51
|
von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020; 20. [PMID: 31925943 DOI: 10.1111/1755-0998.13136] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/24/2019] [Accepted: 01/05/2020] [Indexed: 01/16/2023]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
Collapse
Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| |
Collapse
|
52
|
Carreras C, García‐Cisneros A, Wangensteen OS, Ordóñez V, Palacín C, Pascual M, Turon X. East is East and West is West: Population genomics and hierarchical analyses reveal genetic structure and adaptation footprints in the keystone species
Paracentrotus lividus
(Echinoidea). DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.13016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Carlos Carreras
- Department de Genètica Microbiologia i Estadística and IRBio Universitat de Barcelona Barcelona Spain
| | - Alex García‐Cisneros
- Centre d'Estudis Avançats de Blanes (CEAB, CSIC) Girona Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences and IRBIo University of Barcelona Barcelona Spain
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Víctor Ordóñez
- Department de Genètica Microbiologia i Estadística and IRBio Universitat de Barcelona Barcelona Spain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences and IRBIo University of Barcelona Barcelona Spain
| | - Marta Pascual
- Department de Genètica Microbiologia i Estadística and IRBio Universitat de Barcelona Barcelona Spain
| | - Xavier Turon
- Centre d'Estudis Avançats de Blanes (CEAB, CSIC) Girona Spain
| |
Collapse
|
53
|
van Riemsdijk I, Butlin RK, Wielstra B, Arntzen JW. Testing an hypothesis of hybrid zone movement for toads in France. Mol Ecol 2019; 28:1070-1083. [PMID: 30609055 DOI: 10.1111/mec.15005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/08/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.
Collapse
Affiliation(s)
- Isolde van Riemsdijk
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Ben Wielstra
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California
| | - Jan W Arntzen
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands
| |
Collapse
|
54
|
LaCava MEF, Aikens EO, Megna LC, Randolph G, Hubbard C, Buerkle CA. Accuracy of de novo assembly of DNA sequences from double-digest libraries varies substantially among software. Mol Ecol Resour 2019; 20:360-370. [PMID: 31665547 DOI: 10.1111/1755-0998.13108] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 11/29/2022]
Abstract
Advances in DNA sequencing have made it feasible to gather genomic data for non-model organisms and large sets of individuals, often using methods for sequencing subsets of the genome. Several of these methods sequence DNA associated with endonuclease restriction sites (various RAD and GBS methods). For use in taxa without a reference genome, these methods rely on de novo assembly of fragments in the sequencing library. Many of the software options available for this application were originally developed for other assembly types and we do not know their accuracy for reduced representation libraries. To address this important knowledge gap, we simulated data from the Arabidopsis thaliana and Homo sapiens genomes and compared de novo assemblies by six software programs that are commonly used or promising for this purpose (ABySS, CD-HIT, Stacks, Stacks2, Velvet and VSEARCH). We simulated different mutation rates and types of mutations, and then applied the six assemblers to the simulated data sets, varying assembly parameters. We found substantial variation in software performance across simulations and parameter settings. ABySS failed to recover any true genome fragments, and Velvet and VSEARCH performed poorly for most simulations. Stacks and Stacks2 produced accurate assemblies of simulations containing SNPs, but the addition of insertion and deletion mutations decreased their performance. CD-HIT was the only assembler that consistently recovered a high proportion of true genome fragments. Here, we demonstrate the substantial difference in the accuracy of assemblies from different software programs and the importance of comparing assemblies that result from different parameter settings.
Collapse
Affiliation(s)
- Melanie E F LaCava
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Ellen O Aikens
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Libby C Megna
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Gregg Randolph
- Genome Technologies Lab, University of Wyoming, Laramie, WY, USA
| | - Charley Hubbard
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Botany, University of Wyoming, Laramie, WY, USA
| | - C Alex Buerkle
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Botany, University of Wyoming, Laramie, WY, USA
| |
Collapse
|
55
|
Rexer-Huber K, Veale AJ, Catry P, Cherel Y, Dutoit L, Foster Y, McEwan JC, Parker GC, Phillips RA, Ryan PG, Stanworth AJ, van Stijn T, Thompson DR, Waters J, Robertson BC. Genomics detects population structure within and between ocean basins in a circumpolar seabird: The white-chinned petrel. Mol Ecol 2019; 28:4552-4572. [PMID: 31541577 DOI: 10.1111/mec.15248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023]
Abstract
The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (Procellaria aequinoctialis) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and first domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.
Collapse
Affiliation(s)
- Kalinka Rexer-Huber
- Department of Zoology, University of Otago, Dunedin, New Zealand.,Parker Conservation, Dunedin, New Zealand
| | - Andrew J Veale
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Paulo Catry
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Lisboa, Portugal
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, Villiers-en-Bois, France
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Yasmin Foster
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - John C McEwan
- Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand
| | | | - Richard A Phillips
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - Peter G Ryan
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, South Africa
| | | | | | - David R Thompson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Jonathan Waters
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | |
Collapse
|
56
|
Phylogeography of the Rufous Vanga and the role of bioclimatic transition zones in promoting speciation within Madagascar. Mol Phylogenet Evol 2019; 139:106535. [DOI: 10.1016/j.ympev.2019.106535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/12/2019] [Accepted: 06/13/2019] [Indexed: 12/23/2022]
|
57
|
López-Cortegano E, Pouso R, Labrador A, Pérez-Figueroa A, Fernández J, Caballero A. Optimal Management of Genetic Diversity in Subdivided Populations. Front Genet 2019; 10:843. [PMID: 31572448 PMCID: PMC6753960 DOI: 10.3389/fgene.2019.00843] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/13/2019] [Indexed: 11/29/2022] Open
Abstract
One of the main objectives of conservation programs is the maintenance of genetic diversity because this provides the adaptive potential of populations to face new environmental challenges. Genetic diversity is generally assessed by means of neutral molecular markers, and it is usually quantified by the expected heterozygosity under Hardy-Weinberg equilibrium and the number of alleles per locus or allelic diversity. These two measures of genetic diversity are complementary because whereas the former is directly related to genetic variance for quantitative traits and, therefore, to the short-term response to selection and adaptation, the latter is more sensitive to population bottlenecks and relates more strongly to the long-term capacity of adaptation of populations. In the context of structured populations undergoing conservation programs, it is important to decide the optimum management strategy to preserve as much genetic diversity as possible while avoiding inbreeding. Here we examine, through computer simulations, the consequences of choosing a conservation strategy based on maximizing either heterozygosity or allelic diversity of single-nucleotide polymorphism haplotypes in a subdivided population. Our results suggest that maximization of allelic diversity can be more efficient in maintaining the genetic diversity of subdivided populations than maximization of expected heterozygosity because the former maintains a larger number of alleles while making a better control of inbreeding. Thus, maximization of allelic diversity should be a recommended strategy in conservation programs for structured populations.
