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Lorenzana GP, Figueiró HV, Coutinho LL, Villela PMS, Eizirik E. Comparative assessment of genotyping-by-sequencing and whole-exome sequencing for estimating genetic diversity and geographic structure in small sample sizes: insights from wild jaguar populations. Genetica 2024:10.1007/s10709-024-00212-5. [PMID: 39322785 DOI: 10.1007/s10709-024-00212-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 09/12/2024] [Indexed: 09/27/2024]
Abstract
Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. In this study, we empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in a small number of wild jaguar (Panthera onca) samples from South America. Due to its targeted nature, WES allowed for a more straightforward reconstruction of loci compared to GBS, facilitating the identification of true polymorphisms across individuals. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, adjusting parameters for locus assembly and SNP filtering in the latter. We observed significant variation in SNP call rates across samples in GBS datasets, leading to a recurrent miscalling of heterozygous sites. This issue was further amplified by small sample sizes, ultimately impacting the consistency of summary statistics between genotyping methods. Recognizing that the genetic markers obtained from GBS and WES are intrinsically different due to varying evolutionary pressures, particularly selection, we consider that our empirical comparison offers valuable insights and highlights critical considerations for estimating population genetic attributes using reduced representation datasets. Our results emphasize the critical need for careful evaluation of missing data and stringent filtering to achieve reliable estimates of genetic diversity and differentiation in elusive wildlife species.
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Affiliation(s)
- Gustavo P Lorenzana
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Porto Alegre, Brazil.
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA.
| | - Henrique V Figueiró
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Porto Alegre, Brazil
- Environmental Genomics Group, Vale Institute of Technology, Belem, Brazil
| | | | - Priscilla M S Villela
- Centro de Genômica Funcional, ESALQ-USP, Piracicaba, Brazil
- EcoMol Consultoria e Projetos, Piracicaba, Brazil
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, Brazil
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2
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Myburgh AM, Barnes A, Henriques R, Daniels SR. Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki). Mol Phylogenet Evol 2024; 198:108132. [PMID: 38909874 DOI: 10.1016/j.ympev.2024.108132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/24/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.
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Affiliation(s)
- Angus Macgregor Myburgh
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Romina Henriques
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa
| | - Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa.
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3
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Yadav LK, Bellis D, Smith ZC, Ony M, Hale C, Richards C, Klingeman WE, Staton ME, Granger JJ, Hadziabdic D. Genetic diversity and population structure of a rare flowering tree endemic to Appalachia, Stewartia ovata. Ecol Evol 2024; 14:e11547. [PMID: 38932967 PMCID: PMC11199121 DOI: 10.1002/ece3.11547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/08/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
Stewartia ovata (cav.) Weatherby, commonly known as mountain stewartia, is an understory tree native to the southeastern United States (U.S.). This relatively rare species occurs in isolated populations in Virginia, Kentucky, Tennessee, North Carolina, South Carolina, Georgia, Alabama, and Mississippi. As a species, S. ovata has largely been overlooked, and limited information is available regarding its ecology, which presents obstacles to conservation efforts. Stewartia ovata has vibrant, large white flowers that bloom in summer with a variety of filament colors, suggesting potential horticultural traits prized by ornamental industry. However, S. ovata is relatively slow growing and, due to long seed dormancy, propagation is challenging with limited success rates. This has created a need to assess the present genetic diversity in S. ovata populations to inform potential conservation and restoration of the species. Here, we employ a genotyping-by-sequencing (GBS) approach to characterize the spatial distribution and genetic diversity of S. ovata in the southern Appalachia region of the eastern United States. A total of 4475 single nucleotide polymorphisms (SNPs) were identified across 147 individuals from 11 collection sites. Our results indicate low genetic diversity (He = 0.216), the presence of population structure (K = 2), limited differentiation (F ST = 0.039), and high gene flow (Nm = 6.16) between our subpopulations. Principal component analysis corroborated the findings of STRUCTURE, confirming the presence of two distinct S. ovata subpopulations. One subpopulation mainly contains genotypes from the Cumberland Plateau, Tennessee, while the other consists of genotypes present in the Great Smoky Mountain ranges in Tennessee, North Carolina, and portions of Nantahala, Chattahoochee-Oconee national forests in Georgia, highlighting that elevation likely plays a major role in its distribution. Our results further suggested low inbreeding coefficient (F IS = 0.070), which is expected with an outcrossing tree species. This research further provides necessary insight into extant subpopulations and has generated valuable resources needed for conservation efforts of S. ovata.
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Affiliation(s)
- L. K. Yadav
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - D. Bellis
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Z. C. Smith
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - M. Ony
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - C. Hale
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
- Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
| | - C. Richards
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
| | - W. E. Klingeman
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
| | - M. E. Staton
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - J. J. Granger
- Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
| | - D. Hadziabdic
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
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4
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Mishra S, Duarte GT, Horemans N, Ruytinx J, Gudkov D, Danchenko M. Complexity of responses to ionizing radiation in plants, and the impact on interacting biotic factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171567. [PMID: 38460702 DOI: 10.1016/j.scitotenv.2024.171567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
In nature, plants are simultaneously exposed to different abiotic (e.g., heat, drought, and salinity) and biotic (e.g., bacteria, fungi, and insects) stresses. Climate change and anthropogenic pressure are expected to intensify the frequency of stress factors. Although plants are well equipped with unique and common defense systems protecting against stressors, they may compromise their growth and development for survival in such challenging environments. Ionizing radiation is a peculiar stress factor capable of causing clustered damage. Radionuclides are both naturally present on the planet and produced by human activities. Natural and artificial radioactivity affects plants on molecular, biochemical, cellular, physiological, populational, and transgenerational levels. Moreover, the fitness of pests, pathogens, and symbionts is concomitantly challenged in radiologically contaminated areas. Plant responses to artificial acute ionizing radiation exposure and laboratory-simulated or field chronic exposure are often discordant. Acute or chronic ionizing radiation exposure may occasionally prime the defense system of plants to better tolerate the biotic stress or could often exhaust their metabolic reserves, making plants more susceptible to pests and pathogens. Currently, these alternatives are only marginally explored. Our review summarizes the available literature on the responses of host plants, biotic factors, and their interaction to ionizing radiation exposure. Such systematic analysis contributes to improved risk assessment in radiologically contaminated areas.
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Affiliation(s)
- Shubhi Mishra
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia
| | - Gustavo Turqueto Duarte
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium
| | - Nele Horemans
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium; Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Joske Ruytinx
- Department of Bio-engineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dmitri Gudkov
- Institute of Hydrobiology, National Academy of Sciences of Ukraine, 04210 Kyiv, Ukraine
| | - Maksym Danchenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia.
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5
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Alale TY, Sormunen JJ, Vesterinen EJ, Klemola T, Knott KE, Baltazar‐Soares M. Genomic signatures of hybridization between Ixodes ricinus and Ixodes persulcatus in natural populations. Ecol Evol 2024; 14:e11415. [PMID: 38770117 PMCID: PMC11103643 DOI: 10.1002/ece3.11415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
Identifying hybridization between common pathogen vectors is essential due to the major public health implications through risks associated with hybrid's enhanced pathogen transmission potential. The hard-ticks Ixodes ricinus and Ixodes persulcatus are the two most common vectors of tick-borne pathogens that affect human and animal health in Europe. Ixodes ricinus is a known native species in Finland with a well-known distribution, whereas I. persulcatus has expanded in range and abundance over the past 60 years, and currently it appears the most common tick species in certain areas in Finland. Here we used double-digest restriction site-associated DNA (ddRAD) sequencing on 186 ticks (morphologically identified as 92 I. ricinus, and 94 I. persulcatus) collected across Finland to investigate whether RAD generated single nucleotide polymorphisms (SNPs) can discriminate tick species and identify potential hybridization events. Two different clustering methods were used to assign specific species based on how they clustered and identified hybrids among them. We were able to discriminate between the two tick species and identified 11 putative hybrids with admixed genomic proportions ranging from approximately 24 to 76 percent. Four of these hybrids were morphologically identified as I. ricinus while the remaining seven were identified as I. persulcatus. Our results thus indicate that RAD SNPs are robust in identifying both species of the ticks as well as putative hybrids. These results further suggest ongoing hybridization between I. ricinus and I. persulcatus in their natural populations in Finland. The unique ability of RAD markers to discriminate between tick species and hybrids adds a useful aspect to tick evolutionary studies. Our findings align with previous studies and suggest a shared evolutionary history between the species, with instances of individuals possessing a considerable proportion of the other species' genome. This study is a significant step in understanding the formation of hybridization zones due to range expansion potentially associated with climate change.
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Affiliation(s)
- Theophilus Yaw Alale
- Department of BiologyUniversity of TurkuTurkuFinland
- Biodiversity UnitUniversity of TurkuTurkuFinland
| | - Jani J. Sormunen
- Department of BiologyUniversity of TurkuTurkuFinland
- Biodiversity UnitUniversity of TurkuTurkuFinland
| | | | - Tero Klemola
- Department of BiologyUniversity of TurkuTurkuFinland
| | - K. Emily Knott
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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6
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Ollé-Vilanova J, Hajjej G, Macias D, Saber S, Lino PG, Muñoz-Lechuga R, Baibbat S, Sow FN, Diaha NC, Araguas RM, Sanz N, Vinas J. Atlantic bonito (Sarda) genomic analysis reveals population differentiation across Northeast Atlantic and mediterranean locations: Implications for fishery management. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106408. [PMID: 38402010 DOI: 10.1016/j.marenvres.2024.106408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
The Atlantic bonito (Sarda, family Scombridae) is a pelagic species and one of the most exploited small tuna species. Despite its economic importance, biological information is scarce with no associated management directives. In this study, using a population genomic approach resulted in a lack of panmixia of two genetic pools with different effective population sizes (east central-tropical Atlantic and northeast Atlantic-Mediterranean) and an intermixing zone in Atlantic Morocco. The absence of genetic heterogeneity between the locations in Atlantic - Mediterranean transitional zone adds new evidence that challenges the Strait of Gibraltar as a phylogeographic barrier for marine pelagic species. These results are proposed to the ICCAT Commission to establish management areas for this species, although they are not consistent with the recently adopted pelagic ecoregions. Finally, a panel of highly informative SNPs was developed for efficient and low-cost population assignment and the analysis of unresolved population structures.
