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Fuentes‐Pardo AP, Farrell ED, Pettersson ME, Sprehn CG, Andersson L. The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel ( Trachurus trachurus). Evol Appl 2023; 16:1201-1219. [PMID: 37360028 PMCID: PMC10286234 DOI: 10.1111/eva.13559] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 04/21/2023] [Accepted: 05/07/2023] [Indexed: 06/28/2023] Open
Abstract
Understanding how populations adapt to their environment is increasingly important to prevent biodiversity loss due to overexploitation and climate change. Here we studied the population structure and genetic basis of local adaptation of Atlantic horse mackerel, a commercially and ecologically important marine fish that has one of the widest distributions in the eastern Atlantic. We analyzed whole-genome sequencing and environmental data of samples collected from the North Sea to North Africa and the western Mediterranean Sea. Our genomic approach indicated low population structure with a major split between the Mediterranean Sea and the Atlantic Ocean and between locations north and south of mid-Portugal. Populations from the North Sea are the most genetically distinct in the Atlantic. We discovered that most population structure patterns are driven by a few highly differentiated putatively adaptive loci. Seven loci discriminate the North Sea, two the Mediterranean Sea, and a large putative inversion (9.9 Mb) on chromosome 21 underlines the north-south divide and distinguishes North Africa. A genome-environment association analysis indicates that mean seawater temperature and temperature range, or factors correlated to them, are likely the main environmental drivers of local adaptation. Our genomic data broadly support the current stock divisions, but highlight areas of potential mixing, which require further investigation. Moreover, we demonstrate that as few as 17 highly informative SNPs can genetically discriminate the North Sea and North African samples from neighboring populations. Our study highlights the importance of both, life history and climate-related selective pressures in shaping population structure patterns in marine fish. It also supports that chromosomal rearrangements play a key role in local adaptation with gene flow. This study provides the basis for more accurate delineation of the horse mackerel stocks and paves the way for improving stock assessments.
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Affiliation(s)
| | - Edward D. Farrell
- EDF Scientific LimitedCorkIreland
- Killybegs Fishermen's OrganisationDonegalIreland
| | - Mats E. Pettersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - C. Grace Sprehn
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
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2
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Farrell ED, Andersson L, Bekkevold D, Campbell N, Carlsson J, Clarke MW, Egan A, Folkvord A, Gras M, Lusseau SM, Mackinson S, Nolan C, O'Connell S, O'Malley M, Pastoors M, Pettersson ME, White E. A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b-c. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220453. [PMID: 36133150 PMCID: PMC9449477 DOI: 10.1098/rsos.220453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Atlantic herring in International Council for Exploration of the Sea (ICES) Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographical delineators. Outside of spawning the populations form mixed aggregations, which are the subject of acoustic surveys. The inability to distinguish the populations has prevented the development of separate survey indices and separate stock assessments. A panel of 45 single-nucleotide polymorphisms, derived from whole-genome sequencing, were used to genotype 3480 baseline spawning samples (2014-2021). A temporally stable baseline comprising 2316 herring from populations known to inhabit Division 6.a was used to develop a genetic assignment method, with a self-assignment accuracy greater than 90%. The long-term temporal stability of the assignment model was validated by assigning archive (2003-2004) baseline samples (270 individuals) with a high level of accuracy. Assignment of non-baseline samples (1514 individuals) from Divisions 6.a, 7.b-c indicated previously unrecognized levels of mixing of populations outside of the spawning season. The genetic markers and assignment models presented constitute a 'toolbox' that can be used for the assignment of herring caught in mixed survey and commercial catches in Division 6.a into their population of origin with a high level of accuracy.
