101
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De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii. G3-GENES GENOMES GENETICS 2020; 10:2585-2592. [PMID: 32586847 PMCID: PMC7407468 DOI: 10.1534/g3.120.401437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 - 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species.
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102
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Cooper L, Bunnefeld L, Hearn J, Cook JM, Lohse K, Stone GN. Low-coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp. Mol Ecol 2020; 29:3649-3666. [PMID: 32567765 DOI: 10.1111/mec.15523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022]
Abstract
Population divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide data sets allows discrimination between alternative scenarios for these processes even in nonmodel taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum [bSFS], the second on the pairwise sequentially Markovian coalescent [PSMC]) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia and are separated into The Northern population is to the north of the Southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of postdivergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196 kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57 kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, nonmodel organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.
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Affiliation(s)
- Lisa Cooper
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Lynsey Bunnefeld
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Jack Hearn
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | - James M Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Graham N Stone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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103
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Bohling J. Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets. Ecol Evol 2020; 10:7585-7601. [PMID: 32760550 PMCID: PMC7391306 DOI: 10.1002/ece3.6483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/29/2022] Open
Abstract
The advent of high-throughput sequencing (HTS) has made genomic-level analyses feasible for nonmodel organisms. A critical step of many HTS pipelines involves aligning reads to a reference genome to identify variants. Despite recent initiatives, only a fraction of species has publically available reference genomes. Therefore, a common practice is to align reads to the genome of an organism related to the target species; however, this could affect read alignment and bias genotyping. In this study, I conducted an experiment using empirical RADseq datasets generated for two species of salmonids (Actinopterygii; Teleostei; Salmonidae) to address these questions. There are currently reference genomes for six salmonids of varying phylogenetic distance. I aligned the RADseq data to all six genomes and identified variants with several different genotypers, which were then fed into population genetic analyses. Increasing phylogenetic distance between target species and reference genome reduced the proportion of reads that successfully aligned and mapping quality. Reference genome also influenced the number of SNPs that were generated and depth at those SNPs, although the affect varied by genotyper. Inferences of population structure were mixed: increasing reference genome divergence reduced estimates of differentiation but similar patterns of population relationships were found across scenarios. These findings reveal how the choice of reference genome can influence the output of bioinformatic pipelines. It also emphasizes the need to identify best practices and guidelines for the burgeoning field of biodiversity genomics.
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Affiliation(s)
- Justin Bohling
- Abernathy Fish Technology Center US Fish and Wildlife Service Longview WA USA
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104
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Sun Y, Deng T, Zhang A, Moore MJ, Landis JB, Lin N, Zhang H, Zhang X, Huang J, Zhang X, Sun H, Wang H. Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization. iScience 2020; 23:101124. [PMID: 32428861 PMCID: PMC7232092 DOI: 10.1016/j.isci.2020.101124] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/20/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.
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Affiliation(s)
- Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Aidi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | | | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA; School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Xiujun Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.
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105
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The long-term restoration of ecosystem complexity. Nat Ecol Evol 2020; 4:676-685. [DOI: 10.1038/s41559-020-1154-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022]
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106
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Van Poelvoorde LA, Saelens X, Thomas I, Roosens NH. Next-Generation Sequencing: An Eye-Opener for the Surveillance of Antiviral Resistance in Influenza. Trends Biotechnol 2020; 38:360-367. [DOI: 10.1016/j.tibtech.2019.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022]
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107
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Feron R, Zahm M, Cabau C, Klopp C, Roques C, Bouchez O, Eché C, Valière S, Donnadieu C, Haffray P, Bestin A, Morvezen R, Acloque H, Euclide PT, Wen M, Jouano E, Schartl M, Postlethwait JH, Schraidt C, Christie MR, Larson WA, Herpin A, Guiguen Y. Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens. Mol Ecol Resour 2020; 20:531-543. [PMID: 31903688 PMCID: PMC7050324 DOI: 10.1111/1755-0998.13133] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]
Abstract
Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long-reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome-scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males (amhr2by+ ) from XX genetic females (amhr2by- ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex-determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.
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Affiliation(s)
- Romain Feron
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Margot Zahm
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
| | - Cédric Cabau
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Céline Roques
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Camille Eché
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Pierrick Haffray
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | - Anastasia Bestin
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | - Romain Morvezen
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | - Hervé Acloque
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Castanet-Tolosan, France
| | - Peter T. Euclide
- Wisconsin Cooperative Fishery Research Unit, University of Wisconsin-Stevens Point, 800 Reserve St., Stevens Point, WI 54481, USA
| | - Ming Wen
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Elodie Jouano
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
| | - Manfred Schartl
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany and The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | - Claire Schraidt
- Department of Forestry and Natural Resources, Purdue University; 715 W. State St., West Lafayette, Indiana 47907-2054 USA
| | - Mark R. Christie
- Department of Forestry and Natural Resources, Purdue University; 715 W. State St., West Lafayette, Indiana 47907-2054 USA
- Department of Biological Sciences, Purdue University; 915 W. State St., West Lafayette, Indiana 47907-2054 USA
| | - Wesley A. Larson
- U.S. Geological Survey Wisconsin Cooperative Fishery Research Unit, University of Wisconsin-Stevens Point, 800 Reserve St., Stevens Point, WI 54481, USA
| | - Amaury Herpin
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
| | - Yann Guiguen
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
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108
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Patton AH, Margres MJ, Stahlke AR, Hendricks S, Lewallen K, Hamede RK, Ruiz-Aravena M, Ryder O, McCallum HI, Jones ME, Hohenlohe PA, Storfer A. Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils. Mol Biol Evol 2020; 36:2906-2921. [PMID: 31424552 PMCID: PMC6878949 DOI: 10.1093/molbev/msz191] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Reconstructing species’ demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods leveraging either the sequentially Markovian coalescent (SMC) or the site-frequency spectrum has been developed to reconstruct population size histories from genomic sequence data. However, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we first present an improved genome assembly for the Tasmanian devil using the Chicago library method. Compared with the original reference genome, our new assembly reduces the number of scaffolds (from 35,975 to 10,010) and increases the scaffold N90 (from 0.101 to 2.164 Mb). Second, we assess the performance of four contemporary genomic methods for inferring population size history (PSMC, MSMC, SMC++, Stairway Plot), using the two devil genome assemblies as well as simulated, artificially fragmented genomes that approximate the hypothesized demographic history of Tasmanian devils. We demonstrate that each method is robust to assembly quality, producing similar estimates of Ne when simulated genomes were fragmented into up to 5,000 scaffolds. Overall, methods reliant on the SMC are most reliable between ∼300 generations before present (gbp) and 100 kgbp, whereas methods exclusively reliant on the site-frequency spectrum are most reliable between the present and 30 gbp. Our results suggest that when used in concert, genomic methods for reconstructing species’ effective population size histories 1) can be applied to nonmodel organisms without highly contiguous reference genomes, and 2) are capable of detecting independently documented effects of historical geological events.