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Affiliation(s)
- Judith Ollé-Vilanova
- Laboratori Ictiologia Genetica, Departament de Biologia, Universitat de Girona, 17003, Girona, Catalunya, Spain
| | - Ghailen Hajjej
- National Institute of Marine Science and Technology, Tunisia
| | - David Macias
- Centro Oceanográfico de Málaga. Instituto Espanol de Oceanografía (IEO-CSIC), Spain
| | - Sámar Saber
- Centro Oceanográfico de Málaga. Instituto Espanol de Oceanografía (IEO-CSIC), Spain
| | - Pedro G Lino
- Instituto Portugues Do Mar e da Atmosfera (IPMA), Avenida 5 de Outubro S/n, 8700-305, Olhão, Portugal
| | - Rubén Muñoz-Lechuga
- Instituto Portugues Do Mar e da Atmosfera (IPMA), Avenida 5 de Outubro S/n, 8700-305, Olhão, Portugal; Department of Biology, Faculty of Marine and Environmental Sciences, University of Cádiz, 11510, Puerto Real, Cádiz, Spain
| | | | | | | | - Rosa M Araguas
- Laboratori Ictiologia Genetica, Departament de Biologia, Universitat de Girona, 17003, Girona, Catalunya, Spain
| | - Núria Sanz
- Laboratori Ictiologia Genetica, Departament de Biologia, Universitat de Girona, 17003, Girona, Catalunya, Spain
| | - Jordi Vinas
- Laboratori Ictiologia Genetica, Departament de Biologia, Universitat de Girona, 17003, Girona, Catalunya, Spain.
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7
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Deakin S, Coltman DW. Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep ( Ovis canadensis canadensis). PeerJ 2024; 12:e16946. [PMID: 38426129 PMCID: PMC10903336 DOI: 10.7717/peerj.16946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, high-density, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped ~45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.
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Affiliation(s)
- Samuel Deakin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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8
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Rojas-Araos F, Rojas-Hernández N, Cornejo-Guzmán S, Ernst B, Dewitte B, Parada C, Veliz D. Population genomic and biophysical modeling show different patterns of population connectivity in the spiny lobster Jasus frontalis inhabiting oceanic islands. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106253. [PMID: 37979403 DOI: 10.1016/j.marenvres.2023.106253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/20/2023]
Abstract
Knowledge about connectivity between populations is essential for the fisheries management of commercial species. The lobster Jasus frontalis inhabits two oceanic island groups, the Juan Fernández Archipelago and the Desventuradas Islands, separated by 800 km. Since this species is primarily exploited in the Juan Fernández Archipelago, knowledge of the connectivity patterns among islands is foundational for species management. Here, we used variability at single-nucleotide polymorphisms (SNPs) and individual-based modeling (IBM) to estimate the genetic structure and connectivity between J. frontalis populations in these island groups. The variability at 9090 SNPs suggests two genetic populations, one in the Juan Fernández Archipelago and one in the Desventuradas Islands. Furthermore, IBM suggests an asymmetric connectivity pattern, with particles moving from the Juan Fernández Archipelago to the Desventuradas Islands but not vice versa. Since the IBM analysis suggests asymmetric larval movement between the islands, and the genetic analysis indicates isolation between the Juan Fernández Archipelago and the Desventuradas Islands, larval retention mechanisms such as small-scale oceanographic processes or behavior could hinder larval movement between islands. This study highlights the importance of using more than one methodology to estimate population connectivity.
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Affiliation(s)
- Felipe Rojas-Araos
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Noemi Rojas-Hernández
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Billy Ernst
- Centro Milenio de Ecología y Manejo Sustentable (ESMOI), Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile; Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Boris Dewitte
- Centro Milenio de Ecología y Manejo Sustentable (ESMOI), Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile; Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile; Université de Toulouse III, CERFACS/CNRS, Toulouse, France
| | - Carolina Parada
- Departamento de Geofísica, Universidad de Concepción, Concepción, Chile; Centro Milenio de Ecología y Manejo Sustentable (ESMOI), Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
| | - David Veliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Centro Milenio de Ecología y Manejo Sustentable (ESMOI), Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
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9
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Rahi ML, Mather PB, de Bello Cioffi M, Ezaz T, Hurwood DA. Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events. J Mol Evol 2023; 91:976-989. [PMID: 38010517 DOI: 10.1007/s00239-023-10149-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Adaptation to different salinity environments can enhance morphological and genomic divergence between related aquatic taxa. Species of prawns in the genus Macrobrachium naturally inhabit different osmotic niches and possess distinctive lifecycle traits associated with salinity tolerance. This study was conducted to investigate the patterns of adaptive genomic divergence during freshwater colonization in 34 Macrobrachium species collected from four continents; Australia, Asia, North and South America. Genotyping-by-sequencing (GBS) technique identified 5018 loci containing 82,636 single nucleotide polymorphisms (SNPs) that were used to reconstruct a phylogenomic tree. An additional phylogeny was reconstructed based on 43 candidate genes, previously identified as being potentially associated with freshwater adaptation. Comparison of the two phylogenetic trees revealed contrasting topologies. The GBS tree indicated multiple independent continent-specific invasions into freshwater by Macrobrachium lineages following common marine ancestry, as species with abbreviated larval development (ALD), i.e., species having a full freshwater life history, appeared reciprocally monophyletic within each continent. In contrast, the candidate gene tree showed convergent evolution for all ALD species worldwide, forming a single, well-supported clade. This latter pattern is likely the result of common evolutionary pressures selecting key mutations favored in continental freshwater habitats Results suggest that following multiple independent invasions into continental freshwaters at different evolutionary timescales, Macrobrachium taxa experienced adaptive genomic divergence, and in particular, convergence in the same genomic regions with parallel shifts in specific conserved phenotypic traits, such as evolution of larger eggs with abbreviated larval developmental.
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Affiliation(s)
- Md Lifat Rahi
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna, Bangladesh.
| | - Peter B Mather
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, SP, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology (IAE), University of Canberra (UC), Canberra, ACT, 2617, Australia
| | - David A Hurwood
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
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10
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Pronozin AY, Salina EA, Afonnikov DA. GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing. Vavilovskii Zhurnal Genet Selektsii 2023; 27:737-745. [PMID: 38213704 PMCID: PMC10777284 DOI: 10.18699/vjgb-23-86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 01/13/2024] Open
Abstract
The development of next-generation sequencing technologies has provided new opportunities for genotyping various organisms, including plants. Genotyping by sequencing (GBS) is used to identify genetic variability more rapidly, and is more cost-effective than whole-genome sequencing. GBS has demonstrated its reliability and flexibility for a number of plant species and populations. It has been applied to genetic mapping, molecular marker discovery, genomic selection, genetic diversity studies, variety identification, conservation biology and evolutionary studies. However, reduction in sequencing time and cost has led to the need to develop efficient bioinformatics analyses for an ever-expanding amount of sequenced data. Bioinformatics pipelines for GBS data analysis serve the purpose. Due to the similarity of data processing steps, existing pipelines are mainly characterised by a combination of software packages specifically selected either to process data for certain organisms or to process data from any organisms. However, despite the usage of efficient software packages, these pipelines have some disadvantages. For example, there is a lack of process automation (in some pipelines, each step must be started manually), which significantly reduces the performance of the analysis. In the majority of pipelines, there is no possibility of automatic installation of all necessary software packages; for most of them, it is also impossible to switch off unnecessary or completed steps. In the present work, we have developed a GBS-DP bioinformatics pipeline for GBS data analysis. The pipeline can be applied for various species. The pipeline is implemented using the Snakemake workflow engine. This implementation allows fully automating the process of calculation and installation of the necessary software packages. Our pipeline is able to perform analysis of large datasets (more than 400 samples).
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Affiliation(s)
- A Y Pronozin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - E A Salina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State Agrarian University, Novosibirsk, Russia
| | - D A Afonnikov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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11
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Pumpitakkul V, Chetruengchai W, Srichomthong C, Phokaew C, Pootakham W, Sonthirod C, Nawae W, Tongsima S, Wangkumhang P, Wilantho A, Utara Y, Thongpakdee A, Sanannu S, Maikaew U, Khuntawee S, Changpetch W, Phromwat P, Raschasin K, Sarnkhaeveerakul P, Supapannachart P, Buthasane W, Pukazhenthi BS, Koepfli KP, Suriyaphol P, Tangphatsornruang S, Suriyaphol G, Shotelersuk V. Comparative genomics and genome-wide SNPs of endangered Eld's deer provide breeder selection for inbreeding avoidance. Sci Rep 2023; 13:19806. [PMID: 37957263 PMCID: PMC10643696 DOI: 10.1038/s41598-023-47014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/15/2023] Open
Abstract
Eld's deer, a conserved wildlife species of Thailand, is facing inbreeding depression, particularly in the captive Siamese Eld's deer (SED) subspecies. In this study, we constructed genomes of a male SED and a male Burmese Eld's deer (BED), and used genome-wide single nucleotide polymorphisms to evaluate the genetic purity and the inbreeding status of 35 SED and 49 BED with limited pedigree information. The results show that these subspecies diverged approximately 1.26 million years ago. All SED were found to be purebred. A low proportion of admixed SED genetic material was observed in some BED individuals. Six potential breeders from male SED with no genetic relation to any female SED and three purebred male BED with no relation to more than 10 purebred female BED were identified. This study provides valuable insights about Eld's deer populations and appropriate breeder selection in efforts to repopulate this endangered species while avoiding inbreeding.