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Affiliation(s)
- Edward D. Farrell
- EDF Scientific Limited, Rathaha, Ladysbridge, Cork, Ireland
- Area 52 Research Group, School of Biology and Environmental Science/Earth Institute, Science Centre West, University College Dublin, Dublin, Ireland
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Neil Campbell
- Marine Scotland Science, 375 Victoria Road, Aberdeen AB11 9DB, Scotland
| | - Jens Carlsson
- Area 52 Research Group, School of Biology and Environmental Science/Earth Institute, Science Centre West, University College Dublin, Dublin, Ireland
| | | | - Afra Egan
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
| | - Arild Folkvord
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Michaël Gras
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Susan Mærsk Lusseau
- Marine Scotland Science, 375 Victoria Road, Aberdeen AB11 9DB, Scotland
- National Institute of Aquatic Resources, Willemoesvej 2, Hovedbygning, 067, 9850 Hirtshals, Denmark
| | - Steven Mackinson
- Scottish Pelagic Fishermen's Association, Heritage House, 135-139 Shore Street, Fraserburgh, Aberdeenshire, Scotland
| | - Cormac Nolan
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
| | - Steven O'Connell
- Marine Scotland Science, 375 Victoria Road, Aberdeen AB11 9DB, Scotland
| | | | - Martin Pastoors
- Pelagic Freezer-trawler Association, Louis Braillelaan 80, 2719 EK Zoetermeer, The Netherlands
| | - Mats E. Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Emma White
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
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3
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Baptista L, Meimberg H, Ávila SP, Santos AM, Curto M. Dispersal ability, habitat characteristics, and sea-surface circulation shape population structure of Cingula trifasciata (Gastropoda: Rissoidae) in the remote Azores Archipelago. BMC Ecol Evol 2021; 21:128. [PMID: 34157972 PMCID: PMC8218459 DOI: 10.1186/s12862-021-01862-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/28/2021] [Indexed: 12/14/2022] Open
Abstract
Background In the marine realm, dispersal ability is among the major factors shaping the distribution of species. In the Northeast Atlantic Ocean, the Azores Archipelago is home to a multitude of marine invertebrates which, despite their dispersal limitations, maintain gene flow among distant populations, with complex evolutionary and biogeographic implications. The mechanisms and factors underlying the population dynamics and genetic structure of non-planktotrophic gastropods within the Azores Archipelago and related mainland populations are still poorly understood. The rissoid Cingula trifasciata is herewith studied to clarify its population structure in the Northeast Atlantic Ocean and factors shaping it, with a special focus in intra-archipelagic dynamics. Results Coupling microsatellite genotyping by amplicon sequencing (SSR-GBAS) and mitochondrial datasets, our results suggest the differentiation between insular and continental populations of Cingula trifasciata, supporting previously raised classification issues and detecting potential cryptic diversity. The finding of connectivity between widely separated populations was startling. In unique ways, dispersal ability, habitat type, and small-scale oceanographic currents appear to be the key drivers of C. trifasciata’s population structure in the remote Azores Archipelago. Dispersal as non-planktotrophic larvae is unlikely, but its small-size adults easily engage in rafting. Although the typical habitat of C. trifasciata, with low hydrodynamics, reduces the likelihood of rafting, individuals inhabiting algal mats are more prone to dispersal. Sea-surface circulation might create dispersal pathways for rafts, even between widely separated populations/islands. Conclusions Our results show that gene flow of a marine non-planktotrophic gastropod within a remote archipelago can reveal unanticipated patterns, such that the understanding of life in such areas is far from well-understood. We expect this work to be the starting of the application of SSR-GBAS in other non-model marine invertebrates, providing insights on their population dynamics at distinct geographical scales and on hidden diversity. How transversal is the role played by the complex interaction between functional traits, ecological features, and sea-surface circulation in the population structure of marine invertebrates can be further addressed by expanding this approach to more taxa. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01862-1.
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Affiliation(s)
- L Baptista
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria. .,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-801, Ponta Delgada, Azores, Portugal. .,MPB-Marine Palaeontology and Biogeography Lab, Universidade Dos Açores, 9501-801, Ponta Delgada, Azores, Portugal. .,Faculdade de Ciências da Universidade do Porto, Rua Do Campo Alegre, 1021/1055, 4169-007, Porto, Portugal.