Collapse
Affiliation(s)
- Eugenio López-Cortegano
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Ramón Pouso
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Adriana Labrador
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain
| | - Jesús Fernández
- Departamento de Mejora Genética, Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| |
Collapse
|
58
|
Theodoridis S, Nogués‐Bravo D, Conti E. The role of cryptic diversity and its environmental correlates in global conservation status assessments: Insights from the threatened bird's‐eye primrose (
Primula farinosa
L.). DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12953] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Spyros Theodoridis
- Department of Systematic and Evolutionary Botany and Botanic Garden University of Zurich Zurich Switzerland
| | - David Nogués‐Bravo
- Department of Biology, Center for Macroecology, Evolution and Climate University of Copenhagen Copenhagen Ø Denmark
| | - Elena Conti
- Department of Systematic and Evolutionary Botany and Botanic Garden University of Zurich Zurich Switzerland
| |
Collapse
|
59
|
Development of SNVs and indels markers mined out of the first multi-organ transcriptomes from Hypancistrus zebra (Loricariidae), an endangered Amazonian catfish. Genomics 2019; 112:971-980. [PMID: 31220586 DOI: 10.1016/j.ygeno.2019.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/26/2019] [Accepted: 06/15/2019] [Indexed: 12/30/2022]
Abstract
Hypancistrus zebra is a catfish, endemic from the Xingu River, threatened with extinction due to the impacts of Belo Monte dam, of its illegal capture, of gold mining activities and of climate change. Currently, there are three nucleotide sequences from this species in GenBank, what impedes the development of genetic markers to assist on its conservation. A total of 217 million RNA-Seq reads from seven organs were sequenced and used to assemble 566,607 transcripts, including 98% of BUSCO vertebrates orthologs, 11,321 transcripts with SNVs and 1,724 transcripts with indels. Three transcripts with SNVs and five transcripts with indels were validated as the best candidate markers to conservation practices. This work illustrates the use of transcriptomics in conservation, by the development of a bigger toolbox for an endangered fish, and shall further contribute to studies on this and others related species reproduction, physiology, and adaptability to environmental changes.
Collapse
|
60
|
Gervais L, Perrier C, Bernard M, Merlet J, Pemberton JM, Pujol B, Quéméré E. RAD-sequencing for estimating genomic relatedness matrix-based heritability in the wild: A case study in roe deer. Mol Ecol Resour 2019; 19:1205-1217. [PMID: 31058463 DOI: 10.1111/1755-0998.13031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 01/02/2023]
Abstract
Estimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree-free estimation of trait heritabilities in wild populations. However, until now, most quantitative genetic studies based on a genomic relatedness matrix (GRM) have focused on long-term monitored populations for which traditional pedigrees were also available, and have often had access to knowledge of genome sequence and variability. Here, we investigated the potential of RAD-sequencing for estimating heritability in a free-ranging roe deer (Capreolous capreolus) population for which no prior genomic resources were available. We propose a step-by-step analytical framework to optimize the quality and quantity of the genomic data and explore the impact of the single nucleotide polymorphism (SNP) calling and filtering processes on the GRM structure and GRM-based heritability estimates. As expected, our results show that sequence coverage strongly affects the number of recovered loci, the genotyping error rate and the amount of missing data. Ultimately, this had little effect on heritability estimates and their standard errors, provided that the GRM was built from a minimum number of loci (above 7,000). Genomic relatedness matrix-based heritability estimates thus appear robust to a moderate level of genotyping errors in the SNP data set. We also showed that quality filters, such as the removal of low-frequency variants, affect the relatedness structure of the GRM, generating lower h2 estimates. Our work illustrates the huge potential of RAD-sequencing for estimating GRM-based heritability in virtually any natural population.
Collapse
Affiliation(s)
- Laura Gervais
- CEFS, INRA, Université de Toulouse, Castanet-Tolosan, Cedex, France.,Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), CNRS, IRD, UPS, Université Fédérale de Toulouse Midi-Pyrénées, Toulouse, France
| | | | - Maria Bernard
- SIGENAE, INRA, Jouy-en-Josas, France.,GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Joël Merlet
- CEFS, INRA, Université de Toulouse, Castanet-Tolosan, Cedex, France
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Benoit Pujol
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), CNRS, IRD, UPS, Université Fédérale de Toulouse Midi-Pyrénées, Toulouse, France.,PSL Université Paris: EPHE-UPVD-CNRS, Université de Perpignan, Perpignan, France
| | - Erwan Quéméré
- CEFS, INRA, Université de Toulouse, Castanet-Tolosan, Cedex, France
| |
Collapse
|
61
|
Xuereb A, Benestan L, Normandeau É, Daigle RM, Curtis JMR, Bernatchez L, Fortin MJ. Asymmetric oceanographic processes mediate connectivity and population genetic structure, as revealed by RADseq, in a highly dispersive marine invertebrate (Parastichopus californicus). Mol Ecol 2019; 27:2347-2364. [PMID: 29654703 DOI: 10.1111/mec.14589] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 01/02/2023]
Abstract
Marine populations are typically characterized by weak genetic differentiation due to the potential for long-distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the coast of North America in the northeastern Pacific Ocean. Then, we tested two hypotheses regarding spatial processes influencing population structure: (i) isolation by distance (IBD: genetic structure is explained by geographic distance) and (ii) isolation by resistance (IBR: genetic structure is driven by ocean circulation). Using RADseq, we genotyped 717 individuals from 24 sampling locations across 2,719 neutral SNPs to assess the degree of population differentiation and integrated estimates of genetic variation with inferred connectivity probabilities from a biophysical model of larval dispersal mediated by ocean currents. We identified two clusters separating north and south regions, as well as significant, albeit weak, substructure within regions (FST = 0.002, p = .001). After modelling the asymmetric nature of ocean currents, we demonstrated that local oceanography (IBR) was a better predictor of genetic variation (R2 = .49) than geographic distance (IBD) (R2 = .18), and directional processes played an important role in shaping fine-scale structure. Our study contributes to the growing body of literature identifying significant population structure in marine systems and has important implications for the spatial management of P. californicus and other exploited marine species.