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Affiliation(s)
- Vichayanee Pumpitakkul
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chureerat Phokaew
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Wanapinun Nawae
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Alisa Wilantho
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Yongchai Utara
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute, Bangkok, 10800, Thailand
| | - Ampika Thongpakdee
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute, Bangkok, 10800, Thailand
| | - Saowaphang Sanannu
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute, Bangkok, 10800, Thailand
| | - Umaporn Maikaew
- Khao Kheow Open Zoo, Zoological Park Organization of Thailand, Chonburi, 20110, Thailand
| | - Suphattharaphonnaphan Khuntawee
- Ubon Ratchathani Zoo, Zoological Park Organization of Thailand, Ubon Ratchathani District, Ubon Ratchathani, 34000, Thailand
| | - Wirongrong Changpetch
- Nakhon Ratchasima Zoo, Zoological Park Organization of Thailand, Nakhon Ratchasima, 30000, Thailand
| | - Phairot Phromwat
- Huai Kha Khaeng Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Uthai Thani, 61160, Thailand
| | - Kacharin Raschasin
- Chulabhorn Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Sisaket, 33140, Thailand
| | - Phunyaphat Sarnkhaeveerakul
- Banglamung Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Chonburi, 20150, Thailand
| | - Pannawat Supapannachart
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wannapol Buthasane
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, 22630, USA
| | - Prapat Suriyaphol
- Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand.
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
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12
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Meng J, Yang G, Li X, Zhao Y, He S. Population structure of wild soybean ( Glycine soja) based on SLAF-seq have implications for its conservation. PeerJ 2023; 11:e16415. [PMID: 37953790 PMCID: PMC10638924 DOI: 10.7717/peerj.16415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
Background Glycine soja Sieb. & Zucc. is the wild ancestor from which the important crop plant soybean was bred. G. soja provides important germplasm resources for the breeding and improvement of cultivated soybean crops, however the species is threatened by habitat loss and fragmentation, and is experiencing population declines across its natural range. Understanding the patterns of genetic diversity in G. soja populations can help to inform conservation practices. Methods In this study, we analyzed the genetic diversity and differentiation of G. soja at different sites and investigated the gene flow within the species. We obtained 147 G. soja accessions collected from 16 locations across the natural range of the species from China, Korea and Japan. Samples were analyzed using SLAF-seq (Specific-Locus Amplified Fragment Sequencing). Results We obtained a total of 56,489 highly consistent SNPs. Our results suggested that G. soja harbors relatively high diversity and that populations of this species are highly differentiated. The populations harboring high genetic diversity, especially KR, should be considered first when devising conservation plans for the protection of G. soja, and in situ protection should be adopted in KR. G. soja populations from the Yangtze River, the Korean peninsula and northeastern China have a close relationship, although these areas are geographically disconnected. Other populations from north China clustered together. Analysis of gene flow suggested that historical migrations of G. soja may have occurred from the south northwards across the East-Asia land-bridge, but not across north China. All G. soja populations could be divided into one of two lineages, and these two lineages should be treated separately when formulating protection policies.
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Affiliation(s)
- Jing Meng
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Guoqian Yang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yuannan, China
| | - Xuejiao Li
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yan Zhao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shuilian He
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
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13
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Zinevich L, Prommer M, Laczkó L, Rozhkova D, Sorokin A, Karyakin I, Bagyura J, Cserkész T, Sramkó G. Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus). Sci Rep 2023; 13:17800. [PMID: 37853004 PMCID: PMC10584951 DOI: 10.1038/s41598-023-44534-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
The Altai falcon from Central Asia always attracted the attention of humans. Long considered a totemic bird in its native area, modern falconers still much appreciated this large-bodied and mighty bird of prey due to its rarity and unique look. The peculiar body characteristics halfway between the saker falcon (Falco cherrug) and the gyrfalcon (F. rusticolus) triggered debates about its contentious taxonomy. The weak phylogenetic signal associated with traditional genetic methods could not resolve this uncertainty. Here, we address the controversial evolutionary origin of Altai falcons by means of a genome-wide approach, Restriction-site Associated DNA sequencing, using sympatric eastern sakers falcons, allopatric western saker falcons and gyrfalcons as outgroup. This approach provided an unprecedented insight into the phylogenetic relationships of the studied populations by delivering 17,095 unlinked SNPs shedding light on the polyphyletic nature of Altai falcons within eastern sakers. Thus we concluded that the former must correspond to a low taxonomic rank, probably an ecotype or form of the latter. Also, we found that eastern sakers are paraphyletic without gyrfalcons, thus, these latter birds are best regarded as the direct sister lineage of the eastern sakers. This evolutionary relationship, corroborated also by re-analyzing the dataset with the inclusion of outgroup samples (F. biarmicus and F. peregrinus), put eastern sakers into a new light as the potential ancestral genetic source of high latitude and altitude adaptation in descendent populations. Finally, conservation genomic values hint at the stable genetic background of the studied saker populations.
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Affiliation(s)
- Liudmila Zinevich
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - Levente Laczkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Daria Rozhkova
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | - Alexander Sorokin
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - János Bagyura
- MME - BirdLife Hungary, Költő utca 21, Budapest, 1121, Hungary
| | - Tamás Cserkész
- Hungarian Natural History Museum, Baross utca 13, Budapest, 1088, Hungary
| | - Gábor Sramkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary.
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
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14
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Suchocki CR, Ka'apu-Lyons C, Copus JM, Walsh CAJ, Lee AM, Carter JM, Johnson EA, Etter PD, Forsman ZH, Bowen BW, Toonen RJ. Geographic destiny trumps taxonomy in the Roundtail Chub, Gila robusta species complex (Teleostei, Leuciscidae). Sci Rep 2023; 13:15810. [PMID: 37737242 PMCID: PMC10517014 DOI: 10.1038/s41598-023-41719-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
The Gila robusta species complex in the lower reaches of the Colorado River includes three nominal and contested species (G. robusta, G. intermedia, and G. nigra) originally defined by morphological and meristic characters. In subsequent investigations, none of these characters proved diagnostic, and species assignments were based on capture location. Two recent studies applied conservation genomics to assess species boundaries and reached contrasting conclusions: an ezRAD phylogenetic study resolved 5 lineages with poor alignment to species categories and proposed a single species with multiple population partitions. In contrast, a dd-RAD coalescent study concluded that the three nominal species are well-supported evolutionarily lineages. Here we developed a draft genome (~ 1.229 Gbp) to apply genome-wide coverage (10,246 SNPs) with nearly range-wide sampling of specimens (G. robusta N = 266, G. intermedia N = 241, and G. nigra N = 117) to resolve this debate. All three nominal species were polyphyletic, whereas 5 of 8 watersheds were monophyletic. AMOVA partitioned 23.1% of genetic variance among nominal species, 30.9% among watersheds, and the Little Colorado River was highly distinct (FST ranged from 0.79 to 0.88 across analyses). Likewise, DAPC identified watersheds as more distinct than species, with the Little Colorado River having 297 fixed nucleotide differences compared to zero fixed differences among the three nominal species. In every analysis, geography explains more of the observed variance than putative taxonomy, and there are no diagnostic molecular or morphological characters to justify species designation. Our analysis reconciles previous work by showing that species identities based on type location are supported by significant divergence, but natural geographic partitions show consistently greater divergence. Thus, our data confirm Gila robusta as a single polytypic species with roughly a dozen highly isolated geographic populations, providing a strong scientific basis for watershed-based future conservation.
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Affiliation(s)
- Christopher R Suchocki
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cassie Ka'apu-Lyons
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cameron A J Walsh
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Anne M Lee
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Julie Meka Carter
- Arizona Game and Fish Department, 5000 W. Carefree Highway, Phoenix, AZ, 85086, USA
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Paul D Etter
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
- Reefscape Restoration Initiative, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA.
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15
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Zhang K, Wang G, Wang L, Wen B, Fu X, Liu N, Yu Z, Jian W, Guo X, Liu H, Chen SY. A genome-wide association study of coat color in Chinese Rex rabbits. Front Vet Sci 2023; 10:1184764. [PMID: 37655262 PMCID: PMC10467280 DOI: 10.3389/fvets.2023.1184764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Coat color is an important phenotypic characteristic of the domestic rabbit (Oryctolagus cuniculus) and has specific economic importance in the Rex rabbit industry. Coat color varies considerably among different populations of rabbits, and several causal genes for this variation have been thoroughly studied. Nevertheless, the candidate genes affecting coat color variation in Chinese Rex rabbits remained to be investigated. In this study, we collected blood samples from 250 Chinese Rex rabbits with six different coat colors. We performed genome sequencing using a restriction site-associated DNA sequencing approach. A total of 91,546 single nucleotide polymorphisms (SNPs), evenly distributed among 21 autosomes, were identified. Genome-wide association studies (GWAS) were performed using a mixed linear model, in which the individual polygenic effect was fitted as a random effect. We detected a total of 24 significant SNPs that were located within a genomic region on chromosome 4 (OCU4). After re-fitting the most significant SNP (OCU4:13,434,448, p = 1.31e-12) as a covariate, another near-significant SNP (OCU4:11,344,946, p = 7.03e-07) was still present. Hence, we conclude that the 2.1-Mb genomic region located between these two significant SNPs is significantly associated with coat color in Chinese Rex rabbits. The well-studied coat-color-associated agouti signaling protein (ASIP) gene is located within this region. Furthermore, low genetic differentiation was also observed among the six coat color varieties. In conclusion, our results confirmed that ASIP is a putative causal gene affecting coat color variation in Chinese Rex rabbits.