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Affiliation(s)
- Austin H Patton
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, WA.,Department of Organismic and Evolutionary Biology, Harvard University, MA
| | - Amanda R Stahlke
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Sarah Hendricks
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Kevin Lewallen
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Rodrigo K Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | | | - Oliver Ryder
- Institute for Conservation Research, San Diego, CA
| | | | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA
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109
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Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol 2020; 17:95-109. [PMID: 30442909 DOI: 10.1038/s41579-018-0116-y] [Citation(s) in RCA: 393] [Impact Index Per Article: 98.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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Affiliation(s)
- R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Sten Anslan
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, Tartu, Estonia
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110
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Low genetic differentiation despite high fragmentation in the endemic serpentinophyte Minuartia smejkalii (M. verna agg., Caryophyllaceae) revealed by RADSeq SNP markers. CONSERV GENET 2020. [DOI: 10.1007/s10592-019-01239-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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111
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Fu Z, Li Y, Elling AA, Snyder WE. A draft genome of a field-collected Steinernema feltiae strain NW. J Nematol 2020; 52:1-7. [PMID: 32180379 PMCID: PMC7265891 DOI: 10.21307/jofnem-2020-003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 11/26/2022] Open
Abstract
Advances in sequencing technologies have accelerated our understanding of the complex genetic network of organisms and genomic divergences that are linked to evolutionary processes. While many model organisms and laboratory strains have been sequenced, wild populations are underrepresented in the growing list of sequenced genomes. Here, we present a de novo assembly of Steinernema feltiae, strain NW, collected from a working agricultural field in south central Washington, USA. Leveraging Pacific Biosciences (PacBio) long reads, we sequenced strain NW to a high depth (99×). The resulting de novo assembly is significantly larger than the previous assembly generated from the laboratory strain SN, with a noticeable improvement in continuity and completeness. Comparative analysis of two assemblies revealed numerous single nucleotide polymorphisms (SNPs), breakpoints, and indels present between the two genomes. This alternative genome resource and annotation could benefit the research community to examine the genetic foundation of evolutionary processes as well as genomic variation among conspecific populations.
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Affiliation(s)
- Zhen Fu
- Department of Entomology, Washington State University , Pullman, WA ; Current: Department of Entomology, Texas A&M University , College Station, TX
| | - Yuxiang Li
- Department of Plant Pathology, Washington State University , Pullman, WA
| | - Axel A Elling
- Department of Plant Pathology, Washington State University , Pullman, WA ; Current: Bayer Crop Science, Cary, NC
| | - William E Snyder
- Department of Entomology, Washington State University , Pullman, WA ; Current: Department of Entomology, University of Georgia , Athens, GA
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112
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Tan MP, Wong LL, Razali SA, Afiqah-Aleng N, Mohd Nor SA, Sung YY, Van de Peer Y, Sorgeloos P, Danish-Daniel M. Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review. Evol Bioinform Online 2019; 15:1176934319892284. [PMID: 31839703 PMCID: PMC6896124 DOI: 10.1177/1176934319892284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts.
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Affiliation(s)
- Min Pau Tan
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Li Lian Wong
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Siti Aisyah Razali
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Nor Afiqah-Aleng
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Yeong Yik Sung
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Yves Van de Peer
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Patrick Sorgeloos
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Laboratory of Aquaculture & Artemia Reference Center, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Muhd Danish-Daniel
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
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113
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Wang X, Maher KH, Zhang N, Que P, Zheng C, Liu S, Wang B, Huang Q, Chen D, Yang X, Zhang Z, Székely T, Urrutia AO, Liu Y. Demographic Histories and Genome-Wide Patterns of Divergence in Incipient Species of Shorebirds. Front Genet 2019; 10:919. [PMID: 31781152 PMCID: PMC6857203 DOI: 10.3389/fgene.2019.00919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
Understanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the white-faced (C. dealbatus) plovers, which differ in their phenotype, ecology and behavior, are two incipient species and parapatrically distributed in East Asia. Previous studies show evidence of genetic diversification with gene flow between the two plovers. Under this scenario, it is of great importance to explore the patterns of divergence at the genomic level and to determine whether specific regions are involved in reproductive isolation and local adaptation. Here we present the first population genomic analysis of the two incipient species based on the de novo Kentish plover reference genome and resequenced populations. We show that the two plover lineages are distinct in both nuclear and mitochondrial genomes. Using model-based coalescence analysis, we found that population sizes of Kentish plover increased whereas white-faced plovers declined during the Last Glaciation Period. Moreover, the two plovers diverged allopatrically, with gene flow occurring after secondary contact. This has resulted in low levels of genome-wide differentiation, although we found evidence of a few highly differentiated genomic regions in both the autosomes and the Z-chromosome. This study illustrates that incipient shorebird species with gene flow after secondary contact can exhibit discrete divergence at specific genomic regions and provides basis to further exploration on the genetic basis of relevant phenotypic traits.
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Affiliation(s)
- Xuejing Wang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kathryn H Maher
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Nan Zhang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Chenqing Zheng
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Bioinformatics, Shenzhen Realomics Biological Technology Ltd, Shenzhen, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Biao Wang
- School of Biosciences, University of Melbourne, Parkville, VIC, Australia
| | - Qin Huang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - De Chen
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xu Yang
- Department of Bioinformatics, Shenzhen Realomics Biological Technology Ltd, Shenzhen, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tamás Székely
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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114
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Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F. An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity. Mol Ecol Resour 2019; 19:1497-1515. [PMID: 31359622 PMCID: PMC7115901 DOI: 10.1111/1755-0998.13070] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 06/30/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.