Collapse
Affiliation(s)
- Amanda Xuereb
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Laura Benestan
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Rémi M Daigle
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Janelle M R Curtis
- Pacific Biological Station, Ecosystem Sciences Division, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
62
|
Dorant Y, Benestan L, Rougemont Q, Normandeau E, Boyle B, Rochette R, Bernatchez L. Comparing Pool-seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster ( Homarus americanus) as a case study. Ecol Evol 2019; 9:6606-6623. [PMID: 31236247 PMCID: PMC6580275 DOI: 10.1002/ece3.5240] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/10/2019] [Accepted: 04/13/2019] [Indexed: 01/02/2023] Open
Abstract
Unraveling genetic population structure is challenging in species potentially characterized by large population size and high dispersal rates, often resulting in weak genetic differentiation. Genotyping a large number of samples can improve the detection of subtle genetic structure, but this may substantially increase sequencing cost and downstream bioinformatics computational time. To overcome this challenge, alternative, cost-effective sequencing approaches, namely Pool-seq and Rapture, have been developed. We empirically measured the power of resolution and congruence of these two methods in documenting weak population structure in nonmodel species with high gene flow comparatively to a conventional genotyping-by-sequencing (GBS) approach. For this, we used the American lobster (Homarus americanus) as a case study. First, we found that GBS, Rapture, and Pool-seq approaches gave similar allele frequency estimates (i.e., correlation coefficient over 0.90) and all three revealed the same weak pattern of population structure. Yet, Pool-seq data showed F ST estimates three to five times higher than GBS and Rapture, while the latter two methods returned similar F ST estimates, indicating that individual-based approaches provided more congruent results than Pool-seq. We conclude that despite higher costs, GBS and Rapture are more convenient approaches to use in the case of species exhibiting very weak differentiation. While both GBS and Rapture approaches provided similar results with regard to estimates of population genetic parameters, GBS remains more cost-effective in project involving a relatively small numbers of genotyped individuals (e.g., <1,000). Overall, this study illustrates the complexity of estimating genetic differentiation and other summary statistics in complex biological systems characterized by large population size and migration rates.
Collapse
Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Laura Benestan
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Pêches et Océans CanadaInstitut Maurice‐LamontagneMont‐JoliCanada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Plateforme d'analyses génomiques, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Rémy Rochette
- Department of BiologyUniversity of New BrunswickSaint JohnCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| |
Collapse
|
63
|
O'Connell KA, Santo VD, Maldonado J, Molina E, Fujita MK. A Tale of Two Skates: Comparative Phylogeography of North American Skate Species with Implications for Conservation. COPEIA 2019. [DOI: 10.1643/cg-18-114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Kyle A. O'Connell
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Valentina Di Santo
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138
| | - Jose Maldonado
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Erika Molina
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Matthew K. Fujita
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| |
Collapse
|
64
|
López-Cortegano E, Pérez-Figueroa A, Caballero A. metapop2: Re-implementation of software for the analysis and management of subdivided populations using gene and allelic diversity. Mol Ecol Resour 2019; 19:1095-1100. [PMID: 30938911 DOI: 10.1111/1755-0998.13015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 03/07/2019] [Accepted: 03/19/2019] [Indexed: 01/06/2023]
Abstract
Management programmes often have to make decisions based on the analysis of the genetic properties and diversity of populations. Expected heterozygosity (or gene diversity) and population structure parameters are often used to make recommendations for conservation, such as avoidance of inbreeding or migration across subpopulations. Allelic diversity, however, can also provide complementary and useful information for conservation programmes, as it is highly sensitive to population bottlenecks, and is more related to long-term selection response than heterozygosity. Here we present a completely revised and updated re-implementation of the software metapop for the analysis of diversity in subdivided populations, as well as a tool for the management and dynamic estimation of optimal contributions in conservation programmes. This new update includes computation of allelic diversity for population analysis and management, as well as a simulation mode to forecast the consequences of taking different management strategies over time. Furthermore, the new implementation in C++ includes code optimization and improved memory usage, allowing for fast analysis of large data sets including single nucleotide polymorphism markers, as well as enhanced cross-software and cross-platform compatibility.
