101
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Ni G, Kern E, Dong YW, Li Q, Park JK. More than meets the eye: The barrier effect of the Yangtze River outflow. Mol Ecol 2017; 26:4591-4602. [DOI: 10.1111/mec.14235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/15/2017] [Accepted: 06/16/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Gang Ni
- Division of EcoScience; Ewha Womans University; Seodaemun-gu Seoul Korea
| | - Elizabeth Kern
- Division of EcoScience; Ewha Womans University; Seodaemun-gu Seoul Korea
| | - Yun-Wei Dong
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen Fujian Province China
- Marine Biodiversity and Global Change Laboratory; College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian Province China
| | - Qi Li
- The Key Laboratory of Mariculture; Ministry of Education; Ocean University of China; Qingdao China
| | - Joong-Ki Park
- Division of EcoScience; Ewha Womans University; Seodaemun-gu Seoul Korea
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102
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Jacquemyn H, Kort HD, Broeck AV, Brys R. Immigrant and extrinsic hybrid seed inviability contribute to reproductive isolation between forest and dune ecotypes of Epipactis helleborine
(Orchidaceae). OIKOS 2017. [DOI: 10.1111/oik.04329] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hans Jacquemyn
- Dept of Biology; Plant Conservation and Population Biology; BE-3001 Leuven Belgium
| | - Hanne De Kort
- Dept of Biology; Plant Conservation and Population Biology; BE-3001 Leuven Belgium
- Station d'Ecologie Théorique et Expérimentale du CNRS, Centre National de la Recherche Scientifique; Moulis France
| | | | - Rein Brys
- Research Inst. for Forest and Nature; Geraardsbergen Belgium
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103
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Wang Y, Cao X, Zhao Y, Fei J, Hu X, Li N. Optimized double-digest genotyping by sequencing (ddGBS) method with high-density SNP markers and high genotyping accuracy for chickens. PLoS One 2017; 12:e0179073. [PMID: 28598985 PMCID: PMC5466311 DOI: 10.1371/journal.pone.0179073] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/23/2017] [Indexed: 12/04/2022] Open
Abstract
High-density single nucleotide polymorphism (SNP) markers are crucial to improve the resolution and accuracy of genome-wide association study (GWAS) and genomic selection (GS). Numerous approaches, including whole genome sequencing, genome sampling sequencing, and SNP chips are able to discover or genotype markers at different densities and costs. Achieving an optimal balance between sequencing resolution and budgets, especially in large-scale population genetics research, constitutes a major challenge. Here, we performed improved double-enzyme digestion genotyping by sequencing (ddGBS) on chicken. We evaluated eight double-enzyme digestion combinations, and EcoR I- Mse I was chosen as the optimal combination for the chicken genome. We firstly proposed that two parameters, optimal read-count point (ORP) and saturated read-count point (SRP), could be utilized to determine the optimal sequencing volume. A total of 291,772 high-density SNPs from 824 animals were identified. By validation using the SNP chip, we found that the consistency between ddGBS data and the SNP chip is over 99%. The approach that we developed in chickens, which is high-quality, high-density, cost-effective (300 K, $30/sample), and time-saving (within 48 h), will have broad applications in animal breeding programs.
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Affiliation(s)
- Yuzhe Wang
- State Key Laboratories of Agro-biotechnology, College of Biological Science, China Agricultural University, Beijing, China
| | - Xuemin Cao
- State Key Laboratories of Agro-biotechnology, College of Biological Science, China Agricultural University, Beijing, China
| | - Yiqiang Zhao
- State Key Laboratories of Agro-biotechnology, College of Biological Science, China Agricultural University, Beijing, China
| | - Jing Fei
- State Key Laboratories of Agro-biotechnology, College of Biological Science, China Agricultural University, Beijing, China
| | - Xiaoxiang Hu
- State Key Laboratories of Agro-biotechnology, College of Biological Science, China Agricultural University, Beijing, China
- * E-mail:
| | - Ning Li
- State Key Laboratories of Agro-biotechnology, College of Biological Science, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
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104
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Construction of a high-density linkage map and mapping of sex determination and growth-related loci in the mandarin fish (Siniperca chuatsi). BMC Genomics 2017; 18:446. [PMID: 28587594 PMCID: PMC5461734 DOI: 10.1186/s12864-017-3830-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 05/30/2017] [Indexed: 11/10/2022] Open
Abstract
Background The mandarin fish (Siniperca chuatsi) is an important and widely cultured fish in China. However, the lack of selective breeding of mandarin fish in previous decades has resulted in a decline in the growth rate of pond-cultured fish, a shortened period of sexual maturity, and reduced disease resistance; these issues seriously affect the quality and safety of the fish products. Therefore, it is necessary to establish a selective breeding program for the mandarin fish to improve the economical traits of the fish and to sustain the development of the mandarin fish industry. Results We constructed a high-density linkage map for it based on double digest restriction site associated DNA sequencing (ddRAD-Sequencing). This map contained 3283 dimorphic single nucleotide polymorphism markers and 24 linkage groups (LGs). The total map-length was 1972.01 cM, with an average interlocus distance of 0.61 cM. One significant quantitative trait locus (QTL) for sex determination trait was detected on LG23, which was supported by five markers, clustered between 60.27 and 68.71 cM. The highest logarithm of odds value (17.73) was located at 60.27 cM, near the marker r1_73194, accounting for 53.3% of the phenotypic variance. Genotypes of all the male fish on r1_33008 were homozygous, whereas those of all females were heterozygous. Thus, LG23 was considered a sex-related linkage group. Eleven significant QTLs, for three growth traits, at two growth stages and the increased values were distributed on four LGs; their contributions to the phenotypic variation were quite low (12.4–17.2%), suggesting that multiple genes affected the growth traits. Conclusion This high-resolution genetic map provides a valuable resource for fine-mapping of important traits and for identification of sex-related markers that should facilitate breeding of all-female mandarin fish for aquaculture and mechanistic studies on sex determination. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3830-3) contains supplementary material, which is available to authorized users.
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105
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Kang J, Ma X, He S. Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq. Sci Rep 2017; 7:2813. [PMID: 28588195 PMCID: PMC5460224 DOI: 10.1038/s41598-017-02853-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.