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Affiliation(s)
- Kai Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Guozhi Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lihuan Wang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Bin Wen
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiangchao Fu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Ning Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Zhiju Yu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Wensu Jian
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiaolin Guo
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Hanzhong Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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16
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Ramsay MS, Sgarlata GM, Barratt CD, Salmona J, Andriatsitohaina B, Kiene F, Manzi S, Ramilison ML, Rakotondravony R, Chikhi L, Lehman SM, Radespiel U. Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar. Genes (Basel) 2023; 14:1451. [PMID: 37510355 PMCID: PMC10378931 DOI: 10.3390/genes14071451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study, we examined the dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genetic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site, we identified contrasting migration rates for each species, but these did not correspond to habitat-matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.
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Affiliation(s)
- Malcolm S Ramsay
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | | | - Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Jordi Salmona
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Bertrand Andriatsitohaina
- Planet Madagascar, Antananarivo 101, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Frederik Kiene
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Miarisoa L Ramilison
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
- Department of Primate Behavior and Ecology, Central Washington University, Ellensburg, WA 98926, USA
| | - Romule Rakotondravony
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Shawn M Lehman
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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17
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de Ronne M, Légaré G, Belzile F, Boyle B, Torkamaneh D. 3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes. PLANT METHODS 2023; 19:13. [PMID: 36740716 PMCID: PMC9899395 DOI: 10.1186/s13007-023-00990-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Despite the increased efficiency of sequencing technologies and the development of reduced-representation sequencing (RRS) approaches allowing high-throughput sequencing (HTS) of multiplexed samples, the per-sample genotyping cost remains the most limiting factor in the context of large-scale studies. For example, in the context of genomic selection (GS), breeders need genome-wide markers to predict the breeding value of large cohorts of progenies, requiring the genotyping of thousands candidates. Here, we introduce 3D-GBS, an optimized GBS procedure, to provide an ultra-high-throughput and ultra-low-cost genotyping solution for species with small to medium-sized genome and illustrate its use in soybean. Using a combination of three restriction enzymes (PstI/NsiI/MspI), the portion of the genome that is captured was reduced fourfold (compared to a "standard" ApeKI-based protocol) while reducing the number of markers by only 40%. By better focusing the sequencing effort on limited set of restriction fragments, fourfold more samples can be genotyped at the same minimal depth of coverage. This GBS protocol also resulted in a lower proportion of missing data and provided a more uniform distribution of SNPs across the genome. Moreover, we investigated the optimal number of reads per sample needed to obtain an adequate number of markers for GS and QTL mapping (500-1000 markers per biparental cross). This optimization allows sequencing costs to be decreased by ~ 92% and ~ 86% for GS and QTL mapping studies, respectively, compared to previously published work. Overall, 3D-GBS represents a unique and affordable solution for applications requiring extremely high-throughput genotyping where cost remains the most limiting factor.
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Affiliation(s)
- Maxime de Ronne
- Département de Phytologie, Université Laval, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec, Canada
| | - Gaétan Légaré
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada.
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec, Canada.
- Institut intelligence et données (IID), Université Laval, Quebec, Canada.
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18
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Hubbell JP, Schaefer JF, Kreiser BR. The influence of habitat characteristics on the occupancy and dispersal of two headwater fishes in a dendritic network. Ecosphere 2023. [DOI: 10.1002/ecs2.4388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Joshua P. Hubbell
- Department of Biological Sciences Hattiesburg University of Southern Mississippi Hattiesburg Mississippi USA
| | - Jacob F. Schaefer
- Department of Biological Sciences Hattiesburg University of Southern Mississippi Hattiesburg Mississippi USA
| | - Brian R. Kreiser
- Department of Biological Sciences Hattiesburg University of Southern Mississippi Hattiesburg Mississippi USA
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19
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Alvarado-Cerón V, Muñiz-Castillo AI, León-Pech MG, Prada C, Arias-González JE. A decade of population genetics studies of scleractinian corals: A systematic review. MARINE ENVIRONMENTAL RESEARCH 2023; 183:105781. [PMID: 36371949 DOI: 10.1016/j.marenvres.2022.105781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Coral reefs are the most diverse marine ecosystems. However, coral cover has decreased worldwide due to natural disturbances, climate change, and local anthropogenic drivers. In recent decades, various genetic methods and molecular markers have been developed to assess genetic diversity, structure, and connectivity in different coral species to determine the vulnerability of their populations. This review aims to identify population genetic studies of scleractinian corals in the last decade (2010-2020), and the techniques and molecular markers used. Bibliometric analysis was conducted to identify journals and authors working in this field. We then calculated the number of genetic studies by species and ecoregion based on data obtained from 178 studies found in Scopus and Web of Science. Coral Reefs and Molecular Ecology were the main journals published population genetics studies, and microsatellites are the most widely used molecular markers. The Caribbean, Australian Barrier Reef, and South Kuroshio in Japan are among the ecoregions with the most population genetics data. In contrast, we found limited information about the Coral Triangle, a region with the highest biodiversity and key to coral reef conservation. Notably, only 117 (out of 1500 described) scleractinian coral species have genetic studies. This review emphasizes which coral species have been studied and highlights remaining gaps and locations where such data is critical for coral conservation.
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Affiliation(s)
- Viridiana Alvarado-Cerón
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del I.P.N., Unidad Mérida. Km. 6 Antigua carretera a Progreso, Cordemex, 97310, Mérida, Yucatán, Mexico.
| | - Aarón Israel Muñiz-Castillo
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del I.P.N., Unidad Mérida. Km. 6 Antigua carretera a Progreso, Cordemex, 97310, Mérida, Yucatán, Mexico.
| | - María Geovana León-Pech
- Department of Biological Science, University of Rhode Island, 120 Flag Road, Kingston, RI, 02881, USA.
| | - Carlos Prada
- Department of Biological Science, University of Rhode Island, 120 Flag Road, Kingston, RI, 02881, USA.
| | - Jesús Ernesto Arias-González
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del I.P.N., Unidad Mérida. Km. 6 Antigua carretera a Progreso, Cordemex, 97310, Mérida, Yucatán, Mexico.
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20
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T. V. N, S. RP, R. L. R. Population structure and genetic diversity characterization of soybean for seed longevity. PLoS One 2022; 17:e0278631. [PMID: 36472991 PMCID: PMC9725150 DOI: 10.1371/journal.pone.0278631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/19/2022] [Indexed: 12/12/2022] Open
Abstract
Seed longevity is an important trait in the context of germplasm conservation and economics of seed production. The identification of populations with high level of genetic variability for seed longevity and associated traits will become a valuable resource for superior alleles for seed longevity. In this study, Genotyping-by-sequencing (GBS)-single nucleotide polymorphism (SNP) approach, simple sequence repeats (SSR) markers and agro-morphological traits have been explored to investigate the diversity and population structure of assembled 96 genotypes. The GBS technique performed on 96 genotypes of soybean (Glycine max (L.) Merrill) resulted in 37,897 SNPs on sequences aligned to the reference genome sequence. The average genome coverage was 6.81X with a mapping rate of 99.56% covering the entire genome. Totally, 29,955 high quality SNPs were identified after stringent filtering and most of them were detected in non-coding regions. The 96 genotypes were phenotyped for eight quantitative and ten qualitative traits by growing in field by following augmented design. The STRUCTURE (Bayesian-model based algorithm), UPGMA (Un-weighed Pair Group Method with Arithmetic mean) and principal component analysis (PCA) approaches using SSR, SNP as well as quantitative and qualitative traits revealed population structure and diversity in assembled population. The Bayesian-model based STRUCTURE using SNP markers could effectively identify clusters with higher seed longevity associated with seed coat colour and size which were subsequently validated by UPGMA and PCA based on SSR and agro-morphological traits. The results of STRUCTURE, PCA and UPGMA cluster analysis showed high degree of similarity and provided complementary data that helped to identify genotypes with higher longevity. Six black colour genotypes, viz., Local black soybean, Kalitur, ACC Nos. 39, 109, 101 and 37 showed higher seed longevity during accelerated ageing. Higher coefficient of variability observed for plant height, number of pods per plant, seed yield per plant, 100 seed weight and seed longevity confirms the diversity in assembled population and its suitability for quantitative trait loci (QTL) mapping.
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Affiliation(s)
- Naflath T. V.
- Department of Seed Science and Technology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
| | - Rajendra Prasad S.
- Department of Seed Science and Technology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
| | - Ravikumar R. L.
- Department of Plant Biotechnology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
- * E-mail:
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21
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Mandeville EG, Hall RO, Buerkle CA. Ecological outcomes of hybridization vary extensively in Catostomus fishes. Evolution 2022; 76:2697-2711. [PMID: 36097356 PMCID: PMC9801484 DOI: 10.1111/evo.14624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 01/22/2023]
Abstract
Hybridization outcomes vary geographically and can depend on the environment. Hybridization can also reshape biotic interactions, leading to ecological shifts. If hybrids function differently ecologically in ways that enhance or reduce fitness, and those ecological roles vary geographically, ecological factors might explain variation in hybridization outcomes. However, relatively few studies have focused on ecological traits of hybrids. We compared the feeding ecology of Catostomus fish species and hybrids by using stable isotopes (δ13 C and δ15 N) as a proxy for diet and habitat use, and compared two native species, an introduced species, and three interspecific hybrid crosses. We included hybrids and parental species from seven rivers where hybridization outcomes vary. Relative isotopic niches of native species varied geographically, but native species did not fully overlap in isotopic space in any river sampled, suggesting little overlap of resource use between historically sympatric species. The introduced species overlapped with one or both native species in every river, suggesting similar resource use and potential competition. Hybrids occupied intermediate, matching, or more transgressive isotopic niches, and varied within and among rivers. Ecological outcomes of hybridization varied across locations, implying that hybridization might have unpredictable, idiosyncratic ecological effects.