Collapse
Affiliation(s)
- Eugenio López-Cortegano
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| |
Collapse
|
65
|
Baird AB, Robinson MJ, Bickham JW. The role of the American Society of Mammalogists in mammalian conservation: from politics to conservation genetics. J Mammal 2019. [DOI: 10.1093/jmammal/gyz028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Amy B Baird
- Department of Natural Sciences, University of Houston - Downtown, Houston, TX, USA
| | | | - John W Bickham
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| |
Collapse
|
66
|
Bradbury D, Binks RM, Coates DJ, Byrne M. Conservation genomics of range disjunction in a global biodiversity hotspot: a case study of Banksia biterax (Proteaceae) in southwestern Australia. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Donna Bradbury
- Biodiversity and Conservation Science; Department of Biodiversity, Conservation & Attractions, Kensington, WA, Australia
| | - Rachel M Binks
- Biodiversity and Conservation Science; Department of Biodiversity, Conservation & Attractions, Kensington, WA, Australia
| | - David J Coates
- Biodiversity and Conservation Science; Department of Biodiversity, Conservation & Attractions, Kensington, WA, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science; Department of Biodiversity, Conservation & Attractions, Kensington, WA, Australia
| |
Collapse
|
67
|
Hemmer‐Hansen J, Hüssy K, Baktoft H, Huwer B, Bekkevold D, Haslob H, Herrmann J, Hinrichsen H, Krumme U, Mosegaard H, Nielsen EE, Reusch TBH, Storr‐Paulsen M, Velasco A, von Dewitz B, Dierking J, Eero M. Genetic analyses reveal complex dynamics within a marine fish management area. Evol Appl 2019; 12:830-844. [PMID: 30976313 PMCID: PMC6439499 DOI: 10.1111/eva.12760] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 11/20/2018] [Accepted: 11/29/2018] [Indexed: 01/01/2023] Open
Abstract
Genetic data have great potential for improving fisheries management by identifying the fundamental management units-that is, the biological populations-and their mixing. However, so far, the number of practical cases of marine fisheries management using genetics has been limited. Here, we used Atlantic cod in the Baltic Sea to demonstrate the applicability of genetics to a complex management scenario involving mixing of two genetically divergent populations. Specifically, we addressed several assumptions used in the current assessment of the two populations. Through analysis of 483 single nucleotide polymorphisms (SNPs) distributed across the Atlantic cod genome, we confirmed that a model of mechanical mixing, rather than hybridization and introgression, best explained the pattern of genetic differentiation. Thus, the fishery is best monitored as a mixed-stock fishery. Next, we developed a targeted panel of 39 SNPs with high statistical power for identifying population of origin and analyzed more than 2,000 tissue samples collected between 2011 and 2015 as well as 260 otoliths collected in 2003/2004. These data provided high spatial resolution and allowed us to investigate geographical trends in mixing, to compare patterns for different life stages and to investigate temporal trends in mixing. We found similar geographical trends for the two time points represented by tissue and otolith samples and that a recently implemented geographical management separation of the two populations provided a relatively close match to their distributions. In contrast to the current assumption, we found that patterns of mixing differed between juveniles and adults, a signal likely linked to the different reproductive dynamics of the two populations. Collectively, our data confirm that genetics is an operational tool for complex fisheries management applications. We recommend focussing on developing population assessment models and fisheries management frameworks to capitalize fully on the additional information offered by genetically assisted fisheries monitoring.
Collapse
Affiliation(s)
- Jakob Hemmer‐Hansen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Karin Hüssy
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | - Henrik Baktoft
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Bastian Huwer
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | - Dorte Bekkevold
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Jens‐Peter Herrmann
- Institute of Marine Ecosystem and Fishery ScienceUniversity of HamburgHamburgGermany
| | - Hans‐Harald Hinrichsen
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Uwe Krumme
- Thünen Institute of Baltic Sea FisheriesRostockGermany
| | - Henrik Mosegaard
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Thorsten B. H. Reusch
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Marie Storr‐Paulsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | | | - Burkhard von Dewitz
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Jan Dierking
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Margit Eero
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| |
Collapse
|
68
|
|
69
|
Peterson EE, Hanks EM, Hooten MB, Ver Hoef JM, Fortin M. Spatially structured statistical network models for landscape genetics. ECOL MONOGR 2019. [DOI: 10.1002/ecm.1355] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Erin E. Peterson
- ARC Centre for Excellence in Mathematical and Statistical Frontiers (ACEMS) and the Institute for Future Environments Queensland University of Technology (QUT) Brisbane Queensland 4000 Australia
| | - Ephraim M. Hanks
- Department of Statistics Pennsylvania State University University Park Pennsylvania 16801 USA
| | - Mevin B. Hooten
- U.S. Geological Survey Colorado Cooperative Fish and Wildlife Research Unit Department of Fish, Wildlife, and Conservation Biology, and Department of Statistics Colorado State University Fort Collins Colorado 80523 USA
| | - Jay M. Ver Hoef
- Marine Mammal Laboratory NOAA‐NMFS Alaska Fisheries Science Center Seattle Washington 98115 USA
| | - Marie‐Josée Fortin
- Department of Ecology & Evolutionary Biology University of Toronto Toronto Ontario M5S 1A1 Canada
| |
Collapse
|
70
|
Monteiro WP, Veiga JC, Silva AR, Carvalho CDS, Lanes ÉCM, Rico Y, Jaffé R. Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask). PeerJ 2019; 7:e6446. [PMID: 30783576 PMCID: PMC6377592 DOI: 10.7717/peerj.6446] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/15/2019] [Indexed: 11/30/2022] Open
Abstract
The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.
Collapse
Affiliation(s)
| | - Jamille Costa Veiga
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Amanda Reis Silva
- Departamento de Botânica, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
| | | | | | - Yessica Rico
- CONACYT, Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología, A.C., Michoacán, Mexico
| | - Rodolfo Jaffé
- Instituto Tecnológico Vale, Belém, PA, Brazil.,Departamento de Ecologia, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
71
|
Scott PA, Glenn TC, Rissler LJ. Formation of a recent hybrid zone offers insight into the geographic puzzle and maintenance of species boundaries in musk turtles. Mol Ecol 2019; 28:761-771. [DOI: 10.1111/mec.14983] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/11/2018] [Accepted: 12/17/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Peter A. Scott
- Department of Biological Sciences University of Alabama Tuscaloosa Alabama
| | - Travis C. Glenn
- Department of Environmental Health Science and Institute of Bioinformatics University of Georgia Athens Georgia
| | - Leslie J. Rissler
- Department of Biological Sciences University of Alabama Tuscaloosa Alabama
| |
Collapse
|
72
|
Trevoy SAL, Janes JK, Muirhead K, Sperling FAH. Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle ( Dendroctonus ponderosae). Ecol Evol 2019; 9:1147-1159. [PMID: 30805148 PMCID: PMC6374669 DOI: 10.1002/ece3.4803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022] Open
Abstract
Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome-wide single-nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted resampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principal components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex-linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species' genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research.