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Affiliation(s)
- Badr Benjelloun
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Frédéric Boyer
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Wahid Zamani
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, 46417-76489 Noor, Mazandaran, Iran
| | - Stefan Engelen
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Adriana Alberti
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Florian J. Alberto
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Mohamed BenBati
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Mustapha Ibnelbachyr
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Mouad Chentouf
- National Institute of Agronomic Research (INRA Maroc), CRRA Tangier, 90010 Tangier, Morocco
| | - Abdelmajid Bechchari
- National Institute of Agronomic Research (INRA Maroc), CRRA Oujda, 60000 Oujda, Morocco
| | - Hamid R. Rezaei
- Department of Environmental Sci, Gorgan University of Agricultural Sciences & Natural Resources, 41996-13776 Gorgan, Iran
| | - Saeid Naderi
- Environmental Sciences Department, Natural Resources Faculty, University of Guilan, 49138-15749 Guilan, Iran
| | - Alessandra Stella
- PTP Science Park, Bioinformatics Unit, Via Einstein-Loc. Cascina Codazza, 26900 Lodi, Italy
| | - Abdelkader Chikhi
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pierre Taberlet
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Pompanon
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
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115
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Brandies P, Peel E, Hogg CJ, Belov K. The Value of Reference Genomes in the Conservation of Threatened Species. Genes (Basel) 2019; 10:E846. [PMID: 31717707 PMCID: PMC6895880 DOI: 10.3390/genes10110846] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Conservation initiatives are now more crucial than ever-over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.
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Affiliation(s)
| | | | | | - Katherine Belov
- School of Life & Environmental Sciences, The University of Sydney, Sydney 2006, Australia; (P.B.); (E.P.); (C.J.H.)
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116
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Wildt D, Miller P, Koepfli KP, Pukazhenthi B, Palfrey K, Livingston G, Beetem D, Shurter S, Gregory J, Takács M, Snodgrass K. Breeding Centers, Private Ranches, and Genomics for Creating Sustainable Wildlife Populations. Bioscience 2019; 69:928-943. [PMID: 31719713 PMCID: PMC6829018 DOI: 10.1093/biosci/biz091] [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] [Indexed: 11/30/2022] Open
Abstract
Human-induced changes to environments are causing species declines. Beyond preserving habitat (in situ), insurance (ex situ) populations are essential to prevent species extinctions. The Conservation Centers for Species Survival (C2S2) is leveraging space of breeding centers and private ranches to produce “source populations”—genetically diverse reservoirs that also support research and reintroductions. The initial focus is on four African antelopes. C2S2 has developed a program, the Source Population Alliance, that emphasizes animals living in spacious, naturalistic conditions in greater numbers than can be accommodated by urban zoos. Simulation modeling demonstrates how herds can rapidly increase population abundance and retain genetic diversity. Advances in genomics and resulting DNA data allow monitoring of genetic diversity and parentage as well as refined decision-making. This approach, neither pure in situ nor ex situ, but rather “sorta situ”, is an innovative way of linking public and private sector resources to ensure that endangered species survive.
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Affiliation(s)
- David Wildt
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630
| | - Philip Miller
- Conservation Planning Specialist Group of the IUCN-World Conservation Union's Species Survival Commission, Apple Valley, MN 55124
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630
| | - Budhan Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630
| | - Katy Palfrey
- Population Alliance Manager, Conservation Centers for Species Survival, 201 W. 5th Street, 11th Floor, Austin, TX 78701
| | - Gavin Livingston
- Population Alliance Manager, Conservation Centers for Species Survival, 201 W. 5th Street, 11th Floor, Austin, TX 78701
| | - Dan Beetem
- Animal Management, The Wilds, 14000 International Road, Cumberland, OH 43732
| | - Stephen Shurter
- White Oak Conservation, 581705 White Oak Road, Yulee, FL 32097
| | - Jimmy Gregory
- Vice-President and Co-Owner, Austin Savanna, P.O. Box 17126 Austin, TX 78760
| | | | - Kelley Snodgrass
- Fossil Rim Wildlife Center, 2155 County Road 2008, Glen Rose, TX 76043
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117
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Kurland S, Wheat CW, de la Paz Celorio Mancera M, Kutschera VE, Hill J, Andersson A, Rubin C, Andersson L, Ryman N, Laikre L. Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species. Ecol Evol 2019; 9:11448-11463. [PMID: 31641485 PMCID: PMC6802065 DOI: 10.1002/ece3.5646] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F ST) between the two introduced populations exceeds that of the naturally sympatric populations (F ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ ( π ¯ ≈ 0.002 and π ¯ ≈ 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.
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Affiliation(s)
- Sara Kurland
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Christopher W. Wheat
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | | | - Verena E. Kutschera
- Science for Life Laboratory and Department for Biochemistry and BiophysicsStockholm UniversitySolnaSweden
| | - Jason Hill
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Anastasia Andersson
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Carl‐Johan Rubin
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTXUSA
| | - Nils Ryman
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Linda Laikre
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
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118
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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.
