless, there is general consensus that a reaction norm has multiple properties, each of which can be the target of selection. Reaction norms are typically described as consisting of: (1) an intercept, elevation, or offset, which describes the mean trait value across all environments, (2) a slope, which quantifies the degree of trait plasticity, and (3) shape or curvature (e.g., linear, quadratic, monotonic). Evidence that trait means and plasticities can evolve separately underscores the necessity of applying a reaction norm framework for studying ecological and evolutionary responses to the environment, because measuring phenotypes in a single environmental context does not necessarily reflect their relative values or diversities in a different context. These contextual differences are particularly important in a world of rapid anthropogenic change and increasing environmental variability. Therefore, in addition to being fundamental to ecological and evolutionary phenomena, reaction norm evolution is relevant for diverse biological fields, including behavior and psychology, conservation and natural resource management, global change biology, agriculture and breeding programs, and human health. Given that evolutionary change is defined by genetic change, we focus this article on variation among reaction norms from different genotypes (i.e., reaction norms that have potentially evolved to be divergent from one another) as well as the forces that promote and constrain reaction norm evolution. For an overview of the literature on plasticity itself (keeping in mind that reaction norms need not be plastic), see the separate Oxford Bibliographies in Evolutionary Biology article Phenotypic Plasticity.
Collapse
|
10
|
Oomen RA, Kuparinen A, Hutchings JA. Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change. J Hered 2020; 111:319-332. [PMID: 32620014 PMCID: PMC7423069 DOI: 10.1093/jhered/esaa020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/25/2020] [Indexed: 12/26/2022] Open
Abstract
Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modeling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.
Collapse
Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | - Anna Kuparinen
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Jeffrey A Hutchings
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
| |
Collapse
|
11
|
Mérot C, Oomen RA, Tigano A, Wellenreuther M. A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation. Trends Ecol Evol 2020; 35:561-572. [PMID: 32521241 DOI: 10.1016/j.tree.2020.03.002] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/25/2020] [Accepted: 03/03/2020] [Indexed: 12/12/2022]
Abstract
Structural genomic variants (SVs) are ubiquitous and play a major role in adaptation and speciation. Yet, comparative and population genomics have focused predominantly on gene duplications and large-effect inversions. The lack of a common framework for studying all SVs is hampering progress towards a more systematic assessment of their evolutionary significance. Here we (i) review how different types of SVs affect ecological and evolutionary processes; (ii) suggest unifying definitions and recommendations for future studies; and (iii) provide a roadmap for the integration of SVs in ecoevolutionary studies. In doing so, we lay the foundation for population genomics, theoretical, and experimental approaches to understand how the full spectrum of SVs impacts ecological and evolutionary processes.
Collapse
Affiliation(s)
- Claire Mérot
- Université Laval, Institut de Biologie Intégrative des Systèmes, 1030 Avenue de la Médecine, G1V 0A6, Québec, QC, Canada.
| | - Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371 Oslo, Norway; Centre for Coastal Research, University of Agder, Universitetsveien 25, 4630 Kristiansand, Norway.
| | - Anna Tigano
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA.
| | - Maren Wellenreuther
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand.
| |
Collapse
|
12
|
Roney NE, Oomen RA, Knutsen H, Olsen EM, Hutchings JA. Fine-scale population differences in Atlantic cod reproductive success: A potential mechanism for ecological speciation in a marine fish. Ecol Evol 2018; 8:11634-11644. [PMID: 30598762 PMCID: PMC6303701 DOI: 10.1002/ece3.4615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/23/2018] [Accepted: 09/05/2018] [Indexed: 11/30/2022] Open
Abstract
Successful resource-management and conservation outcomes ideally depend on matching the spatial scales of population demography, local adaptation, and threat mitigation. For marine fish with high dispersal capabilities, this remains a fundamental challenge. Based on daily parentage assignments of more than 4,000 offspring, we document fine-scaled temporal differences in individual reproductive success for two spatially adjacent (<10 km) populations of a broadcast-spawning marine fish. Distinguished by differences in genetics and life history, Atlantic cod (Gadus morhua) from inner- and outer-fjord populations were allowed to compete for mating and reproductive opportunities. After accounting for phenotypic variability in several traits, reproductive success of outer-fjord cod was significantly lower than that of inner-fjord cod. This finding, given that genomically different cod ecotypes inhabit inner- and outer-fjord waters, raises the intriguing hypothesis that the populations might be diverging because of ecological speciation. Individual reproductive success, skewed within both sexes (more so among males), was positively affected by body size, which also influenced the timing of reproduction, larger individuals spawning later among females but earlier among males. Our work suggests that spatial mismatches between management and biological units exist in marine fishes and that studies of reproductive interactions between putative populations or ecotypes can provide an informative basis on which determination of the scale of local adaptation can be ascertained.