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Affiliation(s)
- Jingliang Kang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuhui Ma
- College of Animal Science, Guizhou University, Guizhou, 550025, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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106
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Porter CK, Benkman CW. Assessing the Potential Contributions of Reduced Immigrant Viability and Fecundity to Reproductive Isolation. Am Nat 2017; 189:580-591. [DOI: 10.1086/691191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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107
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Affiliation(s)
- Josephine R. Paris
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Jamie R. Stevens
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois at Urbana–Champaign Urbana IL 61801 USA
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108
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de Carvalho DB, Congrains C, Chahad-Ehlers S, Pinotti H, de Brito RA, da Rosa JA. Differential transcriptome analysis supports Rhodnius montenegrensis and Rhodnius robustus (Hemiptera, Reduviidae, Triatominae) as distinct species. PLoS One 2017; 12:e0174997. [PMID: 28406967 PMCID: PMC5390988 DOI: 10.1371/journal.pone.0174997] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/17/2017] [Indexed: 11/18/2022] Open
Abstract
Chagas disease is one of the main parasitic diseases found in Latin America and it is estimated that between six and seven million people are infected worldwide. Its etiologic agent, the protozoan Trypanosoma cruzi, is transmitted by triatomines, some of which from the genus Rhodnius. Twenty species are currently recognized in this genus, including some closely related species with low levels of morphological differentiation, such as Rhodnius montenegrensis and Rhodnius robustus. In order to investigate genetic differences between these two species, we generated large-scale RNA-sequencing data (consisting of four RNA-seq libraries) from the heads and salivary glands of males of R. montenegrensis and R. robustus. Transcriptome assemblies produced for each species resulted in 64,952 contigs for R. montenegrensis and 70,894 contigs for R. robustus, with N50 of approximately 2,100 for both species. SNP calling based on the more complete R. robustus assembly revealed 3,055 fixed interspecific differences and 216 transcripts with high levels of divergence which contained only fixed differences between the two species. A gene ontology enrichment analysis revealed that these highly differentiated transcripts were enriched for eight GO terms related to AP-2 adaptor complex, as well as other interesting genes that could be involved in their differentiation. The results show that R. montenegrensis and R. robustus have a substantial quantity of fixed interspecific polymorphisms, which suggests a high degree of genetic divergence between the two species and likely corroborates the species status of R. montenegrensis.
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Affiliation(s)
- Danila Blanco de Carvalho
- Department of Parasitology, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Carlos Congrains
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Paulo, Brazil
| | - Samira Chahad-Ehlers
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Paulo, Brazil
| | - Heloisa Pinotti
- Department of Parasitology, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Reinaldo Alves de Brito
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Paulo, Brazil
| | - João Aristeu da Rosa
- Department of Parasitology, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
- * E-mail:
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109
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Franchini P, Monné Parera D, Kautt AF, Meyer A. quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage. Mol Ecol 2017; 26:2783-2795. [PMID: 28247584 DOI: 10.1111/mec.14077] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Paolo Franchini
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Daniel Monné Parera
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Andreas F. Kautt
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
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110
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Ma B, Liao L, Peng Q, Fang T, Zhou H, Korban SS, Han Y. Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:190-204. [PMID: 28093854 DOI: 10.1111/jipb.12522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/15/2017] [Indexed: 05/02/2023]
Abstract
Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and 10 wild apples were genotyped using specific-locus amplified fragment sequencing, and 39,635 single nucleotide polymorphisms with no missing genotypes and evenly distributed along the genome were selected to investigate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than cultivated apples. Linkage disequilibrium (LD) decays were observed quite rapidly in cultivated and wild apples, with an r2 -value below 0.2 at 440 and 280 bp, respectively. Moreover, bidirectional gene flow and different distribution patterns of LD blocks were detected between domesticated and wild apples. Most LD blocks unique to cultivated apples were located within QTL regions controlling fruit quality, thus suggesting that fruit quality had probably undergone selection during apple domestication. The genome of the earliest cultivated apple in China, Nai, was highly similar to that of Malus sieversii, and contained a small portion of genetic material from other wild apple species. This suggested that introgression could have been an important driving force during initial domestication of apple. These findings will facilitate future breeding and genetic dissection of complex traits in apple.
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Affiliation(s)
- Baiquan Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Schuyler S Korban
- Department of Biology, University of Massachusetts Boston, Boston Massachusetts 02184, USA
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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111
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Nazareno AG, Bemmels JB, Dick CW, Lohmann LG. Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species. Mol Ecol Resour 2017; 17:1136-1147. [DOI: 10.1111/1755-0998.12654] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/04/2017] [Accepted: 01/09/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Alison G. Nazareno
- Departamento de Botânica Universidade de São Paulo Rua do Matão 277, Cidade Universitária CEP 05508‐900 São Paulo São Paulo Brazil
| | - Jordan B. Bemmels
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI 48109 USA
| | - Christopher W. Dick
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI 48109 USA
| | - Lúcia G. Lohmann
- Departamento de Botânica Universidade de São Paulo Rua do Matão 277, Cidade Universitária CEP 05508‐900 São Paulo São Paulo Brazil
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112
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Willis SC, Hollenbeck CM, Puritz JB, Gold JR, Portnoy DS. Haplotyping RAD loci: an efficient method to filter paralogs and account for physical linkage. Mol Ecol Resour 2017; 17:955-965. [DOI: 10.1111/1755-0998.12647] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/01/2016] [Accepted: 12/14/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Stuart C. Willis
- Marine Genomics Laboratory; Department of Life Sciences; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
| | - Christopher M. Hollenbeck
- Marine Genomics Laboratory; Department of Life Sciences; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
| | - Jonathan B. Puritz
- Marine Genomics Laboratory; Department of Life Sciences; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
- Marine Science Center; Northeastern University; 430 Nahant RD Nahant MA 01908 USA
| | - John R. Gold
- Marine Genomics Laboratory; Department of Life Sciences; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
| | - David S. Portnoy
- Marine Genomics Laboratory; Department of Life Sciences; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
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113
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Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y. The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha
(Myrtaceae). Mol Ecol 2017; 26:1515-1532. [DOI: 10.1111/mec.14016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/13/2016] [Accepted: 12/28/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Ayako Izuno
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Kanehiro Kitayama
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yusuke Onoda
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yuki Tsujii
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Functional Genomics Center Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Atsushi J. Nagano
- Faculty of Agriculture; Ryukoku University; 1-5 Yokatani, Seta Ohe-cho Otsu Shiga 520-2194 Japan
- PRESTO, Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Mie N. Honjo
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Hiroshi Kudoh
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
- Kihara Institute for Biological Research; Yokohama City University; 641-12 Maioka, Totsuka-ward Yokohama Kanagawa 244-0813 Japan
| | - Yuji Isagi
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
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114
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Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae). Mol Phylogenet Evol 2017; 107:345-355. [DOI: 10.1016/j.ympev.2016.11.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 11/19/2016] [Accepted: 11/27/2016] [Indexed: 11/17/2022]
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115
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Ren G, Mateo RG, Liu J, Suchan T, Alvarez N, Guisan A, Conti E, Salamin N. Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing. THE NEW PHYTOLOGIST 2017; 213:1500-1512. [PMID: 27696413 DOI: 10.1111/nph.14221] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/23/2016] [Indexed: 05/28/2023]
Abstract
The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes.