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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
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119
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Grummer JA, Beheregaray LB, Bernatchez L, Hand BK, Luikart G, Narum SR, Taylor EB. Aquatic Landscape Genomics and Environmental Effects on Genetic Variation. Trends Ecol Evol 2019; 34:641-654. [DOI: 10.1016/j.tree.2019.02.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 01/17/2023]
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120
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Parker C, Bernaola L, Lee BW, Elmquist D, Cohen A, Marshall A, Hepler J, Pekarcik A, Justus E, King K, Lee TY, Esquivel C, Hauri K, McCullough C, Hadden W, Ragozzino M, Roth M, Villegas J, Kraus E, Becker M, Mulcahy M, Chen R, Mittapelly P, Clem CS, Skinner R, Josek T, Pearlstein D, Tetlie J, Tran A, Auletta A, Benkert E, Tussey D. Entomology in the 21st Century: Tackling Insect Invasions, Promoting Advancements in Technology, and Using Effective Science Communication-2018 Student Debates. JOURNAL OF INSECT SCIENCE (ONLINE) 2019; 19:4. [PMID: 31268545 PMCID: PMC6608551 DOI: 10.1093/jisesa/iez069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Indexed: 06/09/2023]
Abstract
The 2018 student debates of the Entomological Society of America were held at the Joint Annual Meeting for the Entomological Societies of America, Canada, and British Columbia in Vancouver, BC. Three unbiased introductory speakers and six debate teams discussed and debated topics under the theme 'Entomology in the 21st Century: Tackling Insect Invasions, Promoting Advancements in Technology, and Using Effective Science Communication'. This year's debate topics included: 1) What is the most harmful invasive insect species in the world? 2) How can scientists diffuse the stigma or scare factor surrounding issues that become controversial such as genetically modified organisms, agricultural biotechnological developments, or pesticide chemicals? 3) What new/emerging technologies have the potential to revolutionize entomology (other than Clustered Regularly Interspaced Short Palindromic Repeats)? Introductory speakers and debate teams spent approximately 9 mo preparing their statements and arguments and had the opportunity to share this at the Joint Annual Meeting with an engaged audience.
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Affiliation(s)
- Casey Parker
- University of Florida, Florida Medical Entomology Laboratory, Vero Beach, FL
| | - Lina Bernaola
- Louisiana State University, Department of Entomology, Baton Rouge, LA
| | - Benjamin W Lee
- Washington State University, Department of Entomology, Pullman, WA
| | - Dane Elmquist
- Washington State University, Department of Entomology, Pullman, WA
| | - Abigail Cohen
- Washington State University, Department of Entomology, Pullman, WA
| | - Adrian Marshall
- Washington State University, Department of Entomology, Tree Fruit Research and Extension Center, Wenatchee, WA
| | - James Hepler
- Washington State University, Department of Entomology, Tree Fruit Research and Extension Center, Wenatchee, WA
| | - Adrian Pekarcik
- The Ohio State University, Department of Entomology, Wooster, OH
| | - Emily Justus
- The Ohio State University, Department of Entomology, Wooster, OH
| | - Kendall King
- The Ohio State University, Department of Entomology, Columbus, OH
| | - Tae-Young Lee
- The Ohio State University, Department of Entomology, Columbus, OH
| | - Carlos Esquivel
- The Ohio State University, Department of Entomology, Wooster, OH
| | - Kayleigh Hauri
- Michigan State University, Department of Entomology, East Lansing, MI
| | - Christopher McCullough
- Virginia Polytechnic Institute and State University, Plant and Environmental Science, Blacksburg, VA
| | - Whitney Hadden
- Virginia Polytechnic Institute and State University, Department of Entomology, Also H Smith Jr AREC, Winchester, VA
| | - Max Ragozzino
- Virginia Polytechnic Institute and State University, Department of Entomology, Blacksburg, VA
| | - Morgan Roth
- Virginia Polytechnic Institute and State University, Department of Entomology, Blacksburg, VA
| | - James Villegas
- Louisiana State University, Department of Entomology, Baton Rouge, LA
| | - Emily Kraus
- Louisiana State University, Department of Entomology, Baton Rouge, LA
| | - Michael Becker
- Louisiana State University, Department of Entomology, Baton Rouge, LA
| | - Megan Mulcahy
- Louisiana State University, Department of Entomology, Baton Rouge, LA
| | - Rui Chen
- Louisiana State University, Department of Entomology, Baton Rouge, LA
| | | | - C Scott Clem
- University of Illinois at Urbana-Champaign, Department of Entomology, Urbana, IL
| | - Rachel Skinner
- University of Illinois at Urbana-Champaign, Department of Entomology, Urbana, IL
| | - Tanya Josek
- University of Illinois at Urbana-Champaign, Department of Entomology, Urbana, IL
| | - Daniel Pearlstein
- University of Illinois at Urbana-Champaign, Department of Entomology, Urbana, IL
| | - Jonathan Tetlie
- University of Illinois at Urbana-Champaign, Department of Entomology, Urbana, IL
| | - Anh Tran
- University of Minnesota, Department of Entomology, St Paul, MN
| | - Anthony Auletta
- University of Minnesota, Department of Entomology, St Paul, MN
| | - Edwin Benkert
- University of Minnesota, Department of Entomology, St Paul, MN
| | - Dylan Tussey
- University of Florida, Entomology and Nematology Department, Gainesville, FL
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121
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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.
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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
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122
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Identification of Arabis alpina genomic regions associated with climatic variables along an elevation gradient through whole genome scan. Genomics 2019; 112:729-735. [PMID: 31085222 DOI: 10.1016/j.ygeno.2019.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/24/2019] [Accepted: 05/08/2019] [Indexed: 01/23/2023]
Abstract
We performed a pooled whole-genome sequencing on samples of the alpine plant Arabis alpina, harvested in ten populations along an elevation gradient in the French Alps. A large dataset of genetic variations was produced as single nucleotide polymorphisms (SNPs). A combined genome scan approach enabled detecting genomic regions associated with a synthetic environmental variable characterizing the climate at each sampling location. Positive loci detected by two methods were retained and belong to 19 regions in the Arabis alpina genome. The most significant region harbors an ortholog of the AtNAC062 gene, encoding a membrane-bound transcription factor described as linking the cold response and pathogen resistance that may confer protection to plants under extended snow coverage at high elevations. Other genes involved in the stress response or in flowering regulation were also detected. Altogether, our results indicated that Arabis alpina represent a suitable model for studying genomic adaptation in alpine perennial plants.