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Affiliation(s)
- Elizabeth G. Mandeville
- Department of Integrative Biology, University of Guelph, Guelph, Ontario Canada
- Department of Botany, University of Wyoming, Laramie, Wyoming USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming USA
| | - Robert O. Hall
- Program in Ecology, University of Wyoming, Laramie, Wyoming USA
- Flathead Lake Biological Station, University of Montana, Polson, Montana USA (present address)
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming USA
| | - C. Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, Wyoming USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming USA
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22
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Hart AF, Verbeeck J, Ariza D, Cejas D, Ghisbain G, Honchar H, Radchenko VG, Straka J, Ljubomirov T, Lecocq T, Dániel-Ferreira J, Flaminio S, Bortolotti L, Karise R, Meeus I, Smagghe G, Vereecken N, Vandamme P, Michez D, Maebe K. Signals of adaptation to agricultural stress in the genomes of two European bumblebees. Front Genet 2022; 13:993416. [PMID: 36276969 PMCID: PMC9579324 DOI: 10.3389/fgene.2022.993416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
Human-induced environmental impacts on wildlife are widespread, causing major biodiversity losses. One major threat is agricultural intensification, typically characterised by large areas of monoculture, mechanical tillage, and the use of agrochemicals. Intensification leads to the fragmentation and loss of natural habitats, native vegetation, and nesting and breeding sites. Understanding the adaptability of insects to these changing environmental conditions is critical to predicting their survival. Bumblebees, key pollinators of wild and cultivated plants, are used as model species to assess insect adaptation to anthropogenic stressors. We investigated the effects of agricultural pressures on two common European bumblebees, Bombus pascuorum and B. lapidarius. Restriction-site Associated DNA Sequencing was used to identify loci under selective pressure across agricultural-natural gradients over 97 locations in Europe. 191 unique loci in B. pascuorum and 260 in B. lapidarius were identified as under selective pressure, and associated with agricultural stressors. Further investigation suggested several candidate proteins including several neurodevelopment, muscle, and detoxification proteins, but these have yet to be validated. These results provide insights into agriculture as a stressor for bumblebees, and signal for conservation action in light of ongoing anthropogenic changes.
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Affiliation(s)
- Alex F. Hart
- Ghent University, Faculty of Bioscience Engineering, Department of Plants and Crops, Lab of Agrozoology, Ghent, Belgium
| | - Jaro Verbeeck
- Ghent University, Faculty of Bioscience Engineering, Department of Plants and Crops, Lab of Agrozoology, Ghent, Belgium
| | - Daniel Ariza
- Ghent University, Faculty of Bioscience Engineering, Department of Plants and Crops, Lab of Agrozoology, Ghent, Belgium
| | - Diego Cejas
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Guillaume Ghisbain
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Hanna Honchar
- Institute for Evolutionary Ecology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Vladimir G. Radchenko
- Institute for Evolutionary Ecology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Jakub Straka
- Charles University, Faculty of Science, Department of Zoology, Praha, Czech Republic
| | - Toshko Ljubomirov
- Institute of Biodiversity and Ecosystem Research—Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Thomas Lecocq
- Université de Lorraine, INRAE, URAFPA, Nancy, France
| | | | - Simone Flaminio
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Bologna, Italy
| | - Laura Bortolotti
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Bologna, Italy
| | - Reet Karise
- Estonian University of Life Sciences, Institute of Agricultural and Environmental Sciences, Tartu, Estonia
| | - Ivan Meeus
- Ghent University, Faculty of Bioscience Engineering, Department of Plants and Crops, Lab of Agrozoology, Ghent, Belgium
| | - Guy Smagghe
- Ghent University, Faculty of Bioscience Engineering, Department of Plants and Crops, Lab of Agrozoology, Ghent, Belgium
| | - Nicolas Vereecken
- Agroecology Lab, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Kevin Maebe
- Ghent University, Faculty of Bioscience Engineering, Department of Plants and Crops, Lab of Agrozoology, Ghent, Belgium
- *Correspondence: Kevin Maebe,
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Wilson TC, Rossetto M, Bain D, Yap JS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. AMERICAN JOURNAL OF BOTANY 2022; 109:1652-1671. [PMID: 36164832 PMCID: PMC9828017 DOI: 10.1002/ajb2.16074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
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Affiliation(s)
- Trevor C. Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and ScienceNSW Department of Planning and EnvironmentWollongongAustralia
| | - Jia‐Yee S. Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Peter D. Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Margaret L. Stimpson
- Botany, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia
| | - Peter H. Weston
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelong3125VictoriaAustralia
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24
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Wilson TC, Rossetto M, Bain D, Yap JYS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. AMERICAN JOURNAL OF BOTANY 2022. [PMID: 36164832 DOI: 10.5061/dryad.69p8cz94x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
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Affiliation(s)
- Trevor C Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and Science, NSW Department of Planning and Environment, Wollongong, Australia
| | - Jia-Yee S Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Peter D Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Margaret L Stimpson
- Botany, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Peter H Weston
- Plant Discovery and Evolution, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3125, Victoria, Australia
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25
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Genotyping-by-sequencing (GBS) as a tool for interspecies hybrid detection. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Genotyping-by-sequencing (GBS) is an extremely useful, modern and relatively inexpensive approach to discovering high-quality single-nucleotide polymorphisms (SNPs), which seem to be the most promising markers for identifying hybrid individuals between different species, especially those that can create backcrosses. In addition, GBS could become an invaluable tool in finding backcrosses, even several generations back. Its potential for the use of restriction enzymes and species is almost unlimited. It can also be successfully applied to species for which a reference genome is not established. In this paper, we describe the GBS technique, its main advantages and disadvantages, and the research carried out using this method concerning interspecies hybridisation and the identification of fertile hybrids. We also present future approaches that could be of interest in the context of the GBS method.
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26
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Brooks E, Slender AL, Cu S, Breed MF, Stangoulis JCR. A range-wide analysis of population structure and genomic variation within the critically endangered spiny daisy (Acanthocladium dockeri). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01468-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractUnderstanding population structure and genetic diversity is important for designing effective conservation strategies. As a critically endangered shrub, the six remaining extant populations of spiny daisy (Acanthocladium dockeri) are restricted to country roadsides in the mid-north of South Australia, where the species faces many ongoing abiotic and biotic threats to survival. Currently the spiny daisy is managed by selecting individuals from the extant populations and translocating them to establish insurance populations. However, there is little information available on the genetic differentiation between populations and diversity within source populations, which are essential components of planning translocations. To help fill this knowledge gap, we analysed population structure within and among all six of its known wild populations using 7,742 SNPs generated by a genotyping-by-sequencing approach. Results indicated that each population was strongly differentiated, had low levels of genetic diversity, and there was no evidence of inter-population gene flow. Individuals within each population were generally closely related, however, the Melrose population consisted entirely of clones. Our results suggest genetic rescue should be applied to wild spiny daisy populations to increase genetic diversity that will subsequently lead to greater intra-population fitness and adaptability. As a starting point, we suggest focussing on improving seed viability via inter-population crosses such as through hand pollination experiments to experimentally assess their sexual compatibility with the hope of increasing spiny daisy sexual reproduction and long-term reproductive fitness.
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27
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Sandhu KS, Shiv A, Kaur G, Meena MR, Raja AK, Vengavasi K, Mall AK, Kumar S, Singh PK, Singh J, Hemaprabha G, Pathak AD, Krishnappa G, Kumar S. Integrated Approach in Genomic Selection to Accelerate Genetic Gain in Sugarcane. PLANTS 2022; 11:plants11162139. [PMID: 36015442 PMCID: PMC9412483 DOI: 10.3390/plants11162139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022]
Abstract
Marker-assisted selection (MAS) has been widely used in the last few decades in plant breeding programs for the mapping and introgression of genes for economically important traits, which has enabled the development of a number of superior cultivars in different crops. In sugarcane, which is the most important source for sugar and bioethanol, marker development work was initiated long ago; however, marker-assisted breeding in sugarcane has been lagging, mainly due to its large complex genome, high levels of polyploidy and heterozygosity, varied number of chromosomes, and use of low/medium-density markers. Genomic selection (GS) is a proven technology in animal breeding and has recently been incorporated in plant breeding programs. GS is a potential tool for the rapid selection of superior genotypes and accelerating breeding cycle. However, its full potential could be realized by an integrated approach combining high-throughput phenotyping, genotyping, machine learning, and speed breeding with genomic selection. For better understanding of GS integration, we comprehensively discuss the concept of genetic gain through the breeder’s equation, GS methodology, prediction models, current status of GS in sugarcane, challenges of prediction accuracy, challenges of GS in sugarcane, integrated GS, high-throughput phenotyping (HTP), high-throughput genotyping (HTG), machine learning, and speed breeding followed by its prospective applications in sugarcane improvement.