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Affiliation(s)
- Guangpeng Ren
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Rubén G Mateo
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, 1015, Lausanne, Switzerland
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Tomasz Suchan
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nadir Alvarez
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, 1015, Lausanne, Switzerland
| | - Elena Conti
- Department of Systematic and Evolutionary Botany and Botanic Garden, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
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116
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Garvin MR, Templin WD, Gharrett AJ, DeCovich N, Kondzela CM, Guyon JR, McPhee MV. Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael R. Garvin
- Oregon State University Ringgold Standard Institution ‐ Integrative Biology 3029 Cordley Hall, 2701 SW Campus Way Corvallis OR 97331‐4501 USA
| | - William D. Templin
- Alaska Department of Fish and Game Division of Commercial Fisheries 333 Raspberry Road Anchorage AK 99518 USA
| | - Anthony J. Gharrett
- University of Alaska Fairbanks College Fisheries and Ocean Sciences Juneau AK 99821 USA
| | - Nick DeCovich
- Alaska Department of Fish and Game Division of Commercial Fisheries 333 Raspberry Road Anchorage AK 99518 USA
| | - Christine M. Kondzela
- Auke Bay Laboratories Alaska Fisheries Science Center National Oceanic and Atmospheric Administration National Marine Fisheries Service 17109 Point Lena Loop Road Juneau AK 99801 USA
| | - Jeffrey R. Guyon
- Auke Bay Laboratories Alaska Fisheries Science Center National Oceanic and Atmospheric Administration National Marine Fisheries Service 17109 Point Lena Loop Road Juneau AK 99801 USA
| | - Megan V. McPhee
- University of Alaska Fairbanks College Fisheries and Ocean Sciences Juneau AK 99821 USA
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117
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Grillo MA, De Mita S, Burke PV, Solórzano-Lowell KLS, Heath KD. Intrapopulation genomics in a model mutualist: Population structure and candidate symbiosis genes under selection in Medicago truncatula. Evolution 2016; 70:2704-2717. [PMID: 27757965 DOI: 10.1111/evo.13095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 01/15/2023]
Abstract
Bottom-up evolutionary approaches, including geographically explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here, we conduct a population genomic analysis in the model legume, Medicago truncatula, to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify five distinct genetic clusters with divisions that separate east and west regions in the Mediterranean basin. Much of the genetic variation is maintained within sampling sites, and there is evidence for isolation by distance. Extensive linkage disequilibrium was identified, particularly within populations. We conducted genetic outlier analysis with FST -based genome scans and a Bayesian modeling approach (PCAdapt). There were 70 core outlier loci shared between these distinct methods with one clear candidate symbiosis related gene, DMI1. This work sets that stage for functional experiments to determine the important phenotypes that selection has acted upon and complementary efforts in rhizobium populations.
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Affiliation(s)
- Michael A Grillo
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
| | - Stephane De Mita
- INRA Nancy-Lorraine, UMR 1136 Interactions Arbres Microorganismes, Route d'Amance, 54280, Champenoux, France
| | - Patricia V Burke
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
| | | | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
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118
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Arbizu CI, Ellison SL, Senalik D, Simon PW, Spooner DM. Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae). BMC Evol Biol 2016; 16:234. [PMID: 27793080 PMCID: PMC5084430 DOI: 10.1186/s12862-016-0806-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/14/2016] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex. RESULTS We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 % missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. CONCLUSIONS Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.
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Affiliation(s)
- Carlos I Arbizu
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA
| | - Shelby L Ellison
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA
| | - Douglas Senalik
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA
| | - Philipp W Simon
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA
| | - David M Spooner
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA.
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA.
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119
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Wyss T, Masclaux FG, Rosikiewicz P, Pagni M, Sanders IR. Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis. THE ISME JOURNAL 2016; 10:2514-26. [PMID: 26953600 PMCID: PMC5030683 DOI: 10.1038/ismej.2016.29] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 12/15/2022]
Abstract
Arbuscular mycorrhizal (AM) fungi are symbionts of most plants, increasing plant growth and diversity. The model AM fungus Rhizophagus irregularis (isolate DAOM 197198) exhibits low within-fungus polymorphism. In contrast, another study reported high within-fungus variability. Experiments with other R. irregularis isolates suggest that within-fungus genetic variation can affect the fungal phenotype and plant growth, highlighting the biological importance of such variation. We investigated whether there is evidence of differing levels of within-fungus polymorphism in an R. irregularis population. We genotyped 20 isolates using restriction site-associated DNA sequencing and developed novel approaches for characterizing polymorphism among haploid nuclei. All isolates exhibited higher within-isolate poly-allelic single-nucleotide polymorphism (SNP) densities than DAOM 197198 in repeated and non-repeated sites mapped to the reference genome. Poly-allelic SNPs were independently confirmed. Allele frequencies within isolates deviated from diploids or tetraploids, or that expected for a strict dikaryote. Phylogeny based on poly-allelic sites was robust and mirrored the standard phylogeny. This indicates that within-fungus genetic variation is maintained in AM fungal populations. Our results predict a heterokaryotic state in the population, considerable differences in copy number variation among isolates and divergence among the copies, or aneuploidy in some isolates. The variation may be a combination of all of these hypotheses. Within-isolate genetic variation in R. irregularis leads to large differences in plant growth. Therefore, characterizing genomic variation within AM fungal populations is of major ecological importance.
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Affiliation(s)
- Tania Wyss
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pawel Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marco Pagni
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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120
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Onyango MG, Aitken NC, Jack C, Chuah A, Oguya J, Djikeng A, Kemp S, Bellis GA, Nicholas A, Walker PJ, Duchemin JB. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia. BMC Genomics 2016; 17:769. [PMID: 27716062 PMCID: PMC5045647 DOI: 10.1186/s12864-016-3124-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequencing method, allows highly multiplexed sequencing of genomic subsets. This method has limitations for small organisms with low amounts of genomic DNA, such as the bluetongue virus (BTV) vectors, Culicoides midges. RESULTS This study employed the GBS method to isolate SNP markers de novo from whole genome amplified Culicoides brevitarsis genomic DNA. The individuals were collected from regions representing two different Australian patterns of BTV strain distribution: the Northern Territory (NT) and the east coast. We isolated 8145 SNPs using GBS. Phylogenetic analysis conducted using the filtered 3263 SNPs revealed the presence of a distinct C. brevitarsis sub-population in the NT and this was confirmed by analysis of mitochondrial DNA. Two loci showed a very strong signal for selection and were unique to the NT population. Bayesian analysis with STRUCTURE indicated a possible two-population cluster. CONCLUSIONS The results suggest that genotyping vectors with high density markers in combination with biological and environmental data is useful. However, more extensive sampling over a wider spatial and temporal range is needed. The presence of sub-structure in populations and loci under natural selection indicates the need for further investigation of the role of vectors in shaping the two Australian systems of BTV transmission. The described workflow is transferable to genotyping of small, non-model organisms, including arthropod vectors of pathogens of economic and medical importance.