Collapse
Affiliation(s)
| | - Jasmine K. Janes
- School of Environmental & Rural SciencesUniversity of New EnglandArmidaleNew South WalesAustralia
- Biology DepartmentVancouver Island UniversityNanaimoBritish ColumbiaCanada
| | - Kevin Muirhead
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | |
Collapse
|
73
|
Xuereb A, D’Aloia CC, Daigle RM, Andrello M, Dalongeville A, Manel S, Mouillot D, Guichard F, Côté IM, Curtis JMR, Bernatchez L, Fortin MJ. Marine Conservation and Marine Protected Areas. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2018_63] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
74
|
Stronen AV, Iacolina L, Ruiz-Gonzalez A. Rewilding and conservation genomics: How developments in (re)colonization ecology and genomics can offer mutual benefits for understanding contemporary evolution. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2018.e00502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
75
|
Population Genomics Applied to Fishery Management and Conservation. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2019_66] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
76
|
Clucas GV, Younger JL, Kao D, Emmerson L, Southwell C, Wienecke B, Rogers AD, Bost CA, Miller GD, Polito MJ, Lelliott P, Handley J, Crofts S, Phillips RA, Dunn MJ, Miller KJ, Hart T. Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins. Mol Ecol 2018; 27:4680-4697. [PMID: 30308702 DOI: 10.1111/mec.14896] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 01/02/2023]
Abstract
The mechanisms that determine patterns of species dispersal are important factors in the production and maintenance of biodiversity. Understanding these mechanisms helps to forecast the responses of species to environmental change. Here, we used a comparative framework and genomewide data obtained through RAD-Seq to compare the patterns of connectivity among breeding colonies for five penguin species with shared ancestry, overlapping distributions and differing ecological niches, allowing an examination of the intrinsic and extrinsic barriers governing dispersal patterns. Our findings show that at-sea range and oceanography underlie patterns of dispersal in these penguins. The pelagic niche of emperor (Aptenodytes forsteri), king (A. patagonicus), Adélie (Pygoscelis adeliae) and chinstrap (P. antarctica) penguins facilitates gene flow over thousands of kilometres. In contrast, the coastal niche of gentoo penguins (P. papua) limits dispersal, resulting in population divergences. Oceanographic fronts also act as dispersal barriers to some extent. We recommend that forecasts of extinction risk incorporate dispersal and that management units are defined by at-sea range and oceanography in species lacking genetic data.
Collapse
Affiliation(s)
- Gemma V Clucas
- Department of Zoology, University of Oxford, Oxford, UK.,Ocean & Earth Sciences, University of Southampton, Southampton, UK.,Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire
| | - Jane L Younger
- Department of Zoology, University of Oxford, Oxford, UK.,Department of Biology, Loyola University Chicago, Chicago, Illinois
| | - Damian Kao
- Department of Zoology, University of Oxford, Oxford, UK
| | - Louise Emmerson
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Colin Southwell
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | | | - Alex D Rogers
- Department of Zoology, University of Oxford, Oxford, UK
| | - Charles-André Bost
- Centre d'Études Biologiques de Chizé, UMR -CNRS 7372, Villiers-en-Bois, France
| | - Gary D Miller
- Division of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Michael J Polito
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Patrick Lelliott
- Australian School of Advanced Medicine, Macquarie University, Sydney, New South Wales, Australia
| | - Jonathan Handley
- DST/NRF Centre of Excellence, Percy FitzPatrick Institute of African Ornithology, Department of Zoology, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa.,Marine Apex Predator Research Unit, Institute for Coastal and Marine Research, Port Elizabeth, South Africa
| | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands
| | - Richard A Phillips
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - Michael J Dunn
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - Karen J Miller
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, The University of Western Australia (M096), Crawley, Western Australia, Australia
| | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, UK
| |
Collapse
|
77
|
Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls ( Larus bulleri). Genes (Basel) 2018; 9:genes9110544. [PMID: 30424003 PMCID: PMC6266082 DOI: 10.3390/genes9110544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022] Open
Abstract
Black-billed gulls (Larus bulleri) are endemic to New Zealand and are suspected to be undergoing substantial population declines. They primarily breed on open gravel beds in braided rivers of the South Island—a habitat that is diminishing and becoming increasingly modified. Although management of this species is increasing, little has been published on their movements and demographics. In this study, both mitochondrial DNA (mtDNA) control region domain I and nuclear single nucleotide polymorphisms (SNPs) were examined to help understand the connectivity and population structure of black-billed gulls across the country and to help inform management decisions. Mitochondrial DNA showed no population structure, with high haplotype and low nucleotide diversity, and analyses highlighted mitochondrial introgression with the closely related red-billed gulls (Larus novaehollandiae scopulinus). Nuclear DNA analyses, however, identified two groups, with Rotorua birds in the North Island being distinct from the rest of New Zealand, and isolation-by-distance evident across the South Island populations. Gene flow primarily occurs between nearby colonies with a stepwise movement across the landscape. The importance from a genetic perspective of the more isolated North Island birds (1.6% of total population) needs to be further evaluated. From our results, we infer that the South Island black-billed gull management should focus on maintaining several populations within each region rather than focusing on single specific colonies or river catchments. Future study is needed to investigate the genetic structure of populations at the northern limit of the species’ range, and identify the mechanisms behind, and extent of, the hybridisation between red-billed and black-billed gulls.
Collapse
|
78
|
Abstract
Conservation genetics is a branch of conservation biology that uses molecular data to assist in the conservation and management of imperiled populations, subspecies, and species. In this review, I examine conservation action plans (CAPs)—instrumental documents designed to influence conservation policy—for selected primate species. I use the information contained in CAPs as a means to guide this review. The primary genetics-based topics that are mentioned in CAPs are genetic connectivity, inbreeding, and subspecies/species delimitation. I discuss these topics as well as historical demographic inference and hybridization using examples from wild primate species to illustrate the myriad ways in which genetics can assist in conservation efforts. I also discuss some recent technological advances such as genomic capture techniques and the potential to do molecular work in remote locations.
Collapse
Affiliation(s)
- Richard R. Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia 22807, USA
| |
Collapse
|
79
|
Abstract
"Conservation genomics" encompasses the idea that genome-scale data will improve the capacity of resource managers to protect species. Although genetic approaches have long been used in conservation research, it has only recently become tractable to generate genome-wide data at a scale that is useful for conservation. In this Review, we discuss how genome-scale data can inform species delineation in the face of admixture, facilitate evolution through the identification of adaptive alleles, and enhance evolutionary rescue based on genomic patterns of inbreeding. As genomic approaches become more widely adopted in conservation, we expect that they will have a positive impact on management and policy decisions.