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123
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Allio R, Scornavacca C, Nabholz B, Clamens AL, Sperling FAH, Condamine FL. Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution. Syst Biol 2019; 69:38-60. [DOI: 10.1093/sysbio/syz030] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 01/20/2023] Open
Abstract
Abstract
Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous nonbiological models in parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies—swallowtails of the family Papilionidae—that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced data set (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 Ma (95% credibility interval: 68.6–142.7 Ma) and Papilionidae around 71.4 Ma (49.8–103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Céline Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Institut de Biologie Computationnelle (IBC), Montpellier, France
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Anne-Laure Clamens
- INRA, UMR 1062 Centre de Biologie pour la Gestion des Populations (INRA, IRD, CIRAD, Montpellier SupAgro), 755 Avenue du Campus Agropolis, 34988 Montferrier-sur-Lez, France
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Felix AH Sperling
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Fabien L Condamine
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
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124
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Meek MH, Larson WA. The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era. Mol Ecol Resour 2019; 19:795-803. [PMID: 30681776 DOI: 10.1111/1755-0998.12998] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/21/2023]
Abstract
The genomics revolution has initiated a new era of population genetics where genome-wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Here, amplicon sequencing refers to highly multiplexed PCR followed by high-throughput sequencing (e.g., GTseq), and sequence capture refers to using capture probes to isolate loci from reduced-representation libraries (e.g., Rapture). Both approaches allow sequencing of thousands of individuals at relatively low costs, do not require any specialized equipment for library preparation, and generate data that can be analyzed without sophisticated computational infrastructure. Here, we discuss the advantages and disadvantages of each method and provide a decision framework for geneticists who are looking to integrate these methods into their research programme. While it will always be important to consider the specifics of the biological question and system, we believe that amplicon sequencing is best suited for projects aiming to genotype <500 loci on many individuals (>1,500) or for species where continued monitoring is anticipated (e.g., long-term pedigrees). Sequence capture, on the other hand, is best applied to projects including fewer individuals or where >500 loci are required. Both of these techniques should smooth the transition from traditional genetic techniques to genomics, helping to usher in the conservation genomics era.
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Affiliation(s)
- Mariah H Meek
- Department of Integrative Biology and AgBio Research, Michigan State University, East Lansing, Michigan
| | - Wesley A Larson
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin
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125
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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
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126
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Liu CC, Ji H. PCR Amplification Strategies Towards Full-length HIV-1 Genome Sequencing. Curr HIV Res 2019; 16:98-105. [PMID: 29943704 DOI: 10.2174/1570162x16666180626152252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/05/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
The advent of next-generation sequencing has enabled greater resolution of viral diversity and improved feasibility of full viral genome sequencing allowing routine HIV-1 full genome sequencing in both research and diagnostic settings. Regardless of the sequencing platform selected, successful PCR amplification of the HIV-1 genome is essential for sequencing template preparation. As such, full HIV-1 genome amplification is a crucial step in dictating the successful and reliable sequencing downstream. Here we reviewed existing PCR protocols leading to HIV-1 full genome sequencing. In addition to the discussion on basic considerations on relevant PCR design, the advantages as well as the pitfalls of the published protocols were reviewed.
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Affiliation(s)
- Chao Chun Liu
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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127
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Bernatchez S, Xuereb A, Laporte M, Benestan L, Steeves R, Laflamme M, Bernatchez L, Mallet MA. Seascape genomics of eastern oyster ( Crassostrea virginica) along the Atlantic coast of Canada. Evol Appl 2019; 12:587-609. [PMID: 30828376 PMCID: PMC6383708 DOI: 10.1111/eva.12741] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022] Open
Abstract
Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11,321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean F ST = 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDAs) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype-environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster.
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Affiliation(s)
- Simon Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Fisheries and Oceans CanadaMonctonNew BrunswickCanada
- L’Étang Ruisseau Bar Ltd.ShippaganNew BrunswickCanada
| | - Amanda Xuereb
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Laura Benestan
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Royce Steeves
- Fisheries and Oceans CanadaMonctonNew BrunswickCanada
| | - Mark Laflamme
- Fisheries and Oceans CanadaMonctonNew BrunswickCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
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128
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Adams CIM, Knapp M, Gemmell NJ, Jeunen GJ, Bunce M, Lamare MD, Taylor HR. Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool? Genes (Basel) 2019; 10:E192. [PMID: 30832286 PMCID: PMC6470983 DOI: 10.3390/genes10030192] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 01/23/2023] Open
Abstract
Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.
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Affiliation(s)
- Clare I M Adams
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Knapp
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
| | - Miles D Lamare
- Department of Marine Science, University of Otago, 310 Castle Street, Dunedin, Otago 9016, New Zealand.
| | - Helen R Taylor
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
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129
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Rey-Iglesia A, Gopalakrishan S, Carøe C, Alquezar-Planas DE, Ahlmann Nielsen A, Röder T, Bruhn Pedersen L, Naesborg-Nielsen C, Sinding MHS, Fredensborg Rath M, Li Z, Petersen B, Gilbert MTP, Bunce M, Mourier T, Hansen AJ. MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. Mol Ecol Resour 2019; 19:512-525. [PMID: 30575257 DOI: 10.1111/1755-0998.12984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Abstract
In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site-associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms-enabling the exploration of diverse evolutionary and conservation questions.
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Affiliation(s)
- Alba Rey-Iglesia
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Shyam Gopalakrishan
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David E Alquezar-Planas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Anne Ahlmann Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Timo Röder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lene Bruhn Pedersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Mikkel-Holger S Sinding
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | | | - Zhipeng Li
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Kedah, Malaysia
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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130
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López ME, Benestan L, Moore J, Perrier C, Gilbey J, Di Genova A, Maass A, Diaz D, Lhorente J, Correa K, Neira R, Bernatchez L, Yáñez JM. Comparing genomic signatures of domestication in two Atlantic salmon ( Salmo salar L.) populations with different geographical origins. Evol Appl 2019; 12:137-156. [PMID: 30622641 PMCID: PMC6304691 DOI: 10.1111/eva.12689] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.