| | - H Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - S P Ávila
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-801, Ponta Delgada, Azores, Portugal.,MPB-Marine Palaeontology and Biogeography Lab, Universidade Dos Açores, 9501-801, Ponta Delgada, Azores, Portugal.,Faculdade de Ciências da Universidade do Porto, Rua Do Campo Alegre, 1021/1055, 4169-007, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências e Tecnologia, Universidade Dos Açores, 9501-801, Ponta Delgada, Azores, Portugal
| | - A M Santos
- Faculdade de Ciências da Universidade do Porto, Rua Do Campo Alegre, 1021/1055, 4169-007, Porto, Portugal.,Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, no. 7, 4485-661, Vairão, Portugal
| | - M Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.,MARE, Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
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4
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Lanner J, Gstöttenmayer F, Curto M, Geslin B, Huchler K, Orr MC, Pachinger B, Sedivy C, Meimberg H. Evidence for multiple introductions of an invasive wild bee species currently under rapid range expansion in Europe. BMC Ecol Evol 2021; 21:17. [PMID: 33546597 PMCID: PMC7866639 DOI: 10.1186/s12862-020-01729-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Invasive species are increasingly driving biodiversity decline, and knowledge of colonization dynamics, including both drivers and dispersal modes, are important to prevent future invasions. The bee species Megachile sculpturalis (Hymenoptera: Megachilidae), native to East-Asia, was first recognized in Southeast-France in 2008, and has since spread throughout much of Europe. The spread is very fast, and colonization may result from multiple fronts. RESULT To track the history of this invasion, codominant markers were genotyped using Illumina sequencing and the invasion history and degree of connectivity between populations across the European invasion axis were investigated. Distinctive genetic clusters were detected with east-west differentiations in Middle-Europe. CONCLUSION We hypothesize that the observed cluster formation resulted from multiple, independent introductions of the species to the European continent. This study draws a first picture of an early invasion stage of this wild bee and forms a foundation for further investigations, including studies of the species in their native Asian range and in the invaded range in North America.
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Affiliation(s)
- Julia Lanner
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Straße 33, 1180, Vienna, Austria.
| | - Fabian Gstöttenmayer
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Wagramer Straße 5, 1400, Vienna, Austria
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Straße 33, 1180, Vienna, Austria.,MARE Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Camop Grande, 1749-016, Lisboa, Portugal
| | - Benoît Geslin
- IMBE, Aix Marseille Université, Avignon Université, CNRS, Marseille, France
| | - Katharina Huchler
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Michael C Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Beijing, 100101, China
| | - Bärbel Pachinger
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | | | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Straße 33, 1180, Vienna, Austria
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5
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Motahari B, Shabanian N, Rahmani MS, Mohammad-Hasani F. Genetic diversity and genetic structure of Acer monspessulanum L. across Zagros forests of Iran using molecular markers. Gene 2020; 769:145245. [PMID: 33069803 DOI: 10.1016/j.gene.2020.145245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 11/24/2022]
Abstract
Acer monspessulanum L. is an important tree species found in the temperate Zagros forests of Iran. Despite its importance, the long-term persistence of its small and fragmented populations is jeopardised by genetic erosion and hence, monitoring its genetic resource and variability is practically required for providing conservation measures of the species germplasm in Zagros woodland ecosystem. The present study aimed to provide the first data on genetic diversity and genetic differentiation pattern of 19 natural populations comprising 240 individuals of A. monspessulanum across its growing area in Zagros forests using three molecular tools including inter-simple sequence repeats (ISSR), start codon targeted (SCoT), and simple sequence repeat (SSR). In total, ISSR and SCoT primers generated a total of 141 and 121 clear and scorable bands for analysis with the polymorphism rate of 90.50 and 90.02% and a mean of 10.85 and 11 fragments per marker, respectively. In addition, 73 alleles were achieved using 10 polymorphic SSR loci from the studied accessions with 100% polymorphism, ranging between 5 and 10 alleles per locus. Average percentage of polymorphic alleles per population for ISSR, SCoT, and SSR data was 84.02%, 83%, and 100%, respectively, and generally, Nei's gene diversity (H) and Shannon's index of diversity (I) values for all populations demonstrated moderate to high levels of genetic diversity (H = 0.267-0.707; I = 0.38-1.38). The AMOVA results of the three marker systems attributed higher genetic variation to individuals within in each population than among populations. Furthermore, overall GST value for all populations detected the moderate to high levels of genetic differentiation, indicating a limited gene flow occurrence among the populations. STRUCTURE analysis (K = 5) clustered the populations into four to five distinct groups, in accordance with geographical distances. These results could represent an important contribution for effective germplasm characterization and could be eventually used in in situ or ex situ conservation of A. monspessulanum genetic resources.