Collapse
Affiliation(s)
- Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
| |
Collapse
|
80
|
Hendricks S, Anderson EC, Antao T, Bernatchez L, Forester BR, Garner B, Hand BK, Hohenlohe PA, Kardos M, Koop B, Sethuraman A, Waples RS, Luikart G. Recent advances in conservation and population genomics data analysis. Evol Appl 2018. [PMCID: PMC6099823 DOI: 10.1111/eva.12659] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.
Collapse
Affiliation(s)
- Sarah Hendricks
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Eric C. Anderson
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Santa Cruz California
- University of California Santa Cruz California
| | - Tiago Antao
- Division of Biological Sciences University of Montana Missoula Montana
| | - Louis Bernatchez
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | | | - Brittany Garner
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
- Wildlife Program Fish and Wildlife Genomics Group College of Forestry and Conservation University of Montana Missoula Montana
| | - Brian K. Hand
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Martin Kardos
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
| | - Ben Koop
- Department of Biology Centre for Biomedical Research University of Victoria Victoria British Columbia Canada
| | - Arun Sethuraman
- Department of Biological Sciences California State University San Marcos San Marcos California
| | - Robin S. Waples
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington
| | - Gordon Luikart
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
- Wildlife Program Fish and Wildlife Genomics Group College of Forestry and Conservation University of Montana Missoula Montana
| |
Collapse
|
81
|
Leroy G, Carroll EL, Bruford MW, DeWoody JA, Strand A, Waits L, Wang J. Next-generation metrics for monitoring genetic erosion within populations of conservation concern. Evol Appl 2018; 11:1066-1083. [PMID: 30026798 PMCID: PMC6050182 DOI: 10.1111/eva.12564] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/11/2017] [Indexed: 12/26/2022] Open
Abstract
Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large-effect detrimental alleles, maladaptation and loss of adaptability). Technological advances in genomics now allow the production of data the can be measured by new metrics with improved precision, increased efficiency and the potential to discriminate between neutral diversity (shaped mainly by population size and gene flow) and functional/adaptive diversity (shaped mainly by selection), allowing the assessment of management-relevant genetic markers. The requirements of such studies in terms of sample size and marker density largely depend on the kind of population monitored, the questions to be answered and the metrics employed. We discuss prospects for the integration of this new information and metrics into conservation monitoring programmes.
Collapse
Affiliation(s)
- Gregoire Leroy
- Food and Agriculture Organization (FAO) of the United Nations, Animal Production and Health DivisionRomeItaly
| | - Emma L. Carroll
- Scottish Oceans Institute and School of BiologyUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places InstituteCardiff UniversityCardiffUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
- Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Allan Strand
- Department of BiologyGrice Marine Laboratory, College of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
| |
Collapse
|
82
|
Flanagan SP, Forester BR, Latch EK, Aitken SN, Hoban S. Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation. Evol Appl 2018; 11:1035-1052. [PMID: 30026796 PMCID: PMC6050180 DOI: 10.1111/eva.12569] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/20/2017] [Indexed: 12/14/2022] Open
Abstract
Identifying and monitoring locally adaptive genetic variation can have direct utility for conserving species at risk, especially when management may include actions such as translocations for restoration, genetic rescue, or assisted gene flow. However, genomic studies of local adaptation require careful planning to be successful, and in some cases may not be a worthwhile use of resources. Here, we offer an adaptive management framework to help conservation biologists and managers decide when genomics is likely to be effective in detecting local adaptation, and how to plan assessment and monitoring of adaptive variation to address conservation objectives. Studies of adaptive variation using genomic tools will inform conservation actions in many cases, including applications such as assisted gene flow and identifying conservation units. In others, assessing genetic diversity, inbreeding, and demographics using selectively neutral genetic markers may be most useful. And in some cases, local adaptation may be assessed more efficiently using alternative approaches such as common garden experiments. Here, we identify key considerations of genomics studies of locally adaptive variation, provide a road map for successful collaborations with genomics experts including key issues for study design and data analysis, and offer guidelines for interpreting and using results from genomic assessments to inform monitoring programs and conservation actions.
Collapse
Affiliation(s)
- Sarah P. Flanagan
- National Institute for Mathematical and Biological SynthesisUniversity of TennesseeKnoxvilleTNUSA
| | - Brenna R. Forester
- Duke University, Nicholas School of the EnvironmentDurhamNCUSA
- Present address:
Department of BiologyColorado State UniversityFort CollinsCOUSA
| | - Emily K. Latch
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWIUSA
| | - Sally N. Aitken
- Faculty of ForestryUniversity of British ColumbiaVancouverBCCanada
| | | |
Collapse
|
83
|
Affiliation(s)
- Alex D Twyford
- University of Edinburgh, Institute of Evolutionary Biology, Edinburgh, UK.
| |
Collapse
|
84
|
Yoder AD, Poelstra JW, Tiley GP, Williams RC. Neutral Theory Is the Foundation of Conservation Genetics. Mol Biol Evol 2018; 35:1322-1326. [DOI: 10.1093/molbev/msy076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Anne D Yoder
- Department of Biology, Duke University, Durham, NC
| | | | | | | |
Collapse
|
85
|
Hashemzadeh Segherloo I, Normandeau E, Benestan L, Rougeux C, Coté G, Moore JS, Ghaedrahmati N, Abdoli A, Bernatchez L. Genetic and morphological support for possible sympatric origin of fish from subterranean habitats. Sci Rep 2018; 8:2909. [PMID: 29440653 PMCID: PMC5811452 DOI: 10.1038/s41598-018-20666-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 01/16/2018] [Indexed: 11/09/2022] Open
Abstract
Two blind Iran cave barbs, Garra typhlops and Garra lorestanensis, exist in sympatry in a single subterranean habitat, raising the hypothesis that they may represent a case of sympatric speciation following a colonization event. Their different mental disc forms have prompted some authors to propose the alternative hypothesis of two separate colonization events. In this study, we analysed a genome-wide panel of 11,257 SNPs genotyped by means of genotyping-by-sequencing combined with mitochondrial cytochrome c oxidase sub-unit I sequence data, field observations and morphological traits to test these two hypotheses. Field data suggest some degree of ecological divergence despite some possible niche overlap such that hybridization is possible. According to both nuclear and mtDNA data, the cave barb species are monophyletic with close phylogenetic relationships with Garra gymnothorax from the Karun-Dez and Karkheh river basins. The historical demography analysis revealed that a model of Isolation-with-Migration (IM) best fitted the data, therefore better supporting a scenario of sympatric origin than that of allopatric isolation followed by secondary contact. Overall, our results offer stronger support to the hypothesis that speciation in the subterranean habitat could have occurred in sympatry following a colonization event from the Karun-Dez-Karkheh basins in the Zagros Mountains of Iran.