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Affiliation(s)
- Maria G Onyango
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portalington Road, Geelong, 3220, VIC, Australia.,School of Medicine, Deakin University, 75 Pidgons Road, Waurn Ponds, 3216, VIC, Australia
| | - Nicola C Aitken
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Cameron Jack
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Aaron Chuah
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - James Oguya
- International Livestock Research Institute (ILRI), P.O. Box 30709, 00100, Nairobi, Kenya
| | - Appolinaire Djikeng
- International Livestock Research Institute (ILRI), P.O. Box 30709, 00100, Nairobi, Kenya.,Biosciences eastern and central Africa-ILRI Hub (BecA-ILRI Hub), ILRI, PO Box 30709, 00100, Nairobi, Kenya
| | - Steve Kemp
- International Livestock Research Institute (ILRI), P.O. Box 30709, 00100, Nairobi, Kenya
| | - Glenn A Bellis
- Northern Australia Quarantine Strategy, 1 Pederson Road, Marrara, 0812, NT, Australia.,Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, 0909, NT, Australia
| | - Adrian Nicholas
- NSW Department of Primary Industries, Biosecurity, 4 Marsden Park Road, Calala, 2340, NSW, Australia
| | - Peter J Walker
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portalington Road, Geelong, 3220, VIC, Australia
| | - Jean-Bernard Duchemin
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portalington Road, Geelong, 3220, VIC, Australia.
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121
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Jueterbock A, Franssen SU, Bergmann N, Gu J, Coyer JA, Reusch TBH, Bornberg-Bauer E, Olsen JL. Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures inZostera marina, a globally important seagrass. Mol Ecol 2016; 25:5396-5411. [DOI: 10.1111/mec.13829] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 12/17/2022]
Affiliation(s)
- A. Jueterbock
- Faculty of Biosciences and Aquaculture; Nord University; Universitetsalleen 11 Bodø 8049 Norway
| | - S. U. Franssen
- Institut für Populationsgenetik; Vetmeduni Vienna; Veterinärplatz 1 Vienna 1210 Austria
- Institute for Evolution and Biodiversity; University of Münster; Hüfferstr. 1 Münster 48149 Germany
| | - N. Bergmann
- Integrated School of Ocean Sciences (ISOS); Kiel University; Leibnizstr. 3 Kiel 24098 Germany
| | - J. Gu
- Institute for Evolution and Biodiversity; University of Münster; Hüfferstr. 1 Münster 48149 Germany
| | - J. A. Coyer
- Shoals Marine Laboratory; University of New Hampshire; Durham NH 03824 USA
- Groningen Institute for Evolutionary Life Sciences; Ecological and Evolutionary Genomics Group; University of Groningen; P.O. Box 11103 Groningen 9700 CC The Netherlands
| | - T. B. H. Reusch
- GEOMAR Helmholtz-Centre for Ocean Research Kiel; Evolutionary Ecology of Marine Fishes; Düsternbrooker Weg 20 Kiel 24105 Germany
| | - E. Bornberg-Bauer
- Institute for Evolution and Biodiversity; University of Münster; Hüfferstr. 1 Münster 48149 Germany
| | - J. L. Olsen
- Groningen Institute for Evolutionary Life Sciences; Ecological and Evolutionary Genomics Group; University of Groningen; P.O. Box 11103 Groningen 9700 CC The Netherlands
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122
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Maisano Delser P, Corrigan S, Hale M, Li C, Veuille M, Planes S, Naylor G, Mona S. Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives. Sci Rep 2016; 6:33753. [PMID: 27651217 PMCID: PMC5030670 DOI: 10.1038/srep33753] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/19/2016] [Indexed: 01/23/2023] Open
Abstract
Population genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ~1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported an Nm value ~40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.
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Affiliation(s)
- Pierpaolo Maisano Delser
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Shannon Corrigan
- Department of Biology, College of Charleston, Charleston 29412, SC, USA
| | - Matthew Hale
- Medical University of South Carolina, College of Graduate Studies, Charleston 29403, SC, USA
| | - Chenhong Li
- Department of Biology, College of Charleston, Charleston 29412, SC, USA
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Michel Veuille
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Serge Planes
- CRIOBE-USR 3278, CNRS-EPHE-UPVD, Laboratoire d’Excellence ‘CORAIL’, 58 Avenue Paul Alduy, 66860 Perpignan, France
| | - Gavin Naylor
- Department of Biology, College of Charleston, Charleston 29412, SC, USA
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France
- EPHE, PSL Research University, Paris, France
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123
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Species limits, interspecific hybridization and phylogeny in the cryptic land snail complex Pyramidula: The power of RADseq data. Mol Phylogenet Evol 2016; 101:267-278. [DOI: 10.1016/j.ympev.2016.05.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 04/24/2016] [Accepted: 05/01/2016] [Indexed: 12/31/2022]
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124
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Herrera S, Shank TM. RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa. Mol Phylogenet Evol 2016; 100:70-79. [DOI: 10.1016/j.ympev.2016.03.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/09/2016] [Accepted: 03/11/2016] [Indexed: 11/29/2022]
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125
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Jeffries DL, Copp GH, Lawson Handley L, Olsén KH, Sayer CD, Hänfling B. Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L. Mol Ecol 2016; 25:2997-3018. [PMID: 26971882 DOI: 10.1111/mec.13613] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/19/2016] [Accepted: 02/29/2016] [Indexed: 12/16/2022]
Abstract
The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomized by the freshwater fish Carassius carassius, which is in decline across much of its European range. Restriction site-associated DNA sequencing (RADseq) is increasingly used for such applications; however, RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. This trade-off has previously been examined using simulation studies; however, empirical comparisons between these markers, especially in a phylogeographic context, are lacking. Here, we compare the results from microsatellites and RADseq for the phylogeography of C. carassius to test whether it is more advantageous to genotype fewer markers (microsatellites) in many samples, or many markers (SNPs) in fewer samples. These data sets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns, showing the existence of two previously unidentified C. carassius lineages in Europe: one found throughout northern and central-eastern European drainages and a second almost exclusively confined to the Danubian catchment. These lineages have been isolated for approximately 2.15 m years and should be considered separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with approximate Bayesian computation to show that the postglacial colonization routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology.