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Affiliation(s)
- Maria E. López
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Laura Benestan
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Jean‐Sebastien Moore
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Charles Perrier
- Centre d’Écologie Fonctionnelle et ÉvolutiveUnité Mixte de Recherche CNRS 5175MontpellierFrance
| | - John Gilbey
- Marine Scotland ScienceFreshwater Fisheries LaboratoryFaskallyPitlochryUK
| | - Alex Di Genova
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Alejandro Maass
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Diego Diaz
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | | | | | - Roberto Neira
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Louis Bernatchez
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - José M. Yáñez
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- AquainnovoPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
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131
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Tedersoo L, Drenkhan R, Anslan S, Morales‐Rodriguez C, Cleary M. High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations. Mol Ecol Resour 2019; 19:47-76. [PMID: 30358140 PMCID: PMC7379260 DOI: 10.1111/1755-0998.12959] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/01/2018] [Accepted: 08/28/2018] [Indexed: 12/26/2022]
Abstract
High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state-of-the-art and still evolving methods for diagnostics and population- and community-level ecological research of pathogens and pests.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Rein Drenkhan
- Institute of Forestry and Rural EngineeringEstonian University of Life SciencesTartuEstonia
| | - Sten Anslan
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Michelle Cleary
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesAlnarpSweden
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132
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Cortés AJ, Skeen P, Blair MW, Chacón-Sánchez MI. Does the Genomic Landscape of Species Divergence in Phaseolus Beans Coerce Parallel Signatures of Adaptation and Domestication? FRONTIERS IN PLANT SCIENCE 2018; 9:1816. [PMID: 30619396 PMCID: PMC6306030 DOI: 10.3389/fpls.2018.01816] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/22/2018] [Indexed: 05/10/2023]
Abstract
Exploring the genomic architecture of species and populations divergence aids understanding how lineages evolve and adapt, and ultimately can show the repeatability of evolutionary processes. Yet, the genomic signatures associated with divergence are still relatively unexplored, leading to a knowledge gap on whether species divergence ultimately differs in its genetic architecture from divergence at other spatial scales (i.e., populations, ecotypes). Our goal in this research was to determine whether genomic islands of speciation are more prone to harbor within-species differentiation due to genomic features, suppressed recombination, smaller effective population size or increased drift, across repeated hierarchically nested levels of divergence. We used two species of Phaseolus beans with strong genepool and population sub-structure produced by multiple independent domestications each especially in Andean and Mesoamerican / Middle American geographies. We genotyped 22,531 GBS-derived SNP markers in 209 individuals of wild and cultivated Phaseolus vulgaris and Phaseolus lunatus. We identified six regions for species-associated divergence. Out of these divergence peaks, 21% were recovered in the four within-species between-genepool comparisons and in the five within-genepool wild-cultivated comparisons (some of the latter did retrieve genuine signatures of the well described multiple domestication syndromes). However, genomic regions with overall high relative differentiation (measured by FST) coincided with regions of low SNP density and regions of elevated delta divergence between-genepools (ΔDiv), independent of the scale of divergence. The divergence in chromosome Pv10 further coincided with a between-species pericentric inversion. These convergences suggest that shared variants are being recurrently fixed at replicated regions of the genome, and in a similar manner across different hierarchically nested levels of divergence, likely as result of genomic features that make certain regions more prone to accumulate islands of speciation and within-species divergence. In summary, neighboring signatures of speciation, adaptation and domestication in Phaseolus beans are influenced by ubiquitous genomic constrains, which may continue to fortuitously shape genomic differentiation at various others scales of divergence.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria (Agrosavia) – Centro de Investigación La Selva, Rionegro, Colombia
- Universidad Nacional de Colombia – Sede Medellín, Facultad de Ciencias Agrarias – Departamento de Ciencias
Forestales, Medellín, Colombia
| | - Paola Skeen
- Universidad Nacional de Colombia – Bogotá, Facultad de Ciencias Agrarias – Departamento de Agronomía, Bogotá, Colombia
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Matthew W. Blair
- Department of Agricultural and Environmental Science, Tennessee State University, Nashville, TN, United States
| | - María I. Chacón-Sánchez
- Universidad Nacional de Colombia – Bogotá, Facultad de Ciencias Agrarias – Departamento de Agronomía, Bogotá, Colombia
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133
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Caccavo JA, Papetti C, Wetjen M, Knust R, Ashford JR, Zane L. Along-shelf connectivity and circumpolar gene flow in Antarctic silverfish (Pleuragramma antarctica). Sci Rep 2018; 8:17856. [PMID: 30552350 PMCID: PMC6294782 DOI: 10.1038/s41598-018-36030-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/12/2018] [Indexed: 11/08/2022] Open
Abstract
The Antarctic silverfish (Pleuragramma antarctica) is a critically important forage species with a circumpolar distribution and is unique among other notothenioid species for its wholly pelagic life cycle. Previous studies have provided mixed evidence of population structure over regional and circumpolar scales. The aim of the present study was to test the recent population hypothesis for Antarctic silverfish, which emphasizes the interplay between life history and hydrography in shaping connectivity. A total of 1067 individuals were collected over 25 years from different locations on a circumpolar scale. Samples were genotyped at fifteen microsatellites to assess population differentiation and genetic structuring using clustering methods, F-statistics, and hierarchical analysis of variance. A lack of differentiation was found between locations connected by the Antarctic Slope Front Current (ASF), indicative of high levels of gene flow. However, gene flow was significantly reduced at the South Orkney Islands and the western Antarctic Peninsula where the ASF is absent. This pattern of gene flow emphasized the relevance of large-scale circulation as a mechanism for circumpolar connectivity. Chaotic genetic patchiness characterized population structure over time, with varying patterns of differentiation observed between years, accompanied by heterogeneous standard length distributions. The present study supports a more nuanced version of the genetic panmixia hypothesis that reflects physical-biological interactions over the life history.
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Affiliation(s)
- Jilda Alicia Caccavo
- Department of Biology, University of Padua, Via G. Colombo 3, Padua, 35121, Italy.