Collapse
Affiliation(s)
- Iraj Hashemzadeh Segherloo
- Department of Fisheries and Environmental Sciences, Faculty of Natural Resources and Earth Sciences, Shahr-e-Kord University, Shahr-e-Kord, P. B. 115, Iran.
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Laura Benestan
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Clément Rougeux
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Guillaume Coté
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Jean-Sébastien Moore
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| | | | - Asghar Abdoli
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research center, Shahid Beheshti University, Tehran, Iran
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine Université Laval, Québec, Québec, G1V 0A6, Canada
| |
Collapse
|
86
|
Schell CJ. Urban Evolutionary Ecology and the Potential Benefits of Implementing Genomics. J Hered 2018; 109:138-151. [DOI: 10.1093/jhered/esy001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/06/2018] [Indexed: 01/01/2023] Open
|
87
|
Hohenlohe PA, Hand BK, Andrews KR, Luikart G. Population Genomics Provides Key Insights in Ecology and Evolution. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_20] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
88
|
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]
|
89
|
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: 38] [Impact Index Per Article: 5.4] [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.
Collapse
|
90
|
Aavik T, Helm A. Restoration of plant species and genetic diversity depends on landscape-scale dispersal. Restor Ecol 2017. [DOI: 10.1111/rec.12634] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tsipe Aavik
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
| |
Collapse
|
91
|
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: 152] [Impact Index Per Article: 21.7] [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.
Collapse
|
92
|
Younger JL, Clucas GV, Kao D, Rogers AD, Gharbi K, Hart T, Miller KJ. The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins. Mol Ecol 2017; 26:3883-3897. [PMID: 28488293 DOI: 10.1111/mec.14172] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/09/2017] [Accepted: 04/24/2017] [Indexed: 12/22/2022]
Abstract
Understanding the boundaries of breeding populations is of great importance for conservation efforts and estimates of extinction risk for threatened species. However, determining these boundaries can be difficult when population structure is subtle. Emperor penguins are highly reliant on sea ice, and some populations may be in jeopardy as climate change alters sea-ice extent and quality. An understanding of emperor penguin population structure is therefore urgently needed. Two previous studies have differed in their conclusions, particularly whether the Ross Sea, a major stronghold for the species, is isolated or not. We assessed emperor penguin population structure using 4,596 genome-wide single nucleotide polymorphisms (SNPs), characterized in 110 individuals (10-16 per colony) from eight colonies around Antarctica. In contrast to a previous conclusion that emperor penguins are panmictic around the entire continent, we find that emperor penguins comprise at least four metapopulations, and that the Ross Sea is clearly a distinct metapopulation. Using larger sample sizes and a thorough assessment of the limitations of different analytical methods, we have shown that population structure within emperor penguins does exist and argue that its recognition is vital for the effective conservation of the species. We discuss the many difficulties that molecular ecologists and managers face in the detection and interpretation of subtle population structure using large SNP data sets, and argue that subtle structure should be taken into account when determining management strategies for threatened species, until accurate estimates of demographic connectivity among populations can be made.
Collapse
Affiliation(s)
- Jane L Younger
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Gemma V Clucas
- Department of Zoology, University of Oxford, Oxford, UK
- Ocean & Earth Sciences, University of Southampton Waterfront Campus, Southampton, UK
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Damian Kao
- Department of Zoology, University of Oxford, Oxford, UK
| | - Alex D Rogers
- Department of Zoology, University of Oxford, Oxford, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, UK
| | - Karen J Miller
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, The University of Western Australia (MO96), Crawley, WA, Australia
| |
Collapse
|
93
|
Benestan L, Moore JS, Sutherland BJG, Le Luyer J, Maaroufi H, Rougeux C, Normandeau E, Rycroft N, Atema J, Harris LN, Tallman RF, Greenwood SJ, Clark FK, Bernatchez L. Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems. Mol Ecol 2017; 26:6767-6783. [DOI: 10.1111/mec.14217] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/23/2017] [Accepted: 03/29/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Laura Benestan
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jean-Sébastien Moore
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Ben J. G. Sutherland
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jérémy Le Luyer
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Clément Rougeux
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Eric Normandeau
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | | | - Jelle Atema
- Department of Biology; Boston University; Boston MA USA
| | - Les N. Harris
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Ross F. Tallman
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Spencer J. Greenwood
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Fraser K. Clark
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Louis Bernatchez
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| |
Collapse
|
94
|
Villanueva‐Cañas JL, Rech GE, Cara MAR, González J. Beyond
SNP
s: how to detect selection on transposable element insertions. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12781] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Gabriel E. Rech
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Maria Angeles Rodriguez Cara
- Ecoanthropology and Ethnobiology Laboratory, UMR 7206, CNRS/MNHN/Universite Paris 7 Museum National d'HistoireNaturelle F‐75116 Paris France
| | - Josefa González
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| |
Collapse
|
95
|
Pearse DE. Saving the spandrels? Adaptive genomic variation in conservation and fisheries management. JOURNAL OF FISH BIOLOGY 2016; 89:2697-2716. [PMID: 27723095 DOI: 10.1111/jfb.13168] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of the genome under selection and extend knowledge of the genetic basis of adaptive evolution. What is far less clear, but has been the focus of active discussion, is how such information can or should transfer into conservation practice to complement more typical conservation applications of genetic data. Before such applications can be realized, the evolutionary importance of specific targets of selection relative to the genome-wide diversity of the species as a whole must be evaluated. The key issues for the incorporation of adaptive genomic variation in conservation and management are discussed here, using published examples of adaptive genomic variation associated with specific phenotypes in salmonids and other taxa to highlight practical considerations for incorporating such information into conservation programmes. Scenarios are described in which adaptive genomic data could be used in conservation or restoration, constraints on its utility and the importance of validating inferences drawn from new genomic data before applying them in conservation practice. Finally, it is argued that an excessive focus on preserving the adaptive variation that can be measured, while ignoring the vast unknown majority that cannot, is a modern twist on the adaptationist programme that Gould and Lewontin critiqued almost 40 years ago.