Collapse
Affiliation(s)
- Nancy E. Roney
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Rebekah A. Oomen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
- Institute of Marine ResearchFlødevigen Marine Research StationHisNorway
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
- Institute of Marine ResearchFlødevigen Marine Research StationHisNorway
- Centre for Coastal Research (CCR)University of AgderKristiansandNorway
| | - Esben M. Olsen
- Institute of Marine ResearchFlødevigen Marine Research StationHisNorway
- Centre for Coastal Research (CCR)University of AgderKristiansandNorway
| | - Jeffrey A. Hutchings
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of BiosciencesUniversity of OsloOsloNorway
- Institute of Marine ResearchFlødevigen Marine Research StationHisNorway
| |
Collapse
|
13
|
Abstract
The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.
Collapse
Affiliation(s)
- Rebekah A. Oomen
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
| | - Jeffrey A. Hutchings
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
- Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway
| |
Collapse
|
14
|
Oomen RA, Hutchings JA. Genetic variation in plasticity of life-history traits between Atlantic cod (Gadus morhua) populations exposed to contrasting thermal regimes. CAN J ZOOL 2016. [DOI: 10.1139/cjz-2015-0186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We employed common-garden experiments to test for genetic variation in responses of larval life-history traits to temperature between two populations of Atlantic cod (Gadus morhua L., 1758) that naturally experience contrasting thermal environments during early life due to spatial and temporal differences in spawning. Southern Gulf of St. Lawrence cod larvae experienced faster growth in warmer water and low, uniform survival across all experimental temperatures (3, 7, 11 °C), consistent with previous studies on this spring-spawning population. In contrast, larvae from fall-spawning Southwestern Scotian Shelf cod collected near Sambro, Nova Scotia, lacked plasticity for growth but experienced much lower survival at higher temperatures. Phenotypes that are positively associated with fitness were observed at temperatures closest to those experienced in the wild, consistent with the hypothesis that these populations are adapted to local thermal regimes. The lack of growth plasticity observed in Sambro cod might be due to costly maintenance of plasticity in stable environments or energy savings at cold temperatures. However, additional experiments need to be conducted on Sambro cod and other fall-spawning marine fishes to determine to what extent responses to projected changes in climate will differ among populations.
Collapse
Affiliation(s)
- Rebekah A. Oomen
- Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - Jeffrey A. Hutchings
- Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway
| |
Collapse
|
15
|
Oomen RA, Hutchings JA. Variation in spawning time promotes genetic variability in population responses to environmental change in a marine fish. Conserv Physiol 2015; 3:cov027. [PMID: 27293712 PMCID: PMC4778481 DOI: 10.1093/conphys/cov027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 05/03/2015] [Accepted: 05/09/2015] [Indexed: 05/29/2023]
Abstract
The level of phenotypic plasticity displayed within a population (i.e. the slope of the reaction norm) reflects the short-term response of a population to environmental change, while variation in reaction norm slopes among populations reflects spatial variation in these responses. Thus far, studies of thermal reaction norm variation have focused on geographically driven adaptation among different latitudes, altitudes or habitats. Yet, thermal variability is a function of both space and time. For organisms that reproduce at different times of year, such variation has the potential to promote adaptive variability in thermal responses for critical early life stages. Using common-garden experiments, we examined the spatial scale of genetic variation in thermal plasticity for early life-history traits among five populations of endangered Atlantic cod (Gadus morhua) that spawn at different times of year. Patterns of plasticity for larval growth and survival suggest that population responses to climate change will differ substantially, with increasing water temperatures posing a considerably greater threat to autumn-spawning cod than to those that spawn in winter or spring. Adaptation to seasonal cooling or warming experienced during the larval stage is suggested as a possible cause. Furthermore, populations that experience relatively cold temperatures during early life might be more sensitive to changes in temperature. Substantial divergence in adaptive traits was evident at a smaller spatial scale than has previously been shown for a marine fish with no apparent physical barriers to gene flow (∼200 km). Our findings highlight the need to consider the impact of intraspecific variation in reproductive timing on thermal adaptation when forecasting the effects of climate change on animal populations.