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Affiliation(s)
- Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Aalok Shiv
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Mintu Ram Meena
- Regional Center, ICAR-Sugarcane Breeding Institute, Karnal 132001, India
| | - Arun Kumar Raja
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Krishnapriya Vengavasi
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashutosh Kumar Mall
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Praveen Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Jyotsnendra Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Govind Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashwini Dutt Pathak
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gopalareddy Krishnappa
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
- Correspondence: (G.K.); (S.K.)
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
- Correspondence: (G.K.); (S.K.)
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Laczkó L, Jordán S, Sramkó G. The
RadOrgMiner
pipeline: Automated genotyping of organellar loci from
RADseq
data. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Levente Laczkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
- Department of Metagenomics University of Debrecen Nagyerdei körút 98., Debrecen, H‐4032 Hungary
| | - Sándor Jordán
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- Juhász‐Nagy Pál Doctoral School University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
| | - Gábor Sramkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
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29
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Kurland S, Rafati N, Ryman N, Laikre L. Genomic dynamics of brown trout populations released to a novel environment. Ecol Evol 2022; 12:e9050. [PMID: 35813906 PMCID: PMC9251865 DOI: 10.1002/ece3.9050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/04/2022] [Accepted: 06/04/2022] [Indexed: 11/15/2022] Open
Abstract
Population translocations occur for a variety of reasons, from displacement due to climate change to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (F ST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole-genome sequencing of pooled DNA (Pool-seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool-seq can be used as an initial tool to monitor genome-wide effects.
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Affiliation(s)
- Sara Kurland
- Department of Zoology, Division of Population GeneticsStockholm UniversityStockholmSweden
| | - Nima Rafati
- Department of Medical Biochemistry and MicrobiologyNational Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Nils Ryman
- Department of Zoology, Division of Population GeneticsStockholm UniversityStockholmSweden
| | - Linda Laikre
- Department of Zoology, Division of Population GeneticsStockholm UniversityStockholmSweden
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30
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Mijangos JL, Gruber B, Berry O, Pacioni C, Georges A.
dartR
v2: an accessible genetic analysis platform for conservation, ecology, and agriculture. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Jose Luis Mijangos
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology University of Canberra Bruce ACT Australia
| | - Bernd Gruber
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology University of Canberra Bruce ACT Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Crawley WA Australia
| | - Carlo Pacioni
- Department of Environment, Land, Water, and Planning Arthur Rylah Institute for Environmental Research Heidelberg VIC Australia
- Environmental and Conservation Sciences School of Veterinary and Life Sciences, Murdoch University Murdoch WA Australia
| | - Arthur Georges
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology University of Canberra Bruce ACT Australia
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Iwanycki Ahlstrand N, Gopalakrishnan S, Vieira FG, Bieker VC, Meudt HM, Dunbar-Co S, Rothfels CJ, Martinez-Swatson KA, Maldonado C, Hassemer G, Shipunov A, Bowers MD, Gardner E, Xu M, Ghorbani A, Amano M, Grace OM, Pringle JS, Bishop M, Manzanilla V, Cotrim H, Blaney S, Zubov D, Choi HK, Yesil Y, Bennett B, Vimolmangkang S, El-Seedi HR, Staub PO, Li Z, Boldbaatar D, Hislop M, Caddy LJ, Muasya AM, Saslis-Lagoudakis CH, Gilbert MTP, Zerega NJC, Rønsted N. Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes. FRONTIERS IN PLANT SCIENCE 2022; 13:838166. [PMID: 35755675 PMCID: PMC9218338 DOI: 10.3389/fpls.2022.838166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species' establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.
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Affiliation(s)
| | - Shyam Gopalakrishnan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Filipe G. Vieira
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Vanessa C. Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | | | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | | | - Carla Maldonado
- Herbario Nacional de Bolivia, Universidad Mayor de San Andres, La Paz, Bolivia
| | | | - Alexey Shipunov
- Department of Biology, Minot University, Minot, ND, United States
| | - M. Deane Bowers
- Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
| | - Elliot Gardner
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Chicago, IL, United States
- Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
| | - Maonian Xu
- Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
| | - Abdolbaset Ghorbani
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Makoto Amano
- Natural History Museum and Institute, Chiba, Japan
| | - Olwen M. Grace
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Madonna Bishop
- Memorial University Botanical Garden, St. John’s, NL, Canada
| | | | - Helena Cotrim
- Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Sean Blaney
- Atlantic Canada Conservation Data Centre, Sackville, NB, Canada
| | | | - Hong-Keun Choi
- Department of Life Sciences, Ajou University, Suweon, South Korea
| | - Yeter Yesil
- Department of Pharmaceutical Botany, Istanbul University, Istanbul, Turkey
| | - Bruce Bennett
- Yukon Conservation Data Centre, Yukon Territory, YT, Canada
| | - Sornkanok Vimolmangkang
- Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand
| | - Hesham R. El-Seedi
- Pharmacognosy Group, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Peter O. Staub
- Department of Biomedical Science, University of Cagliari, Cagliari, Italy
| | - Zhu Li
- Chinese Academy of Sciences, Beijing, China
| | - Delgerbat Boldbaatar
- Department of Liver Center, National University of Mongolia, Ulaanbaatar, Mongolia
| | | | - Laura J. Caddy
- Botanical Garden, The University of British Columbia, Vancouver, BC, Canada
| | - A. Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | | | | | - Nyree J. C. Zerega
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Chicago, IL, United States
- Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
| | - Nina Rønsted
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- National Tropical Botanic Garden, Kaua‘i, HI, United States
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Waples RS, Ford MJ, Nichols K, Kardos M, Myers J, Thompson TQ, Anderson EC, Koch IJ, McKinney G, Miller MR, Naish K, Narum SR, O'Malley KG, Pearse DE, Pess GR, Quinn TP, Seamons TR, Spidle A, Warheit KI, Willis SC. Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon. J Hered 2022; 113:121-144. [PMID: 35575083 DOI: 10.1093/jhered/esab069] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/07/2021] [Indexed: 11/13/2022] Open
Abstract
The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California's equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | - Michael J Ford
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | - Krista Nichols
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | | | - Jim Myers
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | | | - Eric C Anderson
- Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Ilana J Koch
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Garrett McKinney
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
- Washington Department of Fish and Wildlife, Olympia, WA, USA
| | | | - Kerry Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WAUSA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | | | - Devon E Pearse
- Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - George R Pess
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | - Thomas P Quinn
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WAUSA
| | - Todd R Seamons
- Washington Department of Fish and Wildlife, Olympia, WA, USA
| | - Adrian Spidle
- Northwest Indian Fisheries Commission, Olympia, WA, USA
| | | | - Stuart C Willis
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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Wright AL, Anson JR, Leo V, Wright BR, Newsome TM, Grueber CE. Urban restoration of common species: population genetics of reintroduced native bush rats
Rattus fuscipes
in Sydney, Australia. Anim Conserv 2022. [DOI: 10.1111/acv.12787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. L. Wright
- School of Life and Environmental Sciences, Faculty of Science The University of Sydney Sydney NSW Australia
| | - J. R. Anson
- Australian Wildlife Conservancy Perth WA Australia
| | - V. Leo
- Australian Wildlife Conservancy Perth WA Australia
| | - B. R. Wright
- School of Life and Environmental Sciences, Faculty of Science The University of Sydney Sydney NSW Australia
- Sydney School of Veterinary Sciences The University of Sydney Faculty of Science, The University of Sydney Sydney NSW Australia
| | - T. M. Newsome
- School of Life and Environmental Sciences, Faculty of Science The University of Sydney Sydney NSW Australia
| | - C. E. Grueber
- School of Life and Environmental Sciences, Faculty of Science The University of Sydney Sydney NSW Australia
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Nazir M, Mahajan R, Mansoor S, Rasool S, Mir RA, Singh R, Thakral V, Kumar V, Sofi PA, El-Serehy HA, Hefft DI, Zargar SM. Identification of QTLs/ Candidate Genes for Seed Mineral Contents in Common Bean (Phaseolus vulgaris L.) Through Genotyping-by-Sequencing. Front Genet 2022; 13:750814. [PMID: 35391791 PMCID: PMC8982075 DOI: 10.3389/fgene.2022.750814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Throughout the ages, the common bean has been consumed by humanity as an important food staple crop and source of nutrition on a global scale. Since its domestication, a wide spectrum of phenotypic and genotypic investigations have been carried out to unravel the potential of this crop and to understand the process of nutrient accumulation along with other desirable characteristics. The common bean is one of the essential legume crops due to its high protein and micronutrient content. The balance in micronutrients is critical for the growth and development of plants as well as humans. Iron (Fe), Zinc (Zn), Copper (Cu), Manganese (Mn), Magnesium (Mg), Calcium (Ca), and Molybdenum (Mo) are some of the important micronutrients present in legumes. Thus, we aimed to investigate the quantitative trait loci’s (QTLs)/single nucleotide polymorphisms (SNPs) to identify the candidate genes associated with micronutrients through genotyping by sequencing (GBS). In our investigation, through GBS we identified SNPs linked with traits and assessed seven micronutrients in 96 selected common bean genotypes for screening nutritionally rich genotypes. Among 96399 SNPs total identified through GBS, 113 SNPs showed significant phenotypic variance, ranging from 13.50 to 21.74%. SNPs associated with most of the seed micronutrients (Mg, Mn, Fe, Ca, Cu) were found on chr3 & chr11 (Mg, Mn, Mo, Ca, Zn). The findings from this study could be used for haplotype-based selection of nutritionally rich genotypes and for marker-assisted genetic enhancement of the common bean. Further, the identified SNPs for candidate genes/transporters associated with micronutrient content may pave the way for the enrichment of seeds by employing genomics-assisted breeding programs.