Collapse
Affiliation(s)
- D E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Road, Santa Cruz, CA, 95060, U.S.A
| |
Collapse
|
96
|
Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
Collapse
Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| |
Collapse
|
97
|
Clucas GV, Younger JL, Kao D, Rogers AD, Handley J, Miller GD, Jouventin P, Nolan P, Gharbi K, Miller KJ, Hart T. Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range. BMC Evol Biol 2016; 16:211. [PMID: 27733109 PMCID: PMC5062852 DOI: 10.1186/s12862-016-0784-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/30/2016] [Indexed: 02/01/2023] Open
Abstract
Background Seabirds are important components of marine ecosystems, both as predators and as indicators of ecological change, being conspicuous and sensitive to changes in prey abundance. To determine whether fluctuations in population sizes are localised or indicative of large-scale ecosystem change, we must first understand population structure and dispersal. King penguins are long-lived seabirds that occupy a niche across the sub-Antarctic zone close to the Polar Front. Colonies have very different histories of exploitation, population recovery, and expansion. Results We investigated the genetic population structure and patterns of colonisation of king penguins across their current range using a dataset of 5154 unlinked, high-coverage single nucleotide polymorphisms generated via restriction site associated DNA sequencing (RADSeq). Despite breeding at a small number of discrete, geographically separate sites, we find only very slight genetic differentiation among colonies separated by thousands of kilometers of open-ocean, suggesting migration among islands and archipelagos may be common. Our results show that the South Georgia population is slightly differentiated from all other colonies and suggest that the recently founded Falkland Island colony is likely to have been established by migrants from the distant Crozet Islands rather than nearby colonies on South Georgia, possibly as a result of density-dependent processes. Conclusions The observed subtle differentiation among king penguin colonies must be considered in future conservation planning and monitoring of the species, and demographic models that attempt to forecast extinction risk in response to large-scale climate change must take into account migration. It is possible that migration could buffer king penguins against some of the impacts of climate change where colonies appear panmictic, although it is unlikely to protect them completely given the widespread physical changes projected for their Southern Ocean foraging grounds. Overall, large-scale population genetic studies of marine predators across the Southern Ocean are revealing more interconnection and migration than previously supposed. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0784-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gemma V Clucas
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. .,Ocean & Earth Sciences, University of Southampton Waterfront Campus, European Way, Southampton, SO14 3ZH, UK.
| | - Jane L Younger
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. .,Department of Biology, Loyola University Chicago, 1032 W. Sheridan Road, Chicago, IL, 60660, USA.
| | - Damian Kao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Alex D Rogers
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Jonathan Handley
- DST/NRF Centre of Excellence, Percy Fitzpatrick Institute of African Ornithology, Department of Zoology, Nelson Mandela Metropolitan University, South Campus, Port Elizabeth, 6031, South Africa
| | - Gary D Miller
- Microbiology and Immunology, PALM, University of Western Australia, Crawley, WA, 6009, Australia
| | - Pierre Jouventin
- Centre National de la Recherche Scientifique, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 du CNRS, 1919 route de Mende, F-34293, Montpellier Cedex 5, France
| | - Paul Nolan
- Department of Biology, The Citadel, 171 Moultrie St, Charleston, SC, 29409, USA
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Karen J Miller
- Australian Institute of Marine Science, The UWA Oceans Institute, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Tom Hart
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| |
Collapse
|
98
|
Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, McGowen MR, Olsen MT, Van Cise AM. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. J Hered 2016; 107:481-95. [PMID: 27511190 DOI: 10.1093/jhered/esw044] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022] Open
Abstract
The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.
Collapse
Affiliation(s)
- Kristina M Cammen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise).
| | - Kimberly R Andrews
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emma L Carroll
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Andrew D Foote
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emily Humble
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Jane I Khudyakov
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Marie Louis
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Michael R McGowen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Morten Tange Olsen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Amy M Van Cise
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| |
Collapse
|
99
|
Kamvar ZN, López-Uribe MM, Coughlan S, Grünwald NJ, Lapp H, Manel S. Developing educational resources for population genetics in R: an open and collaborative approach. Mol Ecol Resour 2016; 17:120-128. [PMID: 27297607 DOI: 10.1111/1755-0998.12558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
The r computing and statistical language community has developed a myriad of resources for conducting population genetic analyses. However, resources for learning how to carry out population genetic analyses in r are scattered and often incomplete, which can make acquiring this skill unnecessarily difficult and time consuming. To address this gap, we developed an online community resource with guidance and working demonstrations for conducting population genetic analyses in r. The resource is freely available at http://popgen.nescent.org and includes material for both novices and advanced users of r for population genetics. To facilitate continued maintenance and growth of this resource, we developed a toolchain, process and conventions designed to (i) minimize financial and labour costs of upkeep; (ii) to provide a low barrier to contribution; and (iii) to ensure strong quality assurance. The toolchain includes automatic integration testing of every change and rebuilding of the website when new vignettes or edits are accepted. The process and conventions largely follow a common, distributed version control-based contribution workflow, which is used to provide and manage open peer review by designated website editors. The online resources include detailed documentation of this process, including video tutorials. We invite the community of population geneticists working in r to contribute to this resource, whether for a new use case of their own, or as one of the vignettes from the 'wish list' we maintain, or by improving existing vignettes.
Collapse
Affiliation(s)
- Zhian N Kamvar
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Margarita M López-Uribe
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Simone Coughlan
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Niklaus J Grünwald
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.,Horticultural Crops Research Unit, USDA Agricultural Research Service, Corvallis, OR, 97330, USA
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Stéphanie Manel
- EPHE, PSL Research University, CNRS, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, F-34293, Montpellier, France
| |
Collapse
|