Collapse
Affiliation(s)
- Rebekah A Oomen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0371, Norway
| | - Jeffrey A Hutchings
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0371, Norway
- Department of Natural Sciences, University of Agder, Kristiansand 4630, Norway
| |
Collapse
|
16
|
Oomen RA, Gillett RM, Kyle CJ. Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage. Mol Ecol Resour 2012; 13:103-16. [PMID: 23095905 DOI: 10.1111/1755-0998.12027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 09/07/2012] [Accepted: 09/11/2012] [Indexed: 12/23/2022]
Abstract
Characterization and population genetic analysis of multilocus genes, such as those found in the major histocompatibility complex (MHC) is challenging in nonmodel vertebrates. The traditional method of extensive cloning and Sanger sequencing is costly and time-intensive and indirect methods of assessment often underestimate total variation. Here, we explored the suitability of 454 pyrosequencing for characterizing multilocus genes for use in population genetic studies. We compared two sample tagging protocols and two bioinformatic procedures for 454 sequencing through characterization of a 185-bp fragment of MHC DRB exon 2 in wolverines (Gulo gulo) and further compared the results with those from cloning and Sanger sequencing. We found 10 putative DRB alleles in the 88 individuals screened with between two and four alleles per individual, suggesting amplification of a duplicated DRB gene. In addition to the putative alleles, all individuals possessed an easily identifiable pseudogene. In our system, sequence variants with a frequency below 6% in an individual sample were usually artefacts. However, we found that sample preparation and data processing procedures can greatly affect variant frequencies in addition to the complexity of the multilocus system. Therefore, we recommend determining a per-amplicon-variant frequency threshold for each unique system. The extremely deep coverage obtained in our study (approximately 5000×) coupled with the semi-quantitative nature of pyrosequencing enabled us to assign all putative alleles to the two DRB loci, which is generally not possible using traditional methods. Our method of obtaining locus-specific MHC genotypes will enhance population genetic analyses and studies on disease susceptibility in nonmodel wildlife species.
Collapse
Affiliation(s)
- Rebekah A Oomen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, Canada.
| | | | | |
Collapse
|
17
|
Oomen RA, Reudink MW, Nocera JJ, Somers CM, Green MC, Kyle CJ. Mitochondrial evidence for panmixia despite perceived barriers to gene flow in a widely distributed waterbird. ACTA ACUST UNITED AC 2011; 102:584-92. [PMID: 21705489 DOI: 10.1093/jhered/esr055] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We examined the mitochondrial genetic structure of American white pelicans (Pelecanus erythrorhynchos) to: 1) verify or refute whether American white pelicans are panmictic and 2) understand if any lack of genetic structure is the result of contemporary processes or historical phenomena. Sequence analysis of mitochondrial DNA control region haplotypes of 367 individuals from 19 colonies located across their North American range revealed a lack of population genetic or phylogeographic structure. This lack of structure was unexpected because: 1) Major geographic barriers such as the North American Continental Divide are thought to limit dispersal; 2) Differences in migratory behavior are expected to promote population differentiation; and 3) Many widespread North American migratory bird species show historic patterns of differentiation resulting from having inhabited multiple glacial refugia. Further, high haplotype diversity and many rare haplotypes are maintained across the species' distribution, despite frequent local extinctions and recolonizations that are expected to decrease diversity. Our findings suggest that American white pelicans have a high effective population size and low natal philopatry. We suggest that the rangewide panmixia we observed in American white pelicans is due to high historical and contemporary gene flow, enabled by high mobility and a lack of effective physical or behavioral barriers.
Collapse
Affiliation(s)
- Rebekah A Oomen
- Forensic Science Department, Trent University, Peterborough, Ontario, Canada.
| | | | | | | | | | | |
Collapse
|