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Affiliation(s)
- Behnaz Motahari
- Laboratory of Forest Tree Genetics, Department of Forestry, Faculty of Natural Resources, University of Kurdistan, Sanandaj 66177-1-5175, Iran
| | - Naghi Shabanian
- Department of Forestry, Faculty of Natural Resources, University of Kurdistan, Sanandaj 66177-1-5175, Iran; The Center for Research and Development of Northern Zagros Forests, University of Kurdistan, Baneh 220, Iran.
| | - Mohammad-Shafie Rahmani
- Laboratory of Forest Tree Genetics, Department of Forestry, Faculty of Natural Resources, University of Kurdistan, Sanandaj 66177-1-5175, Iran.
| | - Farshad Mohammad-Hasani
- Laboratory of Forest Tree Genetics, Department of Forestry, Faculty of Natural Resources, University of Kurdistan, Sanandaj 66177-1-5175, Iran
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6
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The Potential of HTS Approaches for Accurate Genotyping in Grapevine ( Vitis vinifera L.). Genes (Basel) 2020; 11:genes11080917. [PMID: 32785184 PMCID: PMC7464945 DOI: 10.3390/genes11080917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 11/16/2022] Open
Abstract
The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price.
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Lepais O, Chancerel E, Boury C, Salin F, Manicki A, Taillebois L, Dutech C, Aissi A, Bacles CF, Daverat F, Launey S, Guichoux E. Fast sequence-based microsatellite genotyping development workflow. PeerJ 2020; 8:e9085. [PMID: 32411534 PMCID: PMC7204839 DOI: 10.7717/peerj.9085] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022] Open
Abstract
Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.
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Affiliation(s)
- Olivier Lepais
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, France
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | | | - Aurélie Manicki
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | - Laura Taillebois
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | - Cecile F.E. Bacles
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | - Sophie Launey
- INRAE, Agrocampus Ouest, ESE, Ecology and Ecosystem Health, Rennes, France
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Donaldson ME, Jackson K, Rico Y, Sayers JB, Ethier DM, Kyle CJ. Development of a massively parallel, genotyping-by-sequencing assay in American badger (Taxidea taxus) highlights the need for careful validation when working with low template DNA. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01146-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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9
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Maduna SN, Vivian-Smith A, Jónsdóttir ÓDB, Imsland AKD, Klütsch CFC, Nyman T, Eiken HG, Hagen SB. Genome- and transcriptome-derived microsatellite loci in lumpfish Cyclopterus lumpus: molecular tools for aquaculture, conservation and fisheries management. Sci Rep 2020; 10:559. [PMID: 31953426 PMCID: PMC6968997 DOI: 10.1038/s41598-019-57071-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.
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Affiliation(s)
- Simo N Maduna
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway.
| | - Adam Vivian-Smith
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Forestry and Forest Resources, P.O. Box 115, NO-1431, Ås, Norway
| | | | - Albert K D Imsland
- Akvaplan-niva, Iceland Office, Akralind 4, 201, Kópavogur, Iceland.,Department of Biosciences, University of Bergen, 5020, Bergen, Norway
| | - Cornelya F C Klütsch
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway
| | - Tommi Nyman
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway
| | - Snorre B Hagen
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway.
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10
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Murphy SM, Hast JT, Augustine BC, Weisrock DW, Clark JD, Kocka DM, Ryan CW, Sajecki JL, Cox JJ. Early genetic outcomes of American black bear reintroductions in the Central Appalachians, USA. URSUS 2019. [DOI: 10.2192/ursu-d-18-00011.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Sean M. Murphy
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| | - John T. Hast
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| | - Ben C. Augustine
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| | - David W. Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Joseph D. Clark
- United States Geological Survey, Northern Rocky Mountain Science Center, Southern Appalachian Research Branch, University of Tennessee, Knoxville, TN 37996, USA
| | - David M. Kocka
- Virginia Department of Game and Inland Fisheries, Verona, VA 24482, USA
| | - Christopher W. Ryan
- West Virginia Division of Natural Resources, South Charleston, WV 25303, USA
| | - Jaime L. Sajecki
- Virginia Department of Game and Inland Fisheries, Verona, VA 24482, USA
| | - John J. Cox
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
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11
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Curto M, Winter S, Seiter A, Schmid L, Scheicher K, Barthel LMF, Plass J, Meimberg H. Application of a SSR-GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics. Ecol Evol 2019; 9:2814-2832. [PMID: 30891219 PMCID: PMC6405497 DOI: 10.1002/ece3.4960] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 12/10/2018] [Accepted: 12/31/2018] [Indexed: 01/02/2023] Open
Abstract