| | - Chiara Papetti
- Department of Biology, University of Padua, Via G. Colombo 3, Padua, 35121, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, Rome, 00196, Italy
| | - Maj Wetjen
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, Landau, 76829, Germany
| | - Rainer Knust
- Helmholtz Center for Polar and Marine Research, Alfred Wegener Institute, Am Alten Hafen 26, Bremerhaven, 27568, Germany
| | - Julian R Ashford
- Department of Ocean, Earth and Atmospheric Sciences, Center for Quantitative Fisheries Ecology, Old Dominion University, 800 West 46th Street, Norfolk, VA, 23508, United States
| | - Lorenzo Zane
- Department of Biology, University of Padua, Via G. Colombo 3, Padua, 35121, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, Rome, 00196, Italy
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Pouchon C, Fernández A, Nassar JM, Boyer F, Aubert S, Lavergne S, Mavárez J. Phylogenomic Analysis of the Explosive Adaptive Radiation of the Espeletia Complex (Asteraceae) in the Tropical Andes. Syst Biol 2018; 67:1041-1060. [PMID: 30339252 DOI: 10.1093/sysbio/syy022] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/15/2018] [Indexed: 01/17/2023] Open
Abstract
The subtribe Espeletiinae (Asteraceae), endemic to the high-elevations in the Northern Andes, exhibits an exceptional diversity of species, growth-forms, and reproductive strategies. This complex of 140 species includes large trees, dichotomous trees, shrubs and the extraordinary giant caulescent rosettes, considered as a classic example of adaptation in tropical high-elevation ecosystems. The subtribe has also long been recognized as a prominent case of adaptive radiation, but the understanding of its evolution has been hampered by a lack of phylogenetic resolution. Herein, we produce the first fully resolved phylogeny of all morphological groups of Espeletiinae, using whole plastomes and about a million nuclear nucleotides obtained with an original de novo assembly procedure without reference genome, and analyzed with traditional and coalescent-based approaches that consider the possible impact of incomplete lineage sorting and hybridization on phylogenetic inference. We show that the diversification of Espeletiinae started from a rosette ancestor about 2.3 Ma, after the final uplift of the Northern Andes. This was followed by two independent radiations in the Colombian and Venezuelan Andes, with a few trans-cordilleran dispersal events among low-elevation tree lineages but none among high-elevation rosettes. We demonstrate complex scenarios of morphological change in Espeletiinae, usually implying the convergent evolution of growth-forms with frequent loss/gains of various traits. For instance, caulescent rosettes evolved independently in both countries, likely as convergent adaptations to life in tropical high-elevation habitats. Tree growth-forms evolved independently three times from the repeated colonization of lower elevations by high-elevation rosette ancestors. The rate of morphological diversification increased during the early phase of the radiation, after which it decreased steadily towards the present. On the other hand, the rate of species diversification in the best-sampled Venezuelan radiation was on average very high (3.1 spp/My), with significant rate variation among growth-forms (much higher in polycarpic caulescent rosettes). Our results point out a scenario where both adaptive morphological evolution and geographical isolation due to Pleistocene climatic oscillations triggered an exceptionally rapid radiation for a continental plant group.
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Affiliation(s)
- Charles Pouchon
- Laboratoire d'Ecologie Alpine, UMR 5553, Université Grenoble Alpes-CNRS, Grenoble, France
| | - Angel Fernández
- Herbario IVIC, Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020-A, Venezuela
| | - Jafet M Nassar
- Laboratorio de Biología de Organismos, Centro de Ecología, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020-A, Venezuela
| | - Frédéric Boyer
- Laboratoire d'Ecologie Alpine, UMR 5553, Université Grenoble Alpes-CNRS, Grenoble, France
| | - Serge Aubert
- Laboratoire d'Ecologie Alpine, UMR 5553, Université Grenoble Alpes-CNRS, Grenoble, France.,Station alpine Joseph-Fourier, UMS 3370, Université Grenoble Alpes-CNRS, Grenoble, France
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine, UMR 5553, Université Grenoble Alpes-CNRS, Grenoble, France
| | - Jesús Mavárez
- Laboratoire d'Ecologie Alpine, UMR 5553, Université Grenoble Alpes-CNRS, Grenoble, France
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135
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Xuereb A, Kimber CM, Curtis JMR, Bernatchez L, Fortin M. Putatively adaptive genetic variation in the giant California sea cucumber (
Parastichopus californicus
) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data. Mol Ecol 2018; 27:5035-5048. [DOI: 10.1111/mec.14942] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/17/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Amanda Xuereb
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada
| | - Christopher M. Kimber
- AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry, and Biology (IFM) Linköping University Linköping Sweden
| | - Janelle M. R. Curtis
- Pacific Biological Station, Ecosystem Sciences Division Fisheries and Oceans Canada Nanaimo British Columbia Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes Université Laval Québec Québec Canada
| | - Marie‐Josée Fortin
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada
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136
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Mable BK. Conservation of adaptive potential and functional diversity: integrating old and new approaches. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1129-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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137
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Fairweather R, Bradbury IR, Helyar SJ, de Bruyn M, Therkildsen NO, Bentzen P, Hemmer‐Hansen J, Carvalho GR. Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod. Ecol Evol 2018; 8:12140-12152. [PMID: 30598806 PMCID: PMC6303715 DOI: 10.1002/ece3.4672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/11/2022] Open
Abstract
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range-wide examinations suggest significant transatlantic divergence, although the fine-scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data-synthesis approach, integrating multiple genome-wide single-nucleotide polymorphism (SNP) datasets representative of different regions to create a single range-wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post-glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.
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Affiliation(s)
- Robert Fairweather
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- School of Biological SciencesBangor UniversityBangorUK
| | - Ian R. Bradbury
- Science Branch, Department of FisheriesSt John’s, Newfoundland and LabradorCanada
| | - Sarah J. Helyar
- Institute of Global Food SecurityQueen’s University BelfastBelfastUK
| | - Mark de Bruyn
- School of Biological SciencesBangor UniversityBangorUK
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | | | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jakob Hemmer‐Hansen
- Section for Marine Living Resources, National Institute for Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
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138
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Kardos M, Shafer AB. The Peril of Gene-Targeted Conservation. Trends Ecol Evol 2018; 33:827-839. [DOI: 10.1016/j.tree.2018.08.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 01/01/2023]
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139
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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.