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Affiliation(s)
- Muslima Nazir
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Reetika Mahajan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Sheikh Mansoor
- Division of Biochemistry, FBSc, Sher-e Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Sheezan Rasool
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | | | - Ravinder Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Vandana Thakral
- National Agr Food Biotechnology Institute (NABI), Mohali, India
| | - Virender Kumar
- National Agr Food Biotechnology Institute (NABI), Mohali, India
| | - Parvaze A. Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Hamed A. El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Daniel Ingo Hefft
- University Centre Reaseheath, Reaseheath College, Nantwich, United Kingdom
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
- *Correspondence: Sajad Majeed Zargar,
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Van der Heyden H, Dutilleul P, Duceppe M, Bilodeau GJ, Charron J, Carisse O. Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada. MOLECULAR PLANT PATHOLOGY 2022; 23:339-354. [PMID: 34921486 PMCID: PMC8828460 DOI: 10.1111/mpp.13158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 05/19/2023]
Abstract
Several Peronospora species are carried by wind over short and long distances, from warmer climates where they survive on living plants to cooler climates. In eastern Canada, this annual flow of sporangia was thought to be the main source of Peronospora destructor responsible for onion downy mildew. However, the results of a recent study showed that the increasing frequency of onion downy mildew epidemics in eastern Canada is associated with warmer autumns, milder winters, and previous year disease severity, suggesting overwintering of the inoculum in an area where the pathogen is not known to be endogenous. In this study, genotyping by sequencing was used to investigate the population structure of P. destructor at the landscape scale. The study focused on a particular region of southwestern Québec-Les Jardins de Napierville-to determine if the populations were clonal and regionally differentiated. The data were characterized by a high level of linkage disequilibrium, characteristic of clonal organisms. Consequently, the null hypothesis of random mating was rejected when tested on predefined or nonpredefined populations, indicating that linkage disequilibrium was not a function of population structure and suggesting a mixed reproduction mode. Discriminant analysis of principal components performed with predefined population assignment allowed grouping P. destructor isolates by geographical regions, while analysis of molecular variance confirmed that this genetic differentiation was significant at the regional level. Without using a priori population assignment, isolates were clustered into four genetic clusters. These results represent a baseline estimate of the genetic diversity and population structure of P. destructor.
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Affiliation(s)
- Hervé Van der Heyden
- Cie de Recherche PhytodataSherringtonQuébecCanada
- Department of Plant ScienceMcGill UniversityMontrealQuébecCanada
| | - Pierre Dutilleul
- Department of Plant ScienceMcGill UniversityMontrealQuébecCanada
| | | | | | | | - Odile Carisse
- Agriculture and Agri‐Food CanadaSt‐Jean‐sur‐RichelieuQuébecCanada
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Conklin JR, Verkuil YI, Battley PF, Hassell CJ, Ten Horn J, Johnson JA, Tomkovich PS, Baker AJ, Piersma T, Fontaine MC. Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium. Mol Ecol 2022; 31:2124-2139. [PMID: 35106871 PMCID: PMC9545425 DOI: 10.1111/mec.16379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/13/2021] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
Abstract
Present‐day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus, is an arctic‐breeding, long‐distance migratory shorebird with six recognized subspecies defined by differences in morphology, migration behavior, and annual cycle phenology, in a global distribution thought to have arisen just since the last glacial maximum (LGM). We used nextRAD sequencing of 10,881 single‐nucleotide polymorphisms (SNPs) to assess the neutral genetic structure and phylogeographic history of 172 red knots representing all known global breeding populations. Using population genetics approaches, including model‐based scenario‐testing in an approximate Bayesian computation (ABC) framework, we infer that red knots derive from two main lineages that diverged ca. 34,000 years ago, and thus most probably persisted at the LGM in both Palearctic and Nearctic refugia, followed by at least two instances of secondary contact and admixture. Within two Beringian subspecies (C. c. roselaari and rogersi), we detected previously unknown genetic structure among sub‐populations sharing a migratory flyway, reflecting additional complexity in the phylogeographic history of the region. Conversely, we found very weak genetic differentiation between two Nearctic populations (rufa and islandica) with clearly divergent migratory phenotypes and little or no apparent contact throughout the annual cycle. Together, these results suggest that relative gene flow among migratory populations reflects a complex interplay of historical, geographical, and ecological factors.
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Affiliation(s)
- Jesse R Conklin
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Yvonne I Verkuil
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Phil F Battley
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Palmerston North, 4442, New Zealand
| | - Chris J Hassell
- Global Flyway Network, PO Box 3089, Broome, WA, 6725, Australia
| | - Job Ten Horn
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - James A Johnson
- U.S. Fish & Wildlife Service, Migratory Bird Management, 1011 E. Tudor Road, MS 201, Anchorage, Alaska, 99503, USA
| | - Pavel S Tomkovich
- Zoological Museum, Moscow MV Lomonosov State University, Bolshaya Nikitskaya Str. 6, Moscow, 125009, Russia
| | - Allan J Baker
- Department of Natural History, Royal Ontario Museum, 100 Queens Park, Toronto, ON, M5S 2C6, Canada
| | - Theunis Piersma
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.,Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Michaël C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.,MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France.,Montpellier Ecology and Evolution of Diseases Network (MEEDiN), Montpellier, France
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37
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Linking genetic, morphological, and behavioural divergence between inland island and mainland deer mice. Heredity (Edinb) 2022; 128:97-106. [PMID: 34952930 PMCID: PMC8814197 DOI: 10.1038/s41437-021-00492-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/03/2023] Open
Abstract
The island syndrome hypothesis (ISH) stipulates that, as a result of local selection pressures and restricted gene flow, individuals from island populations should differ from individuals within mainland populations. Specifically, island populations are predicted to contain individuals that are larger, less aggressive, more sociable, and that invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here, using a novel set of genome-wide SNP markers in wild deer mice (Peromyscus maniculatus) we conducted a genomic assessment of predictions underlying the ISH in an inland riverine island system: analysing island-mainland population structure, and quantifying heritability of phenotypes thought to underlie the ISH. We found clear genomic differentiation between the island and mainland populations and moderate to high marker-based heritability estimates for overall variation in traits previously found to differ in line with the ISH between mainland and island locations. FST outlier analyses highlighted 12 loci associated with differentiation between mainland and island populations. Together these results suggest that the island populations examined are on independent evolutionary trajectories, the traits considered have a genetic basis (rather than phenotypic variation being solely due to phenotypic plasticity). Coupled with the previous results showing significant phenotypic differentiation between the island and mainland groups in this system, this study suggests that the ISH can hold even on a small spatial scale.
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Brookes B, Jeon H, Derry AM, Post JR, Rogers SM, Humphries S, Fraser DJ. Neutral and adaptive drivers of genomic change in introduced brook trout ( Salvelinus fontinalis) populations revealed by pooled sequencing. Ecol Evol 2022; 12:e8584. [PMID: 35154655 PMCID: PMC8820109 DOI: 10.1002/ece3.8584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/07/2022] [Indexed: 12/22/2022] Open
Abstract
Understanding the drivers of successful species invasions is important for conserving native biodiversity and for mitigating the economic impacts of introduced species. However, whole-genome resolution investigations of the underlying contributions of neutral and adaptive genetic variation in successful introductions are rare. Increased propagule pressure should result in greater neutral genetic variation, while environmental differences should elicit selective pressures on introduced populations, leading to adaptive differentiation. We investigated neutral and adaptive variation among nine introduced brook trout (Salvelinus fontinalis) populations using whole-genome pooled sequencing. The populations inhabit isolated alpine lakes in western Canada and descend from a common source, with an average of ~19 (range of 7-41) generations since introduction. We found some evidence of bottlenecks without recovery, no strong evidence of purifying selection, and little support that varying propagule pressure or differences in local environments shaped observed neutral genetic variation differences. Putative adaptive loci analysis revealed nonconvergent patterns of adaptive differentiation among lakes with minimal putatively adaptive loci (0.001%-0.15%) that did not correspond with tested environmental variables. Our results suggest that (i) introduction success is not always strongly influenced by genetic load; (ii) observed differentiation among introduced populations can be idiosyncratic, population-specific, or stochastic; and (iii) conservatively, in some introduced species, colonization barriers may be overcome by support through one aspect of propagule pressure or benign environmental conditions.
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Affiliation(s)
- Brent Brookes
- Department of BiologyConcordia UniversityMontréalQCCanada
| | - Hyung‐Bae Jeon
- Department of BiologyConcordia UniversityMontréalQCCanada
| | - Alison M. Derry
- Département des sciences biologiquesUniversité du Québec à MontréalMontréalQCCanada
| | - John R. Post
- Department of BiologyUniversity of CalgaryCalgaryABCanada
| | - Sean M. Rogers
- Department of BiologyUniversity of CalgaryCalgaryABCanada
| | - Shelley Humphries
- Parks CanadaNatural Resource Management BranchRadium Hot SpringsBCCanada
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Genomic Hatchery Introgression in Brown Trout (Salmo trutta L.): Development of a Diagnostic SNP Panel for Monitoring the Impacted Mediterranean Rivers. Genes (Basel) 2022; 13:genes13020255. [PMID: 35205298 PMCID: PMC8872556 DOI: 10.3390/genes13020255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/05/2022] [Accepted: 01/27/2022] [Indexed: 02/01/2023] Open
Abstract
Brown trout (Salmo trutta L.) populations have been restocked during recent decades to satisfy angling demand and counterbalance the decline of wild populations. Millions of fertile brown trout individuals were released into Mediterranean and Atlantic rivers from hatcheries with homogeneous central European stocks. Consequently, many native gene pools have become endangered by introgressive hybridization with those hatchery stocks. Different genetic tools have been used to identify and evaluate the degree of introgression starting from pure native and restocking reference populations (e.g., LDH-C* locus, microsatellites). However, due to the high genetic structuring of brown trout, the definition of the "native pool" is hard to achieve. Additionally, although the LDH-C* locus is useful for determining the introgression degree at the population level, its consistency at individual level is far from being accurate, especially after several generations were since releases. Accordingly, the development of a more powerful and cost-effective tool is essential for an appropriate monitoring to recover brown-trout-native gene pools. Here, we used the 2b restriction site-associated DNA sequencing (2b-RADseq) and Stacks 2 with a reference genome to identify single-nucleotide polymorphisms (SNPs) diagnostic for hatchery-native fish discrimination in the Atlantic and Mediterranean drainages of the Iberian Peninsula. A final set of 20 SNPs was validated in a MassARRAY® System genotyping by contrasting data with the whole SNP dataset using samples with different degree of introgression from those previously recorded. Heterogeneous introgression impact was confirmed among and within river basins, and was the highest in the Mediterranean Slope. The SNP tool reported here should be assessed in a broader sample scenario in Southern Europe considering its potential for monitoring recovery plans.