By applying second-generation sequencing technologies to microsatellite genotyping, sequence information is produced which can result in high-resolution population genetics analysis populations and increased replicability between runs and laboratories. In the present study, we establish an approach to study the genetic structure patterns of two European hedgehog species Erinaceaus europaeus and E. roumanicus. These species are usually associated with human settlements and are good models to study anthropogenic impacts on the genetic diversity of wild populations. The short sequence repeats genotyping by sequence (SSR-GBS) method presented uses amplicon sequences to determine genotypes for which allelic variants can be defined according to both length and single nucleotide polymorphisms (SNPs). To evaluate whether complete sequence information improved genetic structure definition, we compared this information with datasets based solely on length information. We identified a total of 42 markers which were successfully amplified in both species. Overall, genotyping based on complete sequence information resulted in a higher number of alleles, as well as greater genetic diversity and differentiation between species. Additionally, the structure patterns were slightly clearer with a division between both species and some potential hybrids. There was some degree of genetic structure within species, although only in E. roumanicus was this related to geographical distance. The statistically significant results obtained by SSR-GBS demonstrate that it is superior to electrophoresis-based methods for SSR genotyping. Moreover, the greater reproducibility and throughput with lower effort which can be obtained with SSR-GBS and the possibility to include degraded DNA into the analysis, allow for continued relevance of SSR markers during the genomic era.
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Affiliation(s)
- Manuel Curto
- Institute for Integrative Nature Conservation ResearchUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Silvia Winter
- Institute for Integrative Nature Conservation ResearchUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Division of Plant ProtectionUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Anna Seiter
- Institute for Integrative Nature Conservation ResearchUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Lukas Schmid
- Institute for Integrative Nature Conservation ResearchUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Klaus Scheicher
- Institute of MathematicsUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Leon M. F. Barthel
- Evolutionary EcologyLeibniz Institute for Zoo and Wildlife Research (IZW)BerlinGermany
| | - Jürgen Plass
- Biologiezentrum LinzOberösterreich LandesmuseumLinzAustria
| | - Harald Meimberg
- Institute for Integrative Nature Conservation ResearchUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
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Manuzzi A, Zane L, Muñoz-Merida A, Griffiths AM, Veríssimo A. Population genomics and phylogeography of a benthic coastal shark (Scyliorhinus canicula) using 2b-RAD single nucleotide polymorphisms. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Alice Manuzzi
- CIBIO – U.P. – Research Center for Biodiversity and Genetic Resources, Vairão, Portugal
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej, Silkeborg, Denmark
| | - Lorenzo Zane
- Department of Biology, University of Padova, Padova, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Antonio Muñoz-Merida
- CIBIO – U.P. – Research Center for Biodiversity and Genetic Resources, Vairão, Portugal
| | | | - Ana Veríssimo
- CIBIO – U.P. – Research Center for Biodiversity and Genetic Resources, Vairão, Portugal
- Virginia Institute of Marine Science, College of William and Mary, VA, USA
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Barbian HJ, Connell AJ, Avitto AN, Russell RM, Smith AG, Gundlapally MS, Shazad AL, Li Y, Bibollet‐Ruche F, Wroblewski EE, Mjungu D, Lonsdorf EV, Stewart FA, Piel AK, Pusey AE, Sharp PM, Hahn BH. CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecol Evol 2018; 8:7946-7963. [PMID: 30250675 PMCID: PMC6145012 DOI: 10.1002/ece3.4302] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/29/2022] Open
Abstract
Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
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Affiliation(s)
- Hannah J. Barbian
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew Jesse Connell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexa N. Avitto
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Ronnie M. Russell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew G. Smith
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Madhurima S. Gundlapally
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexander L. Shazad
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Yingying Li
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Frederic Bibollet‐Ruche
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Emily E. Wroblewski
- Department of AnthropologyWashington University in St. LouisSt. LouisMissouri
| | | | | | - Fiona A. Stewart
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Alexander K. Piel
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Anne E. Pusey
- Department of Evolutionary AnthropologyDuke UniversityDurhamNorth Carolina
| | - Paul M. Sharp
- Institute of Evolutionary Biology and Centre for ImmunityInfection and EvolutionUniversity of EdinburghEdinburghUK
| | - Beatrice H. Hahn
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
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Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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