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Affiliation(s)
- Daniel L Jeffries
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK.,Salmon & Freshwater Team, Cefas, Pakefield Road, Lowestoft, Suffolk, NR33 0HT, UK
| | - Gordon H Copp
- Salmon & Freshwater Team, Cefas, Pakefield Road, Lowestoft, Suffolk, NR33 0HT, UK.,Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Lori Lawson Handley
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK
| | - K Håkan Olsén
- School of Natural Science, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, Flemingsberg, Huddinge, 141 89, Sweden
| | - Carl D Sayer
- Environmental Change Research Centre, Department of Geography, University College London, Pearson Building, Gower Street, London, WC1E 6BT, UK
| | - Bernd Hänfling
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK
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126
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Fu YB, Dong Y, Yang MH. Multiplexed shotgun sequencing reveals congruent three-genome phylogenetic signals for four botanical sections of the flax genus Linum. Mol Phylogenet Evol 2016; 101:122-132. [PMID: 27165939 DOI: 10.1016/j.ympev.2016.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/02/2016] [Accepted: 05/06/2016] [Indexed: 12/11/2022]
Abstract
A genome-wide detection of phylogenetic signals by next generation sequencing (NGS) has recently emerged as a promising genomic approach for phylogenetic analysis of non-model organisms. Here we explored the use of a multiplexed shotgun sequencing method to assess the phylogenetic relationships of 18 Linum samples representing 16 species within four botanical sections of the flax genus Linum. The whole genome DNAs of 18 Linum samples were fragmented, tagged, and sequenced using an Illumina MiSeq. Acquired sequencing reads per sample were further separated into chloroplast, mitochondrial and nuclear sequence reads. SNP calls upon genome-specific sequence data sets revealed 6143 chloroplast, 2673 mitochondrial, and 19,562 nuclear SNPs. Phylogenetic analyses based on three-genome SNP data sets with and without missing observations showed congruent three-genome phylogenetic signals for four botanical sections of the Linum genus. Specifically, two major lineages showing a separation of Linum-Dasylinum sections and Linastrum-Syllinum sections were confirmed. The Linum section displayed three major branches representing two major evolutionary stages leading to cultivated flax. Cultivated flax and its immediate progenitor were formed as its own branch, genetically more closely related to L. decumbens and L. grandiflorum with chromosome count of eight, and distantly apart from six other species with chromosome count of nine. Five species of the Linastrum and Syllinum sections were genetically more distant from cultivated flax, but they appeared to be more closely related to each other, even with variable chromosome counts. These findings not only provide the first evidence of congruent three-genome phylogenetic pathways within the Linum genus, but also demonstrate the utility of the multiplexed shotgun sequencing in acquisition of three-genome phylogenetic signals of non-model organisms.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, AAFC Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N0X2, Canada.
| | - Yibo Dong
- Plant Gene Resources of Canada, AAFC Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N0X2, Canada
| | - Mo-Hua Yang
- Plant Gene Resources of Canada, AAFC Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N0X2, Canada; College of Forestry, Central South University of Forestry & Technology, Changsha, Hunan, China
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127
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Ivy JA, Putnam AS, Navarro AY, Gurr J, Ryder OA. Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs. J Hered 2016; 107:403-12. [PMID: 27208150 DOI: 10.1093/jhered/esw029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/22/2016] [Indexed: 12/24/2022] Open
Abstract
Captive breeding programs for wildlife species typically rely on pedigrees to inform genetic management. Although pedigree-based breeding strategies are quite effective at retaining long-term genetic variation, management of zoo-based breeding programs continues to be hampered when pedigrees are poorly known. The objective of this study was to evaluate 2 options for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships within captive breeding programs. We generated SNP data for a zoo-based population of addax (Addax nasomasculatus) using both the Illumina BovineHD BeadChip and double digest restriction site-associated DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele sharing (AS) between pairs of individuals exhibited low variances. Average AS variances were highest when using 50 loci (SNPchipall = 0.00159; ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling ≥500 loci. Furthermore, the correlation between the SNPchipall and ddRADall AS datasets was 0.88 (95%CI = 0.84-0.91) when subsampling 500 loci. Collectively, our results indicated that both SNP genotyping methods produced sufficient data for accurately estimating relationships, even within an extremely bottlenecked population. Our results also suggested that analytic assumptions historically integrated into the addax pedigree are not adversely impacting long-term pedigree-based management; kinships calculated from the analytic pedigree were significantly correlated (P << 0.001) with AS estimates. Overall, our conclusions are intended to serve as both a proof of concept and a model for applying molecular data to the genetic management of captive breeding programs.
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Affiliation(s)
- Jamie A Ivy
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Andrea S Putnam
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Asako Y Navarro
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Jessica Gurr
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Oliver A Ryder
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
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FUNK WCHRIS, LOVICH ROBERTE, HOHENLOHE PAULA, HOFMAN COURTNEYA, MORRISON SCOTTA, SILLETT TSCOTT, GHALAMBOR CAMERONK, MALDONADO JESUSE, RICK TORBENC, DAY MITCHD, POLATO NICHOLASR, FITZPATRICK SARAHW, COONAN TIMOTHYJ, CROOKS KEVINR, DILLON ADAM, GARCELON DAVIDK, KING JULIEL, BOSER CHRISTINAL, GOULD NICHOLAS, ANDELT WILLIAMF. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Mol Ecol 2016; 25:2176-94. [PMID: 26992010 PMCID: PMC4877267 DOI: 10.1111/mec.13605] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 02/17/2016] [Accepted: 02/23/2016] [Indexed: 01/02/2023]
Abstract
The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.
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Affiliation(s)
- W. CHRIS FUNK
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - ROBERT E. LOVICH
- Naval Facilities Engineering Command Southwest, 1220 Pacific Highway, San Diego, CA 92132, USA
| | - PAUL A. HOHENLOHE
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - COURTNEY A. HOFMAN
- Department of Anthropology, University of Maryland, College Park, MD 20742, USA
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | | | - T. SCOTT SILLETT
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5503, Washington, DC 20013-7012, USA
| | - CAMERON K. GHALAMBOR
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - JESUS E. MALDONADO
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - TORBEN C. RICK
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - MITCH D. DAY
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - NICHOLAS R. POLATO
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - SARAH W. FITZPATRICK
- Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - TIMOTHY J. COONAN
- National Park Service, Channel Islands National Park, 1901 Spinnaker Drive, Ventura, CA 93001, USA
| | - KEVIN R. CROOKS
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA
| | - ADAM DILLON
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA
| | - DAVID K. GARCELON
- Institute for Wildlife Studies, P.O. Box 1104, Arcata, CA 95518, USA
| | - JULIE L. KING
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | | | - NICHOLAS GOULD
- Fisheries, Wildlife, and Conservation Biology, North Carolina State University, Turner House, Box 7646, Raleigh, NC 27695-7646, USA
| | - WILLIAM F. ANDELT
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA
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Hirase S, Takeshima H, Nishida M, Iwasaki W. Parallel Mitogenome Sequencing Alleviates Random Rooting Effect in Phylogeography. Genome Biol Evol 2016; 8:1267-78. [PMID: 27016485 PMCID: PMC4860695 DOI: 10.1093/gbe/evw063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2016] [Indexed: 01/18/2023] Open
Abstract
Reliably rooted phylogenetic trees play irreplaceable roles in clarifying diversification in the patterns of species and populations. However, such trees are often unavailable in phylogeographic studies, particularly when the focus is on rapidly expanded populations that exhibit star-like trees. A fundamental bottleneck is known as the random rooting effect, where a distant outgroup tends to root an unrooted tree "randomly." We investigated whether parallel mitochondrial genome (mitogenome) sequencing alleviates this effect in phylogeography using a case study on the Sea of Japan lineage of the intertidal goby Chaenogobius annularis Eighty-three C. annularis individuals were collected and their mitogenomes were determined by high-throughput and low-cost parallel sequencing. Phylogenetic analysis of these mitogenome sequences was conducted to root the Sea of Japan lineage, which has a star-like phylogeny and had not been reliably rooted. The topologies of the bootstrap trees were investigated to determine whether the use of mitogenomes alleviated the random rooting effect. The mitogenome data successfully rooted the Sea of Japan lineage by alleviating the effect, which hindered phylogenetic analysis that used specific gene sequences. The reliable rooting of the lineage led to the discovery of a novel, northern lineage that expanded during an interglacial period with high bootstrap support. Furthermore, the finding of this lineage suggested the existence of additional glacial refugia and provided a new recent calibration point that revised the divergence time estimation between the Sea of Japan and Pacific Ocean lineages. This study illustrates the effectiveness of parallel mitogenome sequencing for solving the random rooting problem in phylogeographic studies.
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Affiliation(s)
- Shotaro Hirase
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Hirohiko Takeshima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan Center for Research Promotion, Research Institute for Humanity and Nature, National Institutes for the Humanities, Kita-ku, Kyoto, Japan
| | - Mutsumi Nishida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Wataru Iwasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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Patrick HJH, Chomič A, Armstrong KF. Cooled Propylene Glycol as a Pragmatic Choice for Preservation of DNA From Remote Field-Collected Diptera for Next-Generation Sequence Analysis. JOURNAL OF ECONOMIC ENTOMOLOGY 2016; 109:1469-1473. [PMID: 27053702 DOI: 10.1093/jee/tow047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/25/2016] [Indexed: 06/05/2023]
Abstract
Next-generation sequencing (NGS)-based methods can now be applied to large population-scale studies, but this demands very high-quality DNA. For specimens collected from remote field locations, DNA degradation can be a problem, requiring logistically challenging preservation techniques. Simpler preservation techniques are therefore required. Prior to collection of exotic fruit fly (Tephritidae) species, a number of readily available preservatives with storage at either 4°C or room temperature were trialed here to determine the DNA quality for three locally available Diptera species, Fannia canicularis (L.), Musca domestica L., and Lucilia sericata Meigen. Considerable variation was observed between the different preservatives, species, and temperatures, but several preservatives at 4°C were favored. Chilled propylene glycol was subsequently used for the storage and carriage of Australian field-collected Bactrocera fruit fly specimens to New Zealand. When processed up to 20 d later, DNA fragments of ∼10-20 kb were obtained for successful genotyping by sequencing analysis. This protocol is therefore recommended as a logistically simple and safe approach for distant collection of dipteran samples for NGS population genomic studies.
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131
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Torres-Martínez L, Emery NC. Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0524-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing. PLoS One 2016; 11:e0150692. [PMID: 26964097 PMCID: PMC4786213 DOI: 10.1371/journal.pone.0150692] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/18/2016] [Indexed: 11/19/2022] Open
Abstract
Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides 'I-69' and male Populus simonii 'L3'. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population.
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133
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Yang H, Wei CL, Liu HW, Wu JL, Li ZG, Zhang L, Jian JB, Li YY, Tai YL, Zhang J, Zhang ZZ, Jiang CJ, Xia T, Wan XC. Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing. PLoS One 2016; 11:e0151424. [PMID: 26962860 PMCID: PMC4786323 DOI: 10.1371/journal.pone.0151424] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 02/28/2016] [Indexed: 12/19/2022] Open
Abstract
Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants.
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Affiliation(s)
- Hua Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Department of Applied Chemistry, School of Science, Anhui Agricultural University, Hefei, 230036, China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Hong-Wei Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jun-Lan Wu
- School of Information & Computer, Anhui Agricultural University, Hefei, 230036, China
| | - Zheng-Guo Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Liang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | | | - Ye-Yun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yu-Ling Tai
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jing Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Chang-Jun Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- * E-mail:
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134
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Vera M, Díez-del-Molino D, García-Marín JL. Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki). Mol Ecol 2016; 25:1089-105. [PMID: 26825431 DOI: 10.1111/mec.13545] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/10/2015] [Accepted: 01/15/2016] [Indexed: 01/26/2023]
Abstract
Biological invasions rank among the main global threats for biodiversity. The Eastern mosquitofish (Gambusia holbrooki) is considered one of the 100 world worst invasive species due to its high adaptation capability to new environments. Using the restriction-site-associated DNA tags (RADtags), introduced European locations were compared against native US mosquitofish populations to analyse genomic changes that occurred during invasive process of European locations. After filtering, 7724 RADtags containing only one SNP were retained for population studies. Comparative genomics indicated that 186 of these RADtags matched sequences in the transcriptome of Xyphophorus maculatus, the most closely related genome available. Genomic analyses showed that invasive populations show high reductions in diversity. Further, analyses of population structuring based on these data are concordant with previous analyses based on microsatellites. It is concluded that during the invasion process genetic drift was the main evolutionary force affecting patterns of diversity and population structure. While recognizing that positive selection could be masked by the strong drift during founder events, adaptive processes were evidenced in a reduced number of RADtags (<2%), with only one of these in a putative coding region. Surprisingly, balancing selection was detected in several coding RADtags, suggesting that the preservation of polymorphism in specific genes could be more important than the average population diversity for the population maintenance at any location, particularly for the survival of introduced populations.
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Affiliation(s)
- Manuel Vera
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
| | - David Díez-del-Molino
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
| | - José-Luis García-Marín
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
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135
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Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding. PLoS One 2016; 11:e0147187. [PMID: 26799713 PMCID: PMC4723255 DOI: 10.1371/journal.pone.0147187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/30/2015] [Indexed: 11/19/2022] Open
Abstract
Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.
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136
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Lozier JD, Jackson JM, Dillon ME, Strange JP. Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect. Ecol Evol 2016; 6:1075-91. [PMID: 26811748 PMCID: PMC4722823 DOI: 10.1002/ece3.1928] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/08/2015] [Accepted: 12/09/2015] [Indexed: 01/01/2023] Open
Abstract
Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble bee Bombus bifarius comprises two geographically disparate color groups characterized by red‐banded and black‐banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed that B. bifarius in the USA are structured into two major groups concordant with geography and color pattern, but also suggest ongoing gene flow among regional populations. In this study, we better resolve the relationships among major color groups to better understand evolutionary mechanisms promoting and maintaining such polymorphism. We analyze >90,000 and >25,000 single‐nucleotide polymorphisms derived from transcriptome (RNAseq) and double digest restriction site associated DNA sequencing (ddRAD), respectively, in representative samples from spatial and color pattern extremes in B. bifarius as well as phenotypic and geographic intermediates. Both ddRAD and RNAseq data illustrate substantial genome‐wide differentiation of the red‐banded (eastern) color form from both black‐banded (western) and intermediate (central) phenotypes and negligible differentiation among the latter populations, with no obvious admixture among bees from the two major lineages. Results thus indicate much stronger background differentiation among B. bifarius lineages than expected, highlighting potential challenges for revealing loci underlying color polymorphism from population genetic data alone. These findings will have significance for resolving taxonomic confusion in this species and in future efforts to investigate color‐pattern evolution in B. bifarius and other polymorphic bumble bee species.
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Affiliation(s)
- Jeffrey D Lozier
- Department of Biological Sciences University of Alabama Tuscaloosa Alabama
| | - Jason M Jackson
- Department of Biological Sciences University of Alabama Tuscaloosa Alabama
| | - Michael E Dillon
- Department of Zoology & Physiology and Program in Ecology University of Wyoming Laramie Wyoming
| | - James P Strange
- USDA-ARS Pollinating Insect Research Unit Utah State University Logan Utah
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137
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Rivers DM, Darwell CT, Althoff DM. Phylogenetic analysis of RAD-seq data: examining the influence of gene genealogy conflict on analysis of concatenated data. Cladistics 2016; 32:672-681. [DOI: 10.1111/cla.12149] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2015] [Indexed: 01/15/2023] Open
Affiliation(s)
- David M. Rivers
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
| | - Clive T. Darwell
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
| | - David M. Althoff
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
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138
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Abstract
High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.
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139
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Jones MR, Good JM. Targeted capture in evolutionary and ecological genomics. Mol Ecol 2016; 25:185-202. [PMID: 26137993 PMCID: PMC4823023 DOI: 10.1111/mec.13304] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 12/17/2022]
Abstract
The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome-partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole-genome sequencing in ecological and evolutionary genomic studies. High-throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome-partitioning approaches in the light of the increasing accessibility of whole-genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole-genome sequencing.
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Affiliation(s)
- Matthew R. Jones
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
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140
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Pauletto M, Carraro L, Babbucci M, Lucchini R, Bargelloni L, Cardazzo B. Extending RAD tag analysis to microbial ecology: a comparison between MultiLocus Sequence Typing and 2b-RAD to investigate Listeria monocytogenes genetic structure. Mol Ecol Resour 2015; 16:823-35. [PMID: 26613186 DOI: 10.1111/1755-0998.12495] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/14/2015] [Accepted: 11/23/2015] [Indexed: 12/24/2022]
Abstract
The advent of next-generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are quite laborious and time-consuming, especially for large-scale analyses. In this study, a genotyping approach based on restriction site-associated (RAD) tag sequencing, 2b-RAD, was applied to characterize Listeria monocytogenes strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico mlst analysis was conducted as well. Subsequently, 2b-RAD and mlst analyses were experimentally carried out on 58 isolates collected from food samples or food-processing sites. The obtained results demonstrate that 2b-RAD predicts mlst types and often provides more detailed information on population structure than mlst. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although mlst still represents a reliable typing method, large-scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b-RAD analysis proposed here.
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Affiliation(s)
- Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Rosaria Lucchini
- Istituto Zooprofilattico delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
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141
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Winger BM, Hosner PA, Bravo GA, Cuervo AM, Aristizábal N, Cueto LE, Bates JM. Inferring speciation history in the Andes with reduced‐representation sequence data: an example in the bay‐backed antpittas (Aves; Grallariidae;
Grallaria hypoleuca
s. l.). Mol Ecol 2015; 24:6256-77. [DOI: 10.1111/mec.13477] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Benjamin M. Winger
- Committee on Evolutionary Biology The University of Chicago Chicago IL 60637 USA
- Life Sciences Section Integrative Research Center The Field Museum of Natural History Chicago IL 60605 USA
| | - Peter A. Hosner
- Department of Ecology and Evolutionary Biology and Biodiversity Institute University of Kansas Lawrence KS 66045 USA
- Department of Biology University of Florida Gainesville FL 32603 USA
| | - Gustavo A. Bravo
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
- Secão de Aves Museu de Zoologia Universidade de São Paulo (MZUSP) São Paulo SP 04263‐000 Brasil
| | - Andrés M. Cuervo
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
- Department of Ecology and Evolutionary Biology Tulane University New Orleans LA 70118 USA
| | - Natalia Aristizábal
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
- Departamento de Ecologia Instituto de Biociências Universidade de São Paulo São Paulo SP 05508‐900 Brasil
| | - Luis E. Cueto
- Life Sciences Section Integrative Research Center The Field Museum of Natural History Chicago IL 60605 USA
| | - John M. Bates
- Life Sciences Section Integrative Research Center The Field Museum of Natural History Chicago IL 60605 USA
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142
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Pauli M, Chakarov N, Rupp O, Kalinowski J, Goesmann A, Sorenson MD, Krüger O, Hoffman JI. De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite. BMC Genomics 2015; 16:1038. [PMID: 26645667 PMCID: PMC4673757 DOI: 10.1186/s12864-015-2254-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/27/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Studies of non-model species are important for understanding the molecular processes underpinning phenotypic variation under natural ecological conditions. The common buzzard (Buteo buteo; Aves: Accipitriformes) is a widespread and common Eurasian raptor with three distinct plumage morphs that differ in several fitness-related traits, including parasite infestation. To provide a genomic resource for plumage polymorphic birds in general and to search for candidate genes relating to fitness, we generated a transcriptome from a single dead buzzard specimen plus easily accessible, minimally invasive samples from live chicks. RESULTS We not only de novo assembled a near-complete buzzard transcriptome, but also obtained a significant fraction of the transcriptome of its malaria-like parasite, Leucocytozoon buteonis. By identifying melanogenesis-related transcripts that are differentially expressed in light ventral and dark dorsal feathers, but which are also expressed in other regions of the body, we also identified a suite of candidate genes that could be associated with fitness differences among the morphs. These include several immune-related genes, providing a plausible link between melanisation and parasite load. qPCR analysis of a subset of these genes revealed significant differences between ventral and dorsal feathers and an additional effect of morph. CONCLUSION This new resource provides preliminary insights into genes that could be involved in fitness differences between the buzzard colour morphs, and should facilitate future studies of raptors and their malaria-like parasites.
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Affiliation(s)
- Martina Pauli
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
- Present address: Molecular Ecology and Evolution Lab, Lund University, 223 62, Lund, Sweden.
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-University, 35390, Giessen, Germany
- Center for Biotechnology, Bielefeld University, 33501, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33501, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University, 35390, Giessen, Germany
- Center for Biotechnology, Bielefeld University, 33501, Bielefeld, Germany
| | | | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - Joseph Ivan Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
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143
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Ortego J, Noguerales V, Gugger PF, Sork VL. Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach. Mol Ecol 2015; 24:6188-208. [PMID: 26547661 DOI: 10.1111/mec.13457] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 01/17/2023]
Abstract
Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analysed inter- and intraspecific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models (SDMs) and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with SDMs and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors, have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio s/n, E-41092, Seville, Spain
| | - Víctor Noguerales
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio s/n, E-41092, Seville, Spain
| | - Paul F Gugger
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA.,Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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144
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Michels-Boyce M, Zani PA. Lack of supercooling evolution related to winter severity in a lizard. J Therm Biol 2015; 53:72-9. [PMID: 26590458 DOI: 10.1016/j.jtherbio.2015.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 03/22/2015] [Accepted: 08/13/2015] [Indexed: 11/25/2022]
Abstract
As organisms move into higher latitudes, they may evolve physiological mechanisms to survive in harsher climates. One such mechanism is supercooling, the capacity to survive at subzero temperatures without freezing. While interspecific comparisons reveal greater thermal tolerances at higher latitudes in insects and vertebrates, evidence for intraspecific evolution in supercooling related to latitude is only evident in insects. We measured the supercooling points of lizards from 12 populations reared from hatch in common laboratory conditions to test for evolved differences in supercooling related to winter. Results indicate that winter harshness (depth or length) cannot explain supercooling points regardless of how data are analyzed, which suggests that populations have not evolved greater supercooling capacity. While our results are consistent with the idea that thermal physiology is evolutionarily conserved in vertebrates, we cannot reject several alternatives including the possibility that lizards are able to behaviorally avoid the extreme temperatures that would select for thermal evolution.
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Affiliation(s)
- Madeline Michels-Boyce
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI 54481, USA
| | - Peter A Zani
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI 54481, USA.
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145
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Bonatelli IAS, Carstens BC, Moraes EM. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae). PLoS One 2015; 10:e0142602. [PMID: 26561396 PMCID: PMC4641700 DOI: 10.1371/journal.pone.0142602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.
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Affiliation(s)
| | - Bryan C. Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Evandro M. Moraes
- Department of Biology, Federal University of São Carlos, Sorocaba, São Paulo, Brazil
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146
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Herrera S, Reyes-Herrera PH, Shank TM. Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life. Genome Biol Evol 2015; 7:3207-25. [PMID: 26537225 PMCID: PMC4700943 DOI: 10.1093/gbe/evv210] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes--generically known as restriction site associated DNA sequencing (RAD-seq)--is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for nonmodel species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting "neutral" elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced representation data are available (including transcriptomes and neutral RAD-seq data sets). The analytical pipeline developed in this study, PredRAD (https://github.com/phrh/PredRAD), and the resulting databases constitute valuable resources that will help guide the design of any study using RAD-seq or related methods.
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Affiliation(s)
- Santiago Herrera
- Biology Department, Woods Hole Oceanographic Institution Biology Department, Massachusetts Institute of Technology
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147
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Edwards SV, Shultz AJ, Campbell-Staton SC. Next-generation sequencing and the expanding domain of phylogeography. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a2.2015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Shane C. Campbell-Staton
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
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148
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Leaché AD, Banbury BL, Felsenstein J, de Oca ANM, Stamatakis A. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies. Syst Biol 2015. [PMID: 26227865 DOI: 10.5061/dryad.t9r3g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths.
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, WA 98195, USA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA;
| | - Barbara L Banbury
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Joseph Felsenstein
- Department of Biology, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Adrián Nieto-Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, México 04510, Distrito Federal, México
| | - Alexandros Stamatakis
- Exelixis Laboratory, Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany; and Department of Informatics, Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
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149
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Bradbury IR, Hamilton LC, Dempson B, Robertson MJ, Bourret V, Bernatchez L, Verspoor E. Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure. Mol Ecol 2015; 24:5130-44. [DOI: 10.1111/mec.13395] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Ian R. Bradbury
- Science Branch; Department of Fisheries and Oceans Canada; 80 East White Hills Road St. John's Newfoundland Canada A1C 5X1
| | - Lorraine C. Hamilton
- Aquatic Biotechnology Laboratory; Bedford Institute of Oceanography; Dartmouth Halifax Nova Scotia Canada B2Y 4A2
| | - Brian Dempson
- Science Branch; Department of Fisheries and Oceans Canada; 80 East White Hills Road St. John's Newfoundland Canada A1C 5X1
| | - Martha J. Robertson
- Science Branch; Department of Fisheries and Oceans Canada; 80 East White Hills Road St. John's Newfoundland Canada A1C 5X1
| | - Vincent Bourret
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec Canada G1V 0A6
- Direction de la faune aquatique; Ministère du Développement durable, de l'Environnement, de la Faune et des Parcs; Québec Québec Canada G1S 4X4
| | - Louis Bernatchez
- Direction de la faune aquatique; Ministère du Développement durable, de l'Environnement, de la Faune et des Parcs; Québec Québec Canada G1S 4X4
| | - Eric Verspoor
- Rivers and Lochs Institute; Inverness College University of the Highlands and Islands; Inverness IV2 5NA UK
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150
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Shikano T, Järvinen A, Marjamäki P, Kahilainen KK, Merilä J. Genetic Variability and Structuring of Arctic Charr (Salvelinus alpinus) Populations in Northern Fennoscandia. PLoS One 2015; 10:e0140344. [PMID: 26468642 PMCID: PMC4607410 DOI: 10.1371/journal.pone.0140344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/24/2015] [Indexed: 01/01/2023] Open
Abstract
Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean FST ≈ 0.26) differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (Ne) ranged from seven to 228 and were significantly correlated with those of historical Ne but not with lake size. A census size (NC) was estimated to be approximately 300 individuals in a pond (0.14 ha), which exhibited the smallest Ne (i.e. Ne/NC = 0.02). Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.
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Affiliation(s)
- Takahito Shikano
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Antero Järvinen
- Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, Finland
| | - Paula Marjamäki
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Kimmo K. Kahilainen
- Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, Finland
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
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