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40
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Recombinant inbred lines and next-generation sequencing enable rapid identification of candidate genes involved in morphological and agronomic traits in foxtail millet. Sci Rep 2022; 12:218. [PMID: 34997038 PMCID: PMC8742101 DOI: 10.1038/s41598-021-04012-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. We successfully constructed a linkage map using flexible ddRAD-seq with parents and RILs and detected major QTLs for each of three traits: leaf sheath colors, spikelet-tipped bristles (stb), and days to heading (DTH). (1) For leaf sheath colors, we identified the C gene on chromosome IV. (2) We identified a homeobox (HOX14) gene for stb on chromosome II, which shows homology with HvVrs1 in barley. (3) Finally, we identified a QTL with a large effect on DTH on chromosome II. A parent of the RILs from Taiwan and Yugu1 had a Harbinger-like TE in intron 3 of this gene. We also investigated the geographical distribution of the TE insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones.
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Chen Z, Grossfurthner L, Loxterman JL, Masingale J, Richardson BA, Seaborn T, Smith B, Waits LP, Narum SR. Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies. Evol Appl 2022; 15:3-21. [PMID: 35126645 PMCID: PMC8792483 DOI: 10.1111/eva.13335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/01/2022] Open
Abstract
The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.
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Affiliation(s)
- Zhongqi Chen
- Aquaculture Research InstituteUniversity of IdahoHagermanIdahoUSA
| | - Lukas Grossfurthner
- Bioinformatics and Computational Biology Graduate ProgramUniversity of IdahoHagermanIdahoUSA
| | - Janet L. Loxterman
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | | | | | - Travis Seaborn
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Brandy Smith
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
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Sinn BT, Simon SJ, Santee MV, DiFazio SP, Fama NM, Barrett CF. ISSRseq: An extensible method for reduced representation sequencing. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Brandon T. Sinn
- Department of Biology and Earth Science Otterbein University Westerville OH USA
- Department of Biology West Virginia University Morgantown WV USA
| | - Sandra J. Simon
- Department of Biology West Virginia University Morgantown WV USA
- Institute for Sustainability, Energy, and Environment (ISEE) University of Illinois at Urbana‐Champaign Urbana IL USA
- Department of Biology West Virginia University Institute of Technology Beckley WV USA
| | | | | | - Nicole M. Fama
- Department of Biology West Virginia University Morgantown WV USA
- Genetic Immunotherapy Section National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MD USA
| | - Craig F. Barrett
- Department of Biology West Virginia University Morgantown WV USA
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Wang L, Yang J, Zhang H, Tao Q, Zhang Y, Dang Z, Zhang F, Luo Z. Sequence coverage required for accurate genotyping by sequencing in polyploid species. Mol Ecol Resour 2021; 22:1417-1426. [PMID: 34826191 DOI: 10.1111/1755-0998.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/29/2022]
Abstract
Polyploidy plays an important role in the evolution of eukaryotes, especially for flowering plants. Many of ecologically or agronomically important plant or crop species are polyploids, including sycamore maple (tetraploid), the world second and third largest food crops wheat (hexaploid) and potato (tetraploid) as well as economically important aquaculture animals such as Atlantic salmon and trout. The next generation sequencing data enables to allocate genotype at a sequence variant site, known as genotyping by sequencing (GBS). GBS has stimulated enormous interests in population based genomics studies in almost all diploid and many polyploid organisms. DNA sequence polymorphisms are codominant and thus fully informative about the underlying genotype at the polymorphic site, making GBS a straightforward task in diploids. However, sequence data may usually be uninformative in polyploid species, making GBS a far more challenging task in polyploids. This paper presents novel and rigorous statistical methods for predicting the number of sequence reads needed to ensure accurate GBS at a polymorphic site bared by the reads in polyploids and shows that a dozen of reads can ensure a probability of 95% to recover all constituent alleles of any tetraploid genotype but several hundreds of reads are needed to accurately uncover the genotype with probability confidence of 90%, subverting the proposition of GBS using low coverage sequence data in the literature. The theoretical prediction was tested by use of RAD-seq data from tetraploid potato cultivars. The paper provides polyploid experimentalists with theoretical guides and methods for designing and conducting their sequence-based studies.
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Affiliation(s)
- Lin Wang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jixuan Yang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Zhang
- Department of Statistics and Finance, University of Science and Technology of China, Hefei, China
| | - Qin Tao
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuxin Zhang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhenyu Dang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
| | - Fengjun Zhang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
| | - Zewei Luo
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China.,School of Biosciences, University of Birmingham, Birmingham, UK
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Hauser SS, Athrey G, Leberg PL. Waste not, want not: Microsatellites remain an economical and informative technology for conservation genetics. Ecol Evol 2021; 11:15800-15814. [PMID: 34824791 PMCID: PMC8601879 DOI: 10.1002/ece3.8250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/07/2021] [Accepted: 09/16/2021] [Indexed: 11/07/2022] Open
Abstract
Comparisons of microsatellites and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, questioning the continued utility of microsatellites in population and landscape genetics. Yet, highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated previous analyses that used microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.
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Affiliation(s)
- Samantha S. Hauser
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisianaUSA
| | - Giridhar Athrey
- Faculty of Ecology and Evolutionary BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Paul L. Leberg
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisianaUSA
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Schielzeth H, Wolf JBW. Community genomics: a community-wide perspective on within-species genetic diversity. AMERICAN JOURNAL OF BOTANY 2021; 108:2108-2111. [PMID: 34767249 DOI: 10.1002/ajb2.1796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Holger Schielzeth
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Germany
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Germany
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Sebastian W, Sukumaran S, Abdul Azeez S, Muraleedharan KR, Dinesh Kumar PK, Zacharia PU, Gopalakrishnan A. Genomic investigations provide insights into the mechanisms of resilience to heterogeneous habitats of the Indian Ocean in a pelagic fish. Sci Rep 2021; 11:20690. [PMID: 34667208 PMCID: PMC8526693 DOI: 10.1038/s41598-021-00129-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/05/2021] [Indexed: 11/08/2022] Open
Abstract
The adaptive genetic variation in response to heterogeneous habitats of the Indian Ocean was investigated in the Indian oil sardine using ddRAD sequencing to understand the subpopulation structure, stock complexity, mechanisms of resilience, and vulnerability in the face of climate change. Samples were collected from different ecoregions of the Indian ocean and ddRAD sequencing was carried out. Population genetic analyses revealed that samples from the Gulf of Oman significantly diverged from other Indian Ocean samples. SNP allele-environment correlation revealed the presence of candidate loci correlated with the environmental variables like annual sea surface temperature, chlorophyll-a, and dissolved oxygen concentration which might represent genomic regions allegedly diverging as a result of local adaptation. Larval dispersal modelling along the southwest coast of India indicated a high dispersal rate. The two major subpopulations (Gulf of Oman and Indian) need to be managed regionally to ensure the preservation of genetic diversity, which is crucial for climatic resilience.
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Affiliation(s)
- Wilson Sebastian
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
| | - Sandhya Sukumaran
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - S Abdul Azeez
- CSIR-National Institute of Oceanography, Regional Centre Kochi, Dr Salim Ali Road, Post Box No. 1913, Kochi, Kerala, India
| | - K R Muraleedharan
- CSIR-National Institute of Oceanography, Regional Centre Kochi, Dr Salim Ali Road, Post Box No. 1913, Kochi, Kerala, India
| | - P K Dinesh Kumar
- CSIR-National Institute of Oceanography, Regional Centre Kochi, Dr Salim Ali Road, Post Box No. 1913, Kochi, Kerala, India
| | - P U Zacharia
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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Foster Y, Dutoit L, Grosser S, Dussex N, Foster BJ, Dodds KG, Brauning R, Van Stijn T, Robertson F, McEwan JC, Jacobs JME, Robertson BC. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. G3 (BETHESDA, MD.) 2021; 11:jkab307. [PMID: 34542587 PMCID: PMC8527487 DOI: 10.1093/g3journal/jkab307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.
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Affiliation(s)
- Yasmin Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brodie J Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ken G Dodds
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Tracey Van Stijn
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - John C McEwan
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | | | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
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Paula DP. Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution. NEOTROPICAL ENTOMOLOGY 2021; 50:679-696. [PMID: 34374956 DOI: 10.1007/s13744-021-00895-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.
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Neinavaie F, Ibrahim-Hashim A, Kramer AM, Brown JS, Richards CL. The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.
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50
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Forsdick NJ, Martini D, Brown L, Cross HB, Maloney RF, Steeves TE, Knapp M. Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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