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Affiliation(s)
- Richard R. Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia 22807, USA
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140
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Recknagel H, Kamenos NA, Elmer KR. Common lizards break Dollo’s law of irreversibility: Genome-wide phylogenomics support a single origin of viviparity and re-evolution of oviparity. Mol Phylogenet Evol 2018; 127:579-588. [DOI: 10.1016/j.ympev.2018.05.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 04/12/2018] [Accepted: 05/22/2018] [Indexed: 01/03/2023]
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141
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Cayuela H, Rougemont Q, Prunier JG, Moore JS, Clobert J, Besnard A, Bernatchez L. Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review. Mol Ecol 2018; 27:3976-4010. [DOI: 10.1111/mec.14848] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/17/2018] [Accepted: 08/19/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Jérôme G. Prunier
- Station d'Ecologie Théorique et Expérimentale; Unité Mixte de Recherche (UMR) 5321; Centre National de la Recherche Scientifique (CNRS); Université Paul Sabatier (UPS); Moulis France
| | - Jean-Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Jean Clobert
- Station d'Ecologie Théorique et Expérimentale; Unité Mixte de Recherche (UMR) 5321; Centre National de la Recherche Scientifique (CNRS); Université Paul Sabatier (UPS); Moulis France
| | - Aurélien Besnard
- CNRS; PSL Research University; EPHE; UM, SupAgro, IRD; INRA; UMR 5175 CEFE; Montpellier France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
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142
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Tabas-Madrid D, Méndez-Vigo B, Arteaga N, Marcer A, Pascual-Montano A, Weigel D, Xavier Picó F, Alonso-Blanco C. Genome-wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2018; 41:1806-1820. [PMID: 29520809 DOI: 10.1111/pce.13189] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 05/25/2023]
Abstract
Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse Arabidopsis thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million single nucleotide polymorphisms provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome-wide associations supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome-wide associations provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of environmental and phenotypic genome-wide associations identified known (Twin Sister of FT, FRIGIDA-like 1, and Casein Kinase II Beta chain 1) and new (Epithiospecifer Modifier 1 and Voltage-Dependent Anion Channel 5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants.
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Affiliation(s)
- Daniel Tabas-Madrid
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Noelia Arteaga
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Arnald Marcer
- CREAF, 08193, Cerdanyola del Vallès, Spain
- Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Alberto Pascual-Montano
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092, Sevilla, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
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143
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Hunter ME, Hoban SM, Bruford MW, Segelbacher G, Bernatchez L. Next-generation conservation genetics and biodiversity monitoring. Evol Appl 2018; 11:1029-1034. [PMID: 30026795 PMCID: PMC6050179 DOI: 10.1111/eva.12661] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
This special issue of Evolutionary Applications consists of 10 publications investigating the use of next-generation tools and techniques in population genetic analyses and biodiversity assessment. The special issue stems from a 2016 Next Generation Genetic Monitoring Workshop, hosted by the National Institute for Mathematical and Biological Synthesis (NIMBioS) in Tennessee, USA. The improved accessibility of next-generation sequencing platforms has allowed molecular ecologists to rapidly produce large amounts of data. However, with the increased availability of new genomic markers and mathematical techniques, care is needed in selecting appropriate study designs, interpreting results in light of conservation concerns, and determining appropriate management actions. This special issue identifies key attributes of successful genetic data analyses in biodiversity evaluation and suggests ways to improve analyses and their application in current population and conservation genetics research.
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Affiliation(s)
- Margaret E. Hunter
- U.S. Geological SurveyWetland and Aquatic Research CenterGainesvilleFlorida
| | | | - Michael W. Bruford
- Cardiff School of Biosciences and Sustainable Places InstituteCardiff UniversityCardiffUK
| | | | - Louis Bernatchez
- GIROQDépartement de BiologieUniversité LavalSte‐Foy, QuébecQCCanada
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144
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Measuring Genetic Differentiation from Pool-seq Data. Genetics 2018; 210:315-330. [PMID: 30061425 DOI: 10.1534/genetics.118.300900] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/21/2018] [Indexed: 12/26/2022] Open
Abstract
The advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many nonmodel species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of [Formula: see text] for Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Finally, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper, we show how the use of an unbiased [Formula: see text] estimator may question the interpretation of population structure inferred from previous analyses.
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145
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Campbell CR, Poelstra JW, Yoder AD. What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly063] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - J W Poelstra
- Department of Biology, Duke University, Durham, NC, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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146
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Obregón C, Lyndon AR, Barker J, Christiansen H, Godley BJ, Kurland S, Piccolo JJ, Potts R, Short R, Tebb A, Mariani S. Valuing and understanding fish populations in the Anthropocene: key questions to address. JOURNAL OF FISH BIOLOGY 2018; 92:828-845. [PMID: 29411379 DOI: 10.1111/jfb.13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/09/2017] [Indexed: 06/08/2023]
Abstract
Research on the values of fish populations and fisheries has primarily focused on bio-economic aspects; a more nuanced and multidimensional perspective is mostly neglected. Although a range of social aspects is increasingly being considered in fisheries research, there is still no clear understanding as to how to include these additional values within management policies nor is there a cogent appreciation of the major knowledge gaps that should be tackled by future research. This paper results from a workshop held during the 50th anniversary symposium of the Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017. Here, we aim to highlight the current knowledge gaps on the values of fish populations and fisheries thus directing future research. To this end, we present eight questions that are deeply relevant to understanding the values of fish populations and fisheries. These can be applied to all habitats and fisheries, including freshwater, estuarine and marine.
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Affiliation(s)
- C Obregón
- Estuaries & Wetlands Conservation Programmes, Conservation Programmes Department, Zoological Society of London, Regents Park, London NW1 4RY, U.K
- Centre for Fish and Fisheries Research, Department of Biological Sciences, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - A R Lyndon
- Centre for Marine Biodiversity and Biotechnology, Institute of Life and Earth Sciences, John Muir Building, Heriot-Watt University, Edinburgh, EH14 4AS, U.K
| | - J Barker
- Estuaries & Wetlands Conservation Programmes, Conservation Programmes Department, Zoological Society of London, Regents Park, London NW1 4RY, U.K
| | - H Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Charles Deberiotstraat 32 - Box 2439, 3000 Leuven, Belgium
| | - B J Godley
- Centre for Ecology and Conservation, Daphne du Maurier Building, College of Life and Environmental Sciences, Department of Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, U.K
| | - S Kurland
- Populations genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - J J Piccolo
- Institution for Environmental and Life Science, River Ecology and Management Group, Department of Environmental and Life Sciences, Karlstad University, Karlstad, Sweden
| | - R Potts
- Biosciences, College of Life and Environmental Sciences, Department of Biosciences, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, U.K
| | - R Short
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - A Tebb
- Sussex Inshore Fisheries and Conservation Authority, Shoreham-by-Sea, West Sussex, BN43 6RE, U.K
| | - S Mariani
- School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4WT, U.K
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147
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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148
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149
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Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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