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Characterization of highly polymorphic microsatellite markers for the chinese monal (Lophophorus lhuysii, Galliformes) using Illumina MiSeq sequencing. Mol Biol Rep 2023; 50:3903-3908. [PMID: 36652153 DOI: 10.1007/s11033-022-08151-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/23/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND The Chinese monal (Lophophorus lhuysii, Galliformes) is a vulnerable and endemic bird from southwestern China. To better protect this species and increase its population size, genetic markers are urgently needed for investigation and conservation of both wild and captive populations. METHODS AND RESULTS By using next-generation sequencing, we developed and characterized markers for seven microsatellite loci of the Chinese monal. PCR examination and statistical analysis indicated that these microsatellites exhibited moderate to high levels of polymorphism, with the expected heterozygosity and polymorphic information content ranging from 0.578 to 0.858 and from 0.540 to 0.841, respectively. Cross-species genome comparison further suggests that these microsatellites are a feature of certain galliform species rather than being specific to the Chinese monal. CONCLUSION A combination of the seven highly polymorphic loci may provide a fundamental genetic toolkit to assess genetic backgrounds and will contribute to design conservation plan, breeding management and other possible studies of the Chinese monal and other evolutionarily related species in the future.
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2
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Campbell DC, Camak DT, Piller KR. Islands in the desert: assessing fine scale population genomic variation of a group of imperiled desert fishes. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01457-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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3
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Mounger JM, van Riemsdijk I, Boquete MT, Wagemaker CAM, Fatma S, Robertson MH, Voors SA, Oberstaller J, Gawehns F, Hanley TC, Grosse I, Verhoeven KJF, Sotka EE, Gehring CA, Hughes AR, Lewis DB, Schmid MW, Richards CL. Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.868826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.
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4
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Kriefall NG, Kanke MR, Aglyamova GV, Davies SW. Reef environments shape microbial partners in a highly connected coral population. Proc Biol Sci 2022; 289:20212459. [PMID: 35042418 PMCID: PMC8767194 DOI: 10.1098/rspb.2021.2459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/15/2021] [Indexed: 01/28/2023] Open
Abstract
Evidence is mounting that composition of microorganisms within a host can play an essential role in total holobiont health. In corals, for instance, studies have identified algal and bacterial taxa that can significantly influence coral host function and these communities depend on environmental context. However, few studies have linked host genetics to algal and microbial partners across environments within a single coral population. Here, using 2b-RAD sequencing of corals and metabarcoding of their associated algal (ITS2) and bacterial (16S) communities, we show evidence that reef zones (locales that differ in proximity to shore and other environmental characteristics) structure algal and bacterial communities at different scales in a highly connected coral population (Acropora hyacinthus) in French Polynesia. Fore reef (FR) algal communities in Mo'orea were more diverse than back reef (BR) communities, suggesting that these BR conditions constrain diversity. Interestingly, in FR corals, host genetic diversity correlated with bacterial diversity, which could imply genotype by genotype interactions between these holobiont members. Our results illuminate that local reef conditions play an important role in shaping unique host-microbial partner combinations, which may have fitness consequences for dispersive coral populations arriving in novel environments.
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Affiliation(s)
| | - M. R. Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - G. V. Aglyamova
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, USA
| | - S. W. Davies
- Biology Department, Boston University, Boston, MA, USA
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5
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Population structure and adaptive variation of Helichrysum italicum (Roth) G. Don along eastern Adriatic temperature and precipitation gradient. Sci Rep 2021; 11:24333. [PMID: 34934087 PMCID: PMC8692458 DOI: 10.1038/s41598-021-03548-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Immortelle (Helichrysum italicum (Roth) G. Don; Asteraceae) is a perennial plant species native to the Mediterranean region, known for many properties with wide application mainly in perfume and cosmetic industry. A total of 18 wild H. italicum populations systematically sampled along the eastern Adriatic environmental gradient were studied using AFLP markers to determine genetic diversity and structure and to identify loci potentially responsible for adaptive divergence. Results showed higher levels of intrapopulation diversity than interpopulation diversity. Genetic differentiation among populations was significant but low, indicating extensive gene flow between populations. Bayesian analysis of population structure revealed the existence of two genetic clusters. Combining the results of FST - outlier analysis (Mcheza and BayeScan) and genome-environment association analysis (Samβada, LFMM) four AFLP loci strongly associated with the bioclimatic variables Bio03 Isothermality, Bio08 Mean temperature of the wettest quarter, Bio15 Precipitation seasonality, and Bio17 Precipitation of driest quarter were found to be the main variables driving potential adaptive genetic variation in H. italicum along the eastern Adriatic environmental gradient. Redundancy analysis revealed that the partitioning of genetic variation was mainly associated with the adaptation to temperature oscillations. The results of the research may contribute to a clearer understanding of the importance of local adaptations for the genetic differentiation of Mediterranean plants and allow the planning of appropriate conservation strategies. However, considering that the identified outlier loci may be linked to genes under selection rather than being the target of natural selection, future studies must aim at their additional analysis.
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6
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Portella RO, Cordeiro EMG, Marques APS, Ming LC, Zucchi MI, Lima MP, Martins ER, Hantao LW, Sawaya ACHF, Semir J, Pinheiro JB, Marques MOM. Evidence of altitudinal gradient modifying genomic and chemical diversity in populations of Lychnophora pinaster Mart. PHYTOCHEMISTRY 2021; 192:112898. [PMID: 34492545 DOI: 10.1016/j.phytochem.2021.112898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/27/2021] [Accepted: 08/03/2021] [Indexed: 05/28/2023]
Abstract
Lychnophora pinaster Mart. (Asteraceae) is endemic to the Brazilian Cerrado. It is distributed along the altitudinal gradient of the mountainous ranges of the state of Minas Gerais. This study aimed to evaluate the influence of altitude on the genetic diversity of L. pinaster populations and the effects of altitude and climatic factors on essential oil chemical composition. Essential oils from L. pinaster populations from the north (North 01, North 02, and North 03, 700-859 m) and the Metropolitan region of Belo Horizonte (MhBH 01 and MrBH 02, 1366-1498 m) were analyzed. SNP markers from L. pinaster in these regions and Campos das Vertentes (CV 01, CV 02, and CV 03, 1055-1292 m) were also analyzed. The main compounds in essential oils were 14-hydroxy-α-humulene (North 01 and North 03), cedr-8(15)-en-9-α-ol (North 02), 14-acetoxy-α-humulene (MrBH 01), and 4-oxo-15-nor-eudesman-11-ene (MrBH 02). Hierarchical cluster and heatmap analyses showed that the North and MrBH populations included five different groups, indicating the chemical composition of essential oils is distinct in each population. Furthermore, principal component analysis showed that higher altitudes (1366 m and 1498 m) in the MrBH influence the chemical composition of essential oils, and climatic factors determine the chemical composition in North region. The genetic diversity showed that most alleles are in Hardy-Weinberg equilibrium and imply high genetic variation and genetic polymorphisms between populations. Furthermore, the results of Mantel tests (R = 0.3861517; p = 0.04709529; R = 0.9423121; p = 0.02739726) also showed that higher altitude (>1360 m) shapes the genetic diversity at the MrBH. The genetic structure showed that higher altitudes (>1360 m) contribute to the structure of the MrBH populations, but not to North and CV populations. Therefore, the altitudinal ranges of Minas Gerais mountainous ranges determine the higher genetic and chemical diversity of L. pinaster populations.
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Affiliation(s)
- Roberto O Portella
- Universidade de Taubaté, Av. Tiradentes, 500, Bom Conselho, CEP: 12030-180, Taubaté, SP, Brazil; Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua Prof. Dr. Antônio Celso Wagner Zanin, 250 - Distrito de Rubião Junior, CEP: 18618-689, Botucatu, SP, Brazil
| | - Erick M G Cordeiro
- Agência Paulista de Tecnologia dos Agronegócios, Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Caixa Postal 28, CEP: 13400-970, Piracicaba, SP, Brazil
| | - Ana Paula S Marques
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua Prof. Dr. Antônio Celso Wagner Zanin, 250 - Distrito de Rubião Junior, CEP: 18618-689, Botucatu, SP, Brazil
| | - Lin C Ming
- Departamento de Horticultura, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua José Barbosa de Barros, 1780, CEP: 18610-307, Botucatu, SP, Brazil
| | - Maria I Zucchi
- Agência Paulista de Tecnologia dos Agronegócios, Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Caixa Postal 28, CEP: 13400-970, Piracicaba, SP, Brazil
| | - Maria P Lima
- Coordenação de Inovação Tecnológica, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Aleixo, CEP: 69011-970, Manaus, AM, Brazil
| | - Ernane R Martins
- Instituto de Ciências Agrárias, Universidade Federal de Minas Gerais, Av. Universitária, 1000, Universitário, CEP: 39404-547, Montes Claros, MG, Brazil
| | - Leandro W Hantao
- Instituto de Química, Universidade Estadual de Campinas, Rua Monteiro Lobato, 270, CEP: 13083-862, Campinas, SP, Brazil
| | - Alexandra C H F Sawaya
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200, Cidade Universitária, CEP: 13083-871, Campinas, SP, Brazil
| | - João Semir
- Departamento de Botânica, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, Barão Geraldo, CEP: 13083-862, Campinas, SP, Brazil
| | - José B Pinheiro
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, CEP: 13418-900, Piracicaba, SP, Brazil
| | - Marcia O M Marques
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico, Avenida Barão de Itapura, 1481, Botafogo, CEP: 13020-902, Campinas, SP, Brazil.
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Mounger J, Boquete MT, Schmid MW, Granado R, Robertson MH, Voors SA, Langanke KL, Alvarez M, Wagemaker CAM, Schrey AW, Fox GA, Lewis DB, Lira CF, Richards CL. Inheritance of DNA methylation differences in the mangrove Rhizophora mangle. Evol Dev 2021; 23:351-374. [PMID: 34382741 DOI: 10.1111/ede.12388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/15/2021] [Accepted: 07/02/2021] [Indexed: 12/11/2022]
Abstract
The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape-level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.
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Affiliation(s)
- Jeannie Mounger
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - M Teresa Boquete
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Department of Evolutionary Ecology, CSIC, Estación Biológica de Doñana, Sevilla, Spain
| | | | - Renan Granado
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Diretoria de Pesquisas, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro/RJ, Brazil
| | - Marta H Robertson
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Sandy A Voors
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Kristen L Langanke
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Mariano Alvarez
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Avalo, Durham, NC, USA
| | | | - Aaron W Schrey
- Department of Biology, Georgia Southern University, Armstrong Campus, Savannah, Georgia, USA
| | - Gordon A Fox
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - David B Lewis
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Catarina Fonseca Lira
- Diretoria de Pesquisas, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro/RJ, Brazil
| | - Christina L Richards
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Plant Evolutionary Ecology, University of Tübingen, Institute of Evolution & Ecology, Tübingen, Germany
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8
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Timm LE, Jackson TL, Browder JA, Bracken-Grissom HD. Population Genomics of the Commercially Important Gulf of Mexico Pink Shrimp Farfantepenaeus duorarum (Burkenroad, 1939) Support Models of Juvenile Transport Around the Florida Peninsula. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.659134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Gulf of Mexico pink shrimp, Farfantepenaeus duorarum, supports large fisheries in the United States and Mexico, with nearly 7,000 tons harvested from the region in 2016. Given the commercial importance of this species, management is critical: in 1997, the southern Gulf of Mexico pink shrimp fishery was declared collapsed and mitigation strategies went into effect, with recovery efforts lasting over a decade. Fisheries management can be informed and improved through a better understanding of how factors associated with early life history impact genetic diversity and population structure in the recruited population. Farfantepenaeus duorarum are short-lived, but highly fecund, and display high variability in recruitment patterns. To date, modeling the impacts of ecological, physical, and behavioral factors on juvenile settlement has focused on recruitment of larval individuals of F. duorarum to nursery grounds in Florida Bay. Here, we articulate testable hypotheses stemming from a recent model of larval transport and evaluate support for each with a population genomics approach, generating reduced representation library sequencing data for F. duorarum collected from seven regions around the Florida Peninsula. Our research represents the first and most molecular data-rich study of population structure in F. duorarum in the Gulf and reveals evidence of a differentiated population in the Dry Tortugas. Our approach largely validates a model of larval transport, allowing us to make management-informative inferences about the impacts of spawning location and recruitment patterns on intraspecific genetic diversity. Such inferences improve our understanding of the roles of non-genetic factors in generating and maintaining genetic diversity in a commercially important penaeid shrimp species.
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9
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Reich HG, Kitchen SA, Stankiewicz KH, Devlin-Durante M, Fogarty ND, Baums IB. Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium 'fitti') among closely related coral hosts. Mol Ecol 2021; 30:3500-3514. [PMID: 33964051 DOI: 10.1111/mec.15952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/20/2022]
Abstract
Mutualisms where hosts are coupled metabolically to their symbionts often exhibit high partner fidelity. Most reef-building coral species form obligate symbioses with a specific species of photosymbionts, dinoflagellates in the family Symbiodiniaceae, despite needing to acquire symbionts early in their development from environmental sources. Three Caribbean acroporids (Acropora palmata, A. cervicornis and their F1 hybrid) are sympatric across much of their range, but often occupy different depth and light habitats. Throughout this range, both species and their hybrid associate with the endosymbiotic dinoflagellate Symbiodinium 'fitti'. Because light (and therefore depth) influences the physiology of dinoflagellates, we investigated whether S. 'fitti' populations from each host taxon were differentiated genetically. Single nucleotide polymorphisms (SNPs) among S. 'fitti' strains were identified by aligning shallow metagenomic sequences of acroporid colonies sampled from across the Caribbean to a ~600-Mb draft assembly of the S. 'fitti' genome (from the CFL14120 A. cervicornis metagenome). Phylogenomic and multivariate analyses revealed that genomic variation among S. 'fitti' strains partitioned to each host taxon rather than by biogeographical origin. This is particularly noteworthy because the hybrid has a sparse fossil record and may be of relatively recent origin. A subset (37.6%) of the SNPs putatively under selection were nonsynonymous mutations predicted to alter protein efficiency. Differences in genomic variation of S. 'fitti' strains from each host taxon may reflect the unique selection pressures created by the microenvironments associated with each host. The nonrandom sorting among S. 'fitti' strains to different hosts could be the basis for lineage diversification via disruptive selection, leading to ecological specialization and ultimately speciation.
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Affiliation(s)
- Hannah G Reich
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sheila A Kitchen
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Nicole D Fogarty
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
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10
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Duckett DJ, Sullivan J, Pirro S, Carstens BC. Genomic Resources for the North American Water Vole ( Microtus richardsoni) and the Montane Vole ( Microtus montanus). GIGABYTE 2021; 2021:gigabyte19. [PMID: 36824326 PMCID: PMC9631978 DOI: 10.46471/gigabyte.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/04/2021] [Indexed: 11/09/2022] Open
Abstract
Voles of the genus Microtus are important research organisms, yet genomic resources are lacking. Such resources would benefit future studies of immunology, phylogeography, cryptic diversity, and more. We sequenced and assembled nuclear genomes from two subspecies of water vole (Microtus richardsoni) and from the montane vole (Microtus montanus). The water vole genomes were sequenced with Illumina and 10× Chromium plus Illumina sequencing, resulting in assemblies with ∼1600,000 and ∼30,000 scaffolds, respectively. The montane vole was also assembled into ∼13,000 scaffolds using Illumina sequencing. Mitochondrial genome assemblies were also performed for both species. Structural and functional annotation for the best water vole nuclear genome resulted in ∼24,500 annotated genes, with 83% of these having functional annotations. Assembly quality statistics for our nuclear assemblies fall within the range of genomes previously published in the genus Microtus, making the water vole and montane vole genomes useful additions to currently available genomic resources.
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Affiliation(s)
- Drew J. Duckett
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 1315 Kinnear Rd., Columbus, OH 43212, USA, Corresponding author. E-mail:
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Box 443051, Moscow, ID 83844-3051, USA
| | - Stacy Pirro
- Iridian Genomes, Inc., 6213 Swords Way, Bethesda, MD 20817, USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 1315 Kinnear Rd., Columbus, OH 43212, USA
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11
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Hussain I, Raza RZ, Ali S, Abrar M, Abbasi AA. Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers. Dev Genes Evol 2021; 231:21-32. [PMID: 33655411 DOI: 10.1007/s00427-021-00672-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/09/2021] [Indexed: 11/25/2022]
Abstract
The zinc finger-containing transcription factor Gli3 is a key mediator of Hedgehog (Hh) signaling pathway. In vertebrates, Gli3 has widespread expression pattern during early embryonic development. Along the anteroposterior axes of the central nervous system (CNS), dorsoventral neural pattern elaboration is achieved through Hh mediated spatio-temporal deployment of Gli3 transcripts. Previously, we and others uncovered a set of enhancers that mediate many of the known aspects of Gli3 expression during neurogenesis. However, the potential role of Gli3 associated enhancers in trait evolution has not yet received any significant attention. Here, we investigate the evolutionary patterns of Gli3 associated CNS-specific enhancers that have been reported so far. A subset of these enhancers has undergone an accelerated rate of molecular evolution in the human lineage in comparison to other primates/mammals. These fast-evolving enhancers have acquired human-specific changes in transcription factor binding sites (TFBSs). These human-unique changes within subset of Gli3 associated CNS-specific enhancers were further validated as single nucleotide polymorphisms through 1000 Genome Project Phase 3 data. This work not only infers the molecular evolutionary patterns of Gli3 associated enhancers but also provides clues for putative genetic basis of the population-specificity of gene expression regulation.
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Affiliation(s)
- Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rabail Zehra Raza
- Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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12
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Baveja P, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Yuda P, Lee JGH, Rheindt FE. Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild. Evol Appl 2021; 14:698-709. [PMID: 33767745 PMCID: PMC7980273 DOI: 10.1111/eva.13149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/13/2020] [Indexed: 11/29/2022] Open
Abstract
Urgent conservation action for terminally endangered species is sometimes hampered by taxonomic uncertainty, especially in illegally traded animals that are often cross-bred in captivity. To overcome these problems, we used a genomic approach to analyze historical DNA from museum samples across the Asian Pied Starling (Gracupica contra) complex in tropical Asia, a popular victim of the ongoing songbird crisis whose distinct Javan population ("Javan Pied Starling") is extinct in the wild and subject to admixture in captivity. Comparing genomic profiles across the entire distribution, we detected three deeply diverged lineages at the species level characterized by a lack of genomic intermediacy near areas of contact. Our study demonstrates that the use of historical DNA can be instrumental in delimiting species in situations of taxonomic uncertainty, especially when modern admixture may obfuscate species boundaries. Results of our research will enable conservationists to commence a dedicated ex situ breeding program for the Javan Pied Starling, and serve as a blueprint for similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.
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Affiliation(s)
- Pratibha Baveja
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Kritika M. Garg
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Institute of Bioinformatics and Applied BiotechnologyBangaloreIndia
| | - Balaji Chattopadhyay
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Keren R. Sadanandan
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | | | - Pramana Yuda
- Fakultas TeknobiologiUniversitas Atma Jaya YogyakartaYogyakartaIndonesia
| | - Jessica G. H. Lee
- Department of Conservation and ResearchWildlife Reserves SingaporeSingaporeSingapore
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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Pespeni MH, Moczek AP. Signals of selection beyond bottlenecks between exotic populations of the bull-headed dung beetle, Onthophagus taurus. Evol Dev 2021; 23:86-99. [PMID: 33522675 DOI: 10.1111/ede.12367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 11/27/2022]
Abstract
Colonization of new environments can lead to population bottlenecks and rapid phenotypic evolution that could be due to neutral and selective processes. Exotic populations of the bull-headed dung beetle (Onthophagus taurus) have differentiated in opposite directions from native beetles in male horn-to-body size allometry and female fecundity. Here we test for genetic and transcriptional differences among two exotic and one native O. taurus populations after three generations in common garden conditions. We sequenced RNA from 24 individuals for each of the three populations including both sexes, and spanning four developmental stages for the two exotic, differentiated populations. Identifying 270,400 high-quality single nucleotide polymorphisms, we revealed a strong signal of genetic differentiation between the three populations, and evidence of recent bottlenecks within and an excess of outlier loci between exotic populations. Differences in gene expression between populations were greatest in prepupae and early adult life stages, stages during which differences in male horn development and female fecundity manifest. Finally, genes differentially expressed between exotic populations also had greater genetic differentiation and performed functions related to chitin biosynthesis and nutrient sensing, possibly underlying allometry and fecundity trait divergences. Our results suggest that beyond bottlenecks, recent introductions have led to genetic and transcriptional differences in genes correlated with observed phenotypic differences.
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Affiliation(s)
- Melissa H Pespeni
- Department of Biology, University of Vermont, Burlington, Vermont, USA.,Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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14
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Maroso F, Gkagkavouzis K, De Innocentiis S, Hillen J, do Prado F, Karaiskou N, Taggart JB, Carr A, Nielsen E, Triantafyllidis A, Bargelloni L. Genome-wide analysis clarifies the population genetic structure of wild gilthead sea bream (Sparus aurata). PLoS One 2021; 16:e0236230. [PMID: 33428622 PMCID: PMC7799848 DOI: 10.1371/journal.pone.0236230] [Citation(s) in RCA: 5] [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: 07/02/2020] [Accepted: 12/22/2020] [Indexed: 11/30/2022] Open
Abstract
Gilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. Its distribution ranges from the Mediterranean to the African and European coasts of the North-East Atlantic. Until now, the population genetic structure of this species in the wild has largely been studied using microsatellite DNA markers, with minimal genetic differentiation being detected. In this geographically widespread study, 958 wild gilthead sea bream from 23 locations within the Mediterranean Sea and Atlantic Ocean were genotyped at 1159 genome-wide SNP markers by RAD sequencing. Outlier analyses identified 18 loci potentially under selection. Neutral marker analyses identified weak subdivision into three genetic clusters: Atlantic, West, and East Mediterranean. The latter group could be further subdivided into an Ionian/Adriatic and an Aegean group using the outlier markers alone. Seascape analysis suggested that this differentiation was mainly due to difference in salinity, this being also supported by preliminary genomic functional analysis. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry.
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Affiliation(s)
- Francesco Maroso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro (PD), Italy
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | | | - Jasmien Hillen
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Leuven, Belgium
| | - Fernanda do Prado
- Department of Biological Sciences, São Paulo State University, Bauru, Brazil
| | - Nikoleta Karaiskou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | | | - Adrian Carr
- Fios Genomics Ltd, Edinburgh, United Kingdom
| | - Einar Nielsen
- Section for Population Ecology and Genetics, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Alexandros Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro (PD), Italy
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15
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Wang Z, Sun Y, Huang X, Li F, Liu Y, Zhu H, Liu Z, Ke W. Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers. PeerJ 2020; 8:e10485. [PMID: 33354429 PMCID: PMC7731653 DOI: 10.7717/peerj.10485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/12/2020] [Indexed: 01/20/2023] Open
Abstract
Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.
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Affiliation(s)
- Zhixin Wang
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yalin Sun
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xinfang Huang
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Feng Li
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yuping Liu
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Honglian Zhu
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Zhengwei Liu
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Weidong Ke
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
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16
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Hanson RL, Van Hout CV, Hsueh WC, Shuldiner AR, Kobes S, Sinha M, Baier LJ, Knowler WC. Assessment of the potential role of natural selection in type 2 diabetes and related traits across human continental ancestry groups: comparison of phenotypic with genotypic divergence. Diabetologia 2020; 63:2616-2627. [PMID: 32886191 PMCID: PMC7642101 DOI: 10.1007/s00125-020-05272-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/22/2020] [Indexed: 11/30/2022]
Abstract
AIMS/HYPOTHESIS Prevalence of type 2 diabetes differs among human ancestry groups, and many hypotheses invoke differential natural selection to account for these differences. We sought to assess the potential role of differential natural selection across major continental ancestry groups for diabetes and related traits, by comparison of genetic and phenotypic differences. METHODS This was a cross-sectional comparison among 734 individuals from an urban sample (none of whom was more closely related to another than third-degree relatives), including 83 African Americans, 523 American Indians and 128 European Americans. Participants were not recruited based on diabetes status or other traits. BMI was calculated, and diabetes was diagnosed by a 75 g oral glucose tolerance test. In those with normal glucose tolerance (n = 434), fasting insulin and 30 min post-load insulin, adjusted for 30 min glucose, were taken as measures of insulin resistance and secretion, respectively. Whole exome sequencing was performed, resulting in 97,388 common (minor allele frequency ≥ 5%) variants; the coancestry coefficient (FST) was calculated across all markers as a measure of genetic divergence among ancestry groups. The phenotypic divergence index (PST) was also calculated from the phenotypic differences and heritability (which was estimated from genetic relatedness calculated empirically across all markers in 761 American Indian participants prior to the exclusion of close relatives). Under evolutionary neutrality, the expectation is PST = FST, while for traits under differential selection PST is expected to be significantly greater than FST. A bootstrap procedure was used to test the hypothesis PST = FST. RESULTS: With adjustment for age and sex, prevalence of type 2 diabetes was 34.0% in American Indians, 12.4% in African Americans and 10.4% in European Americans (p = 2.9 × 10-10 for difference among groups). Mean BMI was 36.3, 33.4 and 33.0 kg/m2, respectively (p = 1.9 × 10-7). Mean fasting insulin was 63.8, 48.4 and 45.2 pmol/l (p = 9.2 × 10-5), while mean 30 min insulin was 559.8, 553.5 and 358.8 pmol/l, respectively (p = 5.7 × 10-8). FST across all markers was 0.130, while PST for liability to diabetes, adjusted for age and sex, was 0.149 (p = 0.35 for difference with FST). PST was 0.094 for BMI (p = 0.54), 0.095 for fasting insulin (p = 0.54) and 0.216 (p = 0.18) for 30 min insulin. For type 2 diabetes and BMI, the maximum divergence between populations was observed between American Indians and European Americans (PST-MAX = 0.22, p = 0.37, and PST-MAX = 0.14, p = 0.61), which suggests that a relatively modest 22% or 14% of the genetic variance, respectively, can potentially be explained by differential selection (assuming the absence of neutral drift). CONCLUSIONS/INTERPRETATION These analyses suggest that while type 2 diabetes and related traits differ significantly among continental ancestry groups, the differences are consistent with neutral expectations based on heritability and genetic distances. While these analyses do not exclude a modest role for natural selection, they do not support the hypothesis that differential natural selection is necessary to explain the phenotypic differences among these ancestry groups. Graphical abstract.
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Affiliation(s)
- Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA.
| | | | - Wen-Chi Hsueh
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | | | - Sayuko Kobes
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Madhumita Sinha
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Leslie J Baier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | | | - William C Knowler
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
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17
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Scott PA, Allison LJ, Field KJ, Averill-Murray RC, Shaffer HB. Individual heterozygosity predicts translocation success in threatened desert tortoises. Science 2020; 370:1086-1089. [DOI: 10.1126/science.abb0421] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 09/11/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Peter A. Scott
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, TX 79016, USA
| | - Linda J. Allison
- U.S. Fish and Wildlife Service, Desert Tortoise Recovery Office, Reno, NV 89502, USA
| | - Kimberleigh J. Field
- U.S. Fish and Wildlife Service, Desert Tortoise Recovery Office, Reno, NV 89502, USA
| | - Roy C. Averill-Murray
- U.S. Fish and Wildlife Service, Desert Tortoise Recovery Office, Reno, NV 89502, USA
| | - H. Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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18
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Tagliamonte MS, Yowell CA, Elbadry MA, Boncy J, Raccurt CP, Okech BA, Goss EM, Salemi M, Dame JB. Genetic Markers of Adaptation of Plasmodium falciparum to Transmission by American Vectors Identified in the Genomes of Parasites from Haiti and South America. mSphere 2020; 5:e00937-20. [PMID: 33087522 PMCID: PMC7580960 DOI: 10.1128/msphere.00937-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/01/2020] [Indexed: 12/30/2022] Open
Abstract
The malaria parasite, Plasmodium falciparum, was introduced into Hispaniola and other regions of the Americas through the slave trade spanning the 16th through the 19th centuries. During this period, more than 12 million Africans were brought across the Atlantic to the Caribbean and other regions of the Americas. Since malaria is holoendemic in West Africa, a substantial percentage of these individuals carried the parasite. St. Domingue on Hispaniola, now modern-day Haiti, was a major port of disembarkation, and malaria is still actively transmitted there. We undertook a detailed study of the phylogenetics of the Haitian parasites and those from Colombia and Peru utilizing whole-genome sequencing. Principal-component and phylogenetic analyses, based upon single nucleotide polymorphisms (SNPs) in protein coding regions, indicate that, despite the potential for millions of introductions from Africa, the Haitian parasites share an ancestral relationship within a well-supported monophyletic clade with parasites from South America, while belonging to a distinct lineage. This result, in stark contrast to the historical record of parasite introductions, is best explained by a severe population bottleneck experienced by the parasites introduced into the Americas. Here, evidence is presented for targeted selection of rare African alleles in genes which are expressed in the mosquito stages of the parasite's life cycle. These genetic markers support the hypothesis that the severe population bottleneck was caused by the required adaptation of the parasite to transmission by new definitive hosts among the Anopheles (Nyssorhynchus) spp. found in the Caribbean and South America.IMPORTANCE Historical data suggest that millions of P. falciparum parasite lineages were introduced into the Americas during the trans-Atlantic slave trade, which would suggest a paraphyletic origin of the extant isolates in the Western Hemisphere. Our analyses of whole-genome variants show that the American parasites belong to a well-supported monophyletic clade. We hypothesize that the required adaptation to American vectors created a severe bottleneck, reducing the effective introduction to a few lineages. In support of this hypothesis, we discovered genes expressed in the mosquito stages of the life cycle that have alleles with multiple, high-frequency or fixed, nonsynonymous mutations in the American populations which are rarely found in African isolates. These alleles appear to be in gene products critical for transmission through the anopheline vector. Thus, these results may inform efforts to develop novel transmission-blocking vaccines by identifying parasite proteins functionally interacting with the vector that are important for successful transmission. Further, to the best of our knowledge, these are the first whole-genome data available from Haitian P. falciparum isolates. Defining the genome of these parasites provides genetic markers useful for mapping parasite populations and monitoring parasite movements/introductions.
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Affiliation(s)
- Massimiliano S Tagliamonte
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Charles A Yowell
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Maha A Elbadry
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Jacques Boncy
- Laboratoire National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Christian P Raccurt
- Department of Tropical Medicine and Infectious Diseases, Faculty of Medicine, University of Quisqueya, Port-au-Prince, Haiti
| | - Bernard A Okech
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Erica M Goss
- Department of Plant Pathology, College of Agricultural and Life Sciences, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - John B Dame
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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19
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Rellstab C, Zoller S, Sailer C, Tedder A, Gugerli F, Shimizu KK, Holderegger R, Widmer A, Fischer MC. Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species. Mol Ecol 2020; 29:4350-4365. [PMID: 32969558 PMCID: PMC7756229 DOI: 10.1111/mec.15648] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/26/2020] [Accepted: 09/04/2020] [Indexed: 01/24/2023]
Abstract
It has long been discussed to what extent related species develop similar genetic mechanisms to adapt to similar environments. Most studies documenting such convergence have either used different lineages within species or surveyed only a limited portion of the genome. Here, we investigated whether similar or different sets of orthologous genes were involved in genetic adaptation of natural populations of three related plant species to similar environmental gradients in the Alps. We used whole-genome pooled population sequencing to study genome-wide SNP variation in 18 natural populations of three Brassicaceae (Arabis alpina, Arabidopsis halleri, and Cardamine resedifolia) from the Swiss Alps. We first de novo assembled draft reference genomes for all three species. We then ran population and landscape genomic analyses with ~3 million SNPs per species to look for shared genomic signatures of selection and adaptation in response to similar environmental gradients acting on these species. Genes with a signature of convergent adaptation were found at significantly higher numbers than expected by chance. The most closely related species pair showed the highest relative over-representation of shared adaptation signatures. Moreover, the identified genes of convergent adaptation were enriched for nonsynonymous mutations, suggesting functional relevance of these genes, even though many of the identified candidate genes have hitherto unknown or poorly described functions based on comparison with Arabidopsis thaliana. We conclude that adaptation to heterogeneous Alpine environments in related species is partly driven by convergent evolution, but that most of the genomic signatures of adaptation remain species-specific.
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Affiliation(s)
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Christian Sailer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Andrew Tedder
- Department of Evolutionary Biology and Environmental Studies, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.,School of Chemistry & Bioscience, University of Bradford, Bradford, UK
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Rolf Holderegger
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Martin C Fischer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
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20
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Guo Y, Warner RM. Dissecting genetic diversity and genomic background of Petunia cultivars with contrasting growth habits. HORTICULTURE RESEARCH 2020; 7:155. [PMID: 33082962 PMCID: PMC7528118 DOI: 10.1038/s41438-020-00373-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/13/2020] [Accepted: 08/05/2020] [Indexed: 05/15/2023]
Abstract
The cultivated petunia (Petunia ×hybrida) is derived from the progenitor species P. axillaris and P. integrifolia. The hybridization dates back only to the 1830s, though intensive breeding efforts have yielded cultivars exhibiting incredible diversity for many traits, including growth habit, flower color, and flower size. Until now, little is known about the genetic diversity and genomic background of modern cultivars. Here we selected a panel of 13 cultivars with contrasting growth habits and three wild species (the progenitors and P. exserta) to estimate the genomic contribution from the ancestral species and to study whether the variation of the genetic origin could be associated with different breeding programs or morphological variability. Transcriptome sequencing identified 1,164,566 SNPs representing 98.4% (32,451) of the transcripts that cover 99.2% (of 52,697,361 bp) of the P. axillaris transcriptome. Cultivars with an upright growth habit had more homozygous alleles and more P. axillaris-derived alleles than trailing cultivars, while mounded cultivars had intermediate heterozygosity. Unlike previous studies, we found the proportions of alleles derived from each progenitor species varied across cultivars but overall were not biased toward one progenitor species, suggesting diverse selection during cultivar development. For trailing cultivars, alleles potentially introgressed from other wild species ("out" alleles) were enriched. The "out" alleles were clustered in particular regions of chromosomes, suggesting that these regions may be hotspots of introgression. Transcripts in these regions were enriched with gene ontology terms associated with growth habit. This study provides novel insight into the contributions of progenitor species to the genomic background of modern petunia cultivars and identifies genome regions that may harbor genes conferring the trailing growth habit for further exploration.
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Affiliation(s)
- Yufang Guo
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Ryan M. Warner
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
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21
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Stuart KC, Cardilini APA, Cassey P, Richardson MF, Sherwin WB, Rollins LA, Sherman CDH. Signatures of selection in a recent invasion reveal adaptive divergence in a highly vagile invasive species. Mol Ecol 2020; 30:1419-1434. [PMID: 33463838 DOI: 10.1111/mec.15601] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/18/2022]
Abstract
A detailed understanding of population genetics in invasive populations helps us to identify drivers of successful alien introductions. Here, we investigate putative signals of selection in Australian populations of invasive common starlings, Sturnus vulgaris, and seek to understand how these have been influenced by introduction history. We used reduced representation sequencing to determine population structure, and identify Single Nucleotide Polymorphisms (SNPs) that are putatively under selection. We found that since their introduction into Australia, starling populations have become genetically differentiated despite the potential for high levels of dispersal, and that starlings have responded to selective pressures imposed by a wide range of environmental conditions across their geographic range. Isolation by distance appears to have played a strong role in determining genetic substructure across the starling's Australian range. Analyses of candidate SNPs that are putatively under selection indicated that aridity, precipitation and temperature may be important factors driving adaptive variation across the starling's invasive range in Australia. However, we also noted that the historic introduction regime may leave footprints on sites flagged as being under adaptive selection, and encourage critical interpretation of selection analyses in non-native populations.
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Affiliation(s)
- Katarina C Stuart
- Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Adam P A Cardilini
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Phillip Cassey
- Centre for Applied Conservation Science and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Mark F Richardson
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.,Genomics Centre, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - William B Sherwin
- Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Lee A Rollins
- Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Craig D H Sherman
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
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22
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Rahman S, Schmidt D, Hughes JM. Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude. PeerJ 2020; 8:e8139. [PMID: 31942250 PMCID: PMC6955102 DOI: 10.7717/peerj.8139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/01/2019] [Indexed: 11/29/2022] Open
Abstract
Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed freshwater shrimp in eastern Australia. The species has been considered as an important stream organism for studying genetics, dispersal, biology, behaviour and evolution in atyids and is a major food source for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of nine highly divergent mitochondrial DNA lineages. Previous studies in southeast Queensland showed that “lineage 4” favours upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify putative selection and population structure between high elevation and low elevation populations of this lineage at relatively small spatial scales. Sample localities were selected from three streams: Booloumba Creek, Broken Bridge Creek and Obi Obi Creek in the Conondale Range, southeast Queensland. Six sample localities, consisting of 142 individuals in total were sequenced using double digest Restriction Site Associated DNA-sequencing (ddRAD-seq) technique. Among the 142 individuals, 131 individuals shared 213 loci. Outlier analysis on 213 loci showed that 27 loci were putatively under selection between high elevation and low elevation populations. Outlier analysis on individual streams was also done to test for parallel patterns of adaptation, but there was no evidence of a parallel pattern. Population structure was observed using both the 27 outliers and 186 neutral loci and revealed similar population structure in both cases. Therefore, we cannot differentiate between selection and drift here. The highest genetic differentiation was observed between high elevation and low elevation populations of Booloumba Creek, with small levels of differentiation in the other two streams.
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Affiliation(s)
- Sharmeen Rahman
- Griffith School of Environment and Australian Rivers Institute, Griffith University, Brisbane, QLD, Australia
| | - Daniel Schmidt
- Griffith School of Environment and Australian Rivers Institute, Griffith University, Brisbane, QLD, Australia
| | - Jane M Hughes
- Griffith School of Environment and Australian Rivers Institute, Griffith University, Brisbane, QLD, Australia
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23
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Zucchi MI, Cordeiro EMG, Wu X, Lamana LM, Brown PJ, Manjunatha S, Viana JPG, Omoto C, Pinheiro JB, Clough SJ. Population Genomics of the Neotropical Brown Stink Bug, Euschistus heros: The Most Important Emerging Insect Pest to Soybean in Brazil. Front Genet 2019; 10:1035. [PMID: 31749834 PMCID: PMC6844245 DOI: 10.3389/fgene.2019.01035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/27/2019] [Indexed: 11/29/2022] Open
Abstract
Recent changes in soybean management like the adoption of transgenic crops and no-till farming, in addition to the expansion of cultivated areas into new virgin frontiers, are some of the hypotheses that can explain the rise of secondary pests, such as the Neotropical brown stink bug, Euschistus heros, in Brazil. To better access the risk of increased pests like E. heros and to determine probabilities for insecticide resistance spreading, it is necessary first to access the levels of the genetic diversity, how the genetic diversity is distributed, and how natural selection is acting upon the natural variation. Using the genotyping by sequencing (GBS) technique, we generated ~60,000 single-nucleotide polymorphisms (SNPs) distributed across the E. heros genome to answer some of those questions. The SNP data was used to investigate the pattern of genetic structure, hybridization and natural selection of this emerging pest. We found that E. heros populations presented similar levels of genetic diversity with slightly higher values at several central locations in Brazil. Our results also showed strong genetic structure separating northern and southern Brazilian regions (FST = 0.22; p-value = 0.000) with a very distinct hybrid zone at the central region. The analyses also suggest the possibility that GABA channels and odorant receptors might play a role in the process of natural selection. At least one marker was associated with soybean and beans crops, but no association between allele frequency and cotton was found. We discuss the implications of these findings in the management of emerging pests in agriculture, particularly in the context of large areas of monoculture such as soybean and cotton.
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Affiliation(s)
- Maria I Zucchi
- Institute of Biology, University of Campinas, Campinas, Brazil.,Agência Paulista de Tecnologia dos Agronegócios, Pólo Regional Centro-Sul, Piracicaba, Brazil
| | - Erick M G Cordeiro
- Department of Entomology, University of São Paulo-ESALQ/USP, Piracicaba, Brazil
| | - Xing Wu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Letícia Marise Lamana
- Department of Fitotecnia e Fitossanidade, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Patrick J Brown
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Shilpa Manjunatha
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - João Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Celso Omoto
- Department of Entomology, University of São Paulo-ESALQ/USP, Piracicaba, Brazil
| | - José B Pinheiro
- Department of Genetics, University of São Paulo-ESALQ/USP, Piracicaba, Brazil
| | - Steven J Clough
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,US Department of Agriculture, Agricultural Research Services, Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, Urbana, IL, United States
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25
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Estrada-Reyes ZM, Tsukahara Y, Amadeu RR, Goetsch AL, Gipson TA, Sahlu T, Puchala R, Wang Z, Hart SP, Mateescu RG. Signatures of selection for resistance to Haemonchus contortus in sheep and goats. BMC Genomics 2019; 20:735. [PMID: 31615414 PMCID: PMC6792194 DOI: 10.1186/s12864-019-6150-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/29/2019] [Indexed: 11/20/2022] Open
Abstract
Background Gastrointestinal nematode infection (GNI) is the most important disease affecting the small ruminant industry in U.S. The environmental conditions in the southern United States are ideal for the survival of the most pathogenic gastrointestinal nematode, Haemonchus contortus. Host genetic variation for resistance to H. contortus allows selective breeding for increased resistance of animals. This selection process increases the prevalence of particular alleles in sheep and goats and creates unique genetic patterns in the genome of these species. The aim of this study was to identify loci with divergent allelic frequencies in a candidate gene panel of 100 genes using two different approaches (frequentist and Bayesian) to estimate Fst outliers in three different breeds of sheep and goats exposed to H. contortus. Results Our results for sheep populations showed SNPs under selection in C3AR1, CSF3, SOCS2, NOS2, STAT5B, TGFB2 and IL2RA genes using frequentist and Bayesian approaches. For goats, SNPs in CD1D, ITGA9, IL12A, IL13RA1, CD86 and TGFB2 genes were under selection. Common signatures of selection in both species were observed in NOS2, TGFB2 and TLR4 genes. Directional selection was present in all SNPs evaluated in the present study. Conclusions A total of 13 SNPs within 7 genes of our candidate gene panel related to H. contortus exposure were identified under selection in sheep populations. For goats, 11 SNPs within 7 genes were identified under selection. Results from this study support the hypothesis that resistance to H. contortus is likely to be controlled by many loci. Shared signatures of selection related to mechanisms of immune protection against H. contortus infection in sheep and goats could be useful targets in breeding programs aimed to produce resistant animals with low FEC.
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Affiliation(s)
| | - Yoko Tsukahara
- American Institute for Goat Research, Langston University, Langston, OK, USA
| | - Rodrigo R Amadeu
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Arthur L Goetsch
- American Institute for Goat Research, Langston University, Langston, OK, USA
| | - Terry A Gipson
- American Institute for Goat Research, Langston University, Langston, OK, USA
| | - Tilahun Sahlu
- American Institute for Goat Research, Langston University, Langston, OK, USA
| | - Richard Puchala
- American Institute for Goat Research, Langston University, Langston, OK, USA
| | - Zaisen Wang
- American Institute for Goat Research, Langston University, Langston, OK, USA
| | - Steve P Hart
- American Institute for Goat Research, Langston University, Langston, OK, USA
| | - Raluca G Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
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26
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Grdiša M, Radosavljević I, Liber Z, Stefkov G, Ralli P, Chatzopoulou PS, Carović-Stanko K, Šatović Z. Divergent selection and genetic structure of Sideritis scardica populations from southern Balkan Peninsula as revealed by AFLP fingerprinting. Sci Rep 2019; 9:12767. [PMID: 31484938 PMCID: PMC6726656 DOI: 10.1038/s41598-019-49097-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/19/2019] [Indexed: 01/04/2023] Open
Abstract
Sideritis scardica Giseb. is a subalpine/alpine plant species endemic to the central part of the Balkan Peninsula. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) and environmental data to examine the adaptive genetic variations in S. scardica natural populations sampled in contrasting environments. A total of 226 AFLP loci were genotyped in 166 individuals from nine populations. The results demonstrated low gene diversity, ranging from 0.095 to 0.133 and significant genetic differentiation ranging from 0.115 to 0.408. Seven genetic clusters were revealed by Bayesian clustering methods as well as by Discriminant Analysis of Principal Components and each population formed its respective cluster. The exception were populations P02 Mt. Shara and P07 Mt. Vermio, that were admixed between two clusters. Both landscape genetic methods Mcheza and BayeScan identified a total of seven (3.10%) markers exhibiting higher levels of genetic differentiation among populations. The spatial analysis method Samβada detected 50 individual markers (22.12%) associated with bioclimatic variables, among them seven were identified by both Mcheza and BayeScan as being under directional selection. Four bioclimatic variables associated with five out of seven outliers were related to precipitation, suggesting that this variable is the key factor affecting the adaptive variation of S. scardica.
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Affiliation(s)
- Martina Grdiša
- University of Zagreb, Faculty of Agriculture, Department of Seed Science and Technology Svetošimunska 25, 10000, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia
| | - Ivan Radosavljević
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia.
- University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Marulićev trg 9A, 10000, Zagreb, Croatia.
| | - Zlatko Liber
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia
- University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Marulićev trg 9A, 10000, Zagreb, Croatia
| | - Gjoshe Stefkov
- University Ss. Cyril and Methodius Skopje, Faculty of Pharmacy, Vodnjanska 17, 1000, Skopje, Republic of North Macedonia
| | - Parthenopi Ralli
- Hellenic Agricultural Organization DEMETER, Institute of Breeding and Plant Genetic Resources, Thermi - Thessalonikis, PO Box 60411, 57001, Thessaloniki, Greece
| | - Paschalina S Chatzopoulou
- Hellenic Agricultural Organization DEMETER, Institute of Breeding and Plant Genetic Resources, Thermi - Thessalonikis, PO Box 60411, 57001, Thessaloniki, Greece
| | - Klaudija Carović-Stanko
- University of Zagreb, Faculty of Agriculture, Department of Seed Science and Technology Svetošimunska 25, 10000, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia
| | - Zlatko Šatović
- University of Zagreb, Faculty of Agriculture, Department of Seed Science and Technology Svetošimunska 25, 10000, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia
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27
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van Moorsel SJ, Schmid MW, Wagemaker NCAM, van Gurp T, Schmid B, Vergeer P. Evidence for rapid evolution in a grassland biodiversity experiment. Mol Ecol 2019; 28:4097-4117. [PMID: 31336411 DOI: 10.1111/mec.15191] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 12/14/2022]
Abstract
In long-term grassland experiments, positive biodiversity effects on plant productivity commonly increase with time. Subsequent glasshouse experiments showed that these strengthened positive biodiversity effects persist not only in the local environment but also when plants are transferred into a common environment. Thus, we hypothesized that community diversity had acted as a selective agent, resulting in the emergence of plant monoculture and mixture types with differing genetic composition. To test our hypothesis, we grew offspring from plants that were grown for eleven years in monoculture or mixture environments in a biodiversity experiment (Jena Experiment) under controlled glasshouse conditions in monocultures or two-species mixtures. We used epiGBS, a genotyping-by-sequencing approach combined with bisulphite conversion, to provide integrative genetic and epigenetic (i.e., DNA methylation) data. We observed significant divergence in genetic and DNA methylation data according to selection history in three out of five perennial grassland species, namely Galium mollugo, Prunella vulgaris and Veronica chamaedrys, with DNA methylation differences mostly reflecting the genetic differences. In addition, current diversity levels in the glasshouse had weak effects on epigenetic variation. However, given the limited genome coverage of the reference-free bisulphite method epiGBS, it remains unclear how much of the differences in DNA methylation was independent of underlying genetic differences. Our results thus suggest that selection of genetic variants, and possibly epigenetic variants, caused the rapid emergence of monoculture and mixture types within plant species in the Jena Experiment.
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Affiliation(s)
- Sofia J van Moorsel
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
| | - Marc W Schmid
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland.,MWSchmid GmbH, Zürich, Switzerland
| | - Niels C A M Wagemaker
- Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Bernhard Schmid
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland.,Department of Geography, University of Zürich, Zürich, Switzerland
| | - Philippine Vergeer
- Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Environmental Sciences, Plant Ecology and Nature Conservation Group, Wageningen University, Wageningen, The Netherlands
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28
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Choquet M, Smolina I, Dhanasiri AKS, Blanco-Bercial L, Kopp M, Jueterbock A, Sundaram AYM, Hoarau G. Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton Calanus finmarchicus. ROYAL SOCIETY OPEN SCIENCE 2019; 6:180608. [PMID: 30891252 PMCID: PMC6408391 DOI: 10.1098/rsos.180608] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 01/07/2019] [Indexed: 05/09/2023]
Abstract
Advances in next-generation sequencing technologies and the development of genome-reduced representation protocols have opened the way to genome-wide population studies in non-model species. However, species with large genomes remain challenging, hampering the development of genomic resources for a number of taxa including marine arthropods. Here, we developed a genome-reduced representation method for the ecologically important marine copepod Calanus finmarchicus (haploid genome size of 6.34 Gbp). We optimized a capture enrichment-based protocol based on 2656 single-copy genes, yielding a total of 154 087 high-quality SNPs in C. finmarchicus including 62 372 in common among the three locations tested. The set of capture probes was also successfully applied to the congeneric C. glacialis. Preliminary analyses of these markers revealed similar levels of genetic diversity between the two Calanus species, while populations of C. glacialis showed stronger genetic structure compared to C. finmarchicus. Using this powerful set of markers, we did not detect any evidence of hybridization between C. finmarchicus and C. glacialis. Finally, we propose a shortened version of our protocol, offering a promising solution for population genomics studies in non-model species with large genomes.
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Affiliation(s)
- Marvin Choquet
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Author for correspondence: Marvin Choquet e-mail:
| | - Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | | | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Arvind Y. M. Sundaram
- Norwegian Sequencing Centre, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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29
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Heimeier D, Alexander A, Hamner RM, Pichler F, Baker CS. The Influence of Selection on MHC DQA and DQB Haplotypes in the Endemic New Zealand Hector’s and Māui Dolphins. J Hered 2018; 109:744-756. [DOI: 10.1093/jhered/esy050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/19/2018] [Indexed: 01/15/2023] Open
Affiliation(s)
- Dorothea Heimeier
- School of Biological Sciences, University of Auckland, Private Bag, Auckland, New Zealand
| | - Alana Alexander
- Biodiversity Institute, University of Kansas, Jayhawk Boulevard, Lawrence, KS
| | - Rebecca M Hamner
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, SE Marine Science Drive, Newport, OR
- School of Biological Sciences, University of Auckland, Private Bag, Auckland, New Zealand
| | - Franz Pichler
- School of Biological Sciences, University of Auckland, Private Bag, Auckland, New Zealand
| | - C Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, SE Marine Science Drive, Newport, OR
- School of Biological Sciences, University of Auckland, Private Bag, Auckland, New Zealand
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30
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Parker DJ, Wiberg RAW, Trivedi U, Tyukmaeva VI, Gharbi K, Butlin RK, Hoikkala A, Kankare M, Ritchie MG. Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation. Genome Biol Evol 2018; 10:2086-2101. [PMID: 30010752 PMCID: PMC6107330 DOI: 10.1093/gbe/evy147] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 12/25/2022] Open
Abstract
The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here, we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species known. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm-adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. We also look for evidence of accelerated divergence between D. montana and D. virilis, a previously sequenced relative, but do not find strong evidence for divergent selection on coding sequence variation. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. Finally, we also resequenced three populations of D. montana from across its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.
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Affiliation(s)
- Darren J Parker
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
- Department of Ecology and Evolution, University of Lausanne, Biophore, Switzerland
| | - R Axel W Wiberg
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Venera I Tyukmaeva
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Karim Gharbi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences, The University of Sheffield, UK
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Michael G Ritchie
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
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31
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Nevado B, Contreras-Ortiz N, Hughes C, Filatov DA. Pleistocene glacial cycles drive isolation, gene flow and speciation in the high-elevation Andes. THE NEW PHYTOLOGIST 2018; 219:779-793. [PMID: 29862512 DOI: 10.1111/nph.15243] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/30/2018] [Indexed: 05/10/2023]
Abstract
Mountain ranges are amongst the most species-rich habitats, with many large and rapid evolutionary radiations. The tempo and mode of diversification in these systems are key unanswered questions in evolutionary biology. Here we study the Andean Lupinus radiation to understand the processes driving very rapid diversification in montane systems. We use genomic and transcriptomic data of multiple species and populations, and apply phylogenomic and demographic analyses to test whether diversification proceeded without interspecific gene flow - as expected if Andean orogeny and geographic isolation were the main drivers of diversification - or if diversification was accompanied by gene flow, in which case other processes were probably involved. We uncover several episodes of gene flow between species, including very recent events likely to have been prompted by changes in habitat connectivity during Pleistocene glacial cycles. Furthermore, we find that gene flow between species was heterogeneously distributed across the genome. We argue that exceptionally fast diversification of Andean Lupinus was partly a result of Late Pleistocene glacial cycles, with associated cycles of expansion and contraction driving geographic isolation or secondary contact of species. Furthermore, heterogeneous gene flow across the genome suggests a role for selection and ecological speciation in rapid diversification in this system.
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Affiliation(s)
- Bruno Nevado
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Natalia Contreras-Ortiz
- Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Apartado Aéreo, 4976, Bogotá, Colombia
- Jardín Botánico de Bogotá 'José Celestino Mutis', Avenida Calle 63 No. 68-95, Bogotá DC, Colombia
| | - Colin Hughes
- Department of Systematic & Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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32
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Folkertsma R, Westbury MV, Eccard JA, Hofreiter M. The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:446-447. [PMID: 33474199 PMCID: PMC7800005 DOI: 10.1080/23802359.2018.1457994] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus.
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Affiliation(s)
- Remco Folkertsma
- Department of Mathematics and Natural Science, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Department of Mathematics and Natural Sciences, Animal Ecology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael V Westbury
- Department of Mathematics and Natural Science, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jana A Eccard
- Department of Mathematics and Natural Sciences, Animal Ecology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Department of Mathematics and Natural Science, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes. G3-GENES GENOMES GENETICS 2018; 8:887-897. [PMID: 29343494 PMCID: PMC5844309 DOI: 10.1534/g3.117.300493] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vector-borne diseases are responsible for > 1 million deaths every year but genomic resources for most species responsible for their transmission are limited. This is true for neglected diseases such as sleeping sickness (Human African Trypanosomiasis), a disease caused by Trypanosoma parasites vectored by several species of tseste flies within the genus Glossina. We describe an integrative approach that identifies statistical associations between trypanosome infection status of Glossina fuscipes fuscipes (Gff) flies from Uganda, for which functional studies are complicated because the species cannot be easily maintained in laboratory colonies, and ∼73,000 polymorphic sites distributed across the genome. Then, we identify candidate genes involved in Gff trypanosome susceptibility by taking advantage of genomic resources from a closely related species, G. morsitans morsitans (Gmm). We compiled a comprehensive transcript library from 72 published and unpublished RNAseq experiments of trypanosome-infected and uninfected Gmm flies, and improved the current Gmm transcriptome assembly. This new assembly was then used to enhance the functional annotations on the Gff genome. As a consequence, we identified 56 candidate genes in the vicinity of the 18 regions associated with Trypanosoma infection status in Gff. Twenty-nine of these genes were differentially expressed (DE) among parasite-infected and uninfected Gmm, suggesting that their orthologs in Gff may correlate with disease transmission. These genes were involved in DNA regulation, neurophysiological functions, and immune responses. We highlight the power of integrating population and functional genomics from related species to enhance our understanding of the genetic basis of physiological traits, particularly in nonmodel organisms.
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Van Bocxlaer B. Hierarchical structure of ecological and non-ecological processes of differentiation shaped ongoing gastropod radiation in the Malawi Basin. Proc Biol Sci 2018; 284:rspb.2017.1494. [PMID: 28904143 DOI: 10.1098/rspb.2017.1494] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/07/2017] [Indexed: 02/03/2023] Open
Abstract
Ecological processes, non-ecological processes or a combination of both may cause reproductive isolation and speciation, but their specific roles and potentially complex interactions in evolutionary radiations remain poorly understood, which defines a central knowledge gap at the interface of microevolution and macroevolution. Here I examine genome scans in combination with phenotypic and environmental data to disentangle how ecological and non-ecological processes contributed to population differentiation and speciation in an ongoing radiation of Lanistes gastropods from the Malawi Basin. I found a remarkable hierarchical structure of differentiation mechanisms in space and time: neutral and mutation-order processes are older and occur mainly between regions, whereas more recent adaptive processes are the main driver of genetic differentiation and reproductive isolation within regions. The strongest differentiation occurs between habitats and between regions, i.e. when ecological and non-ecological processes act synergistically. The structured occurrence of these processes based on the specific geographical setting and ecological opportunities strongly influenced the potential for evolutionary radiation. The results highlight the importance of interactions between various mechanisms of differentiation in evolutionary radiations, and suggest that non-ecological processes are important in adaptive radiations, including those of cichlids. Insight into such interactions is critical to understanding large-scale patterns of organismal diversity.
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Affiliation(s)
- Bert Van Bocxlaer
- CNRS, Université de Lille, UMR 8198 - Evo-Eco-Paléo, 59000 Lille, France .,Limnology Unit, Department of Biology, Ghent University, 9000 Ghent, Belgium.,Department of Animal Ecology and Systematics, Justus Liebig University, 35392 Giessen, Germany
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35
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Meyer X, Chopard B, Salamin N. Accelerating Bayesian inference for evolutionary biology models. Bioinformatics 2017; 33:669-676. [PMID: 28025203 PMCID: PMC5408833 DOI: 10.1093/bioinformatics/btw712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/11/2016] [Indexed: 12/02/2022] Open
Abstract
Motivation Bayesian inference is widely used nowadays and relies largely on Markov chain Monte Carlo (MCMC) methods. Evolutionary biology has greatly benefited from the developments of MCMC methods, but the design of more complex and realistic models and the ever growing availability of novel data is pushing the limits of the current use of these methods. Results We present a parallel Metropolis-Hastings (M-H) framework built with a novel combination of enhancements aimed towards parameter-rich and complex models. We show on a parameter-rich macroevolutionary model increases of the sampling speed up to 35 times with 32 processors when compared to a sequential M-H process. More importantly, our framework achieves up to a twentyfold faster convergence to estimate the posterior probability of phylogenetic trees using 32 processors when compared to the well-known software MrBayes for Bayesian inference of phylogenetic trees. Availability and Implementation https://bitbucket.org/XavMeyer/hogan Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xavier Meyer
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,Department of Computer Science, University of Geneva, 1211 Geneva, Switzerland
| | - Bastien Chopard
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,Department of Computer Science, University of Geneva, 1211 Geneva, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
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De Luca D, Cennamo P, Del Guacchio E, Di Novella R, Caputo P. Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity. Genetica 2017; 146:29-44. [PMID: 29030763 DOI: 10.1007/s10709-017-9994-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/25/2017] [Indexed: 11/26/2022]
Abstract
Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.
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Affiliation(s)
- Daniele De Luca
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, via Foria 223, 80139, Naples, Italy.
| | - Paola Cennamo
- Facoltà di Lettere, Università degli Studi Suor Orsola Benincasa di Napoli, Via Santa Caterina da Siena 37, 80135, Naples, Italy
| | - Emanuele Del Guacchio
- Facoltà di Scienze della Formazione, Università degli Studi Suor Orsola Benincasa di Napoli, Via Santa Caterina da Siena 37, 80135, Naples, Italy
| | | | - Paolo Caputo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, via Foria 223, 80139, Naples, Italy
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RADseq provides evidence for parallel ecotypic divergence in the autotetraploid Cochlearia officinalis in Northern Norway. Sci Rep 2017; 7:5573. [PMID: 28717144 PMCID: PMC5514025 DOI: 10.1038/s41598-017-05794-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/02/2017] [Indexed: 11/08/2022] Open
Abstract
Speciation encompasses a continuum over time from freely interbreeding populations to reproductively isolated species. Along this process, ecotypes - the result of local adaptation - may be on the road to new species. We investigated whether three autotetraploid Cochlearia officinalis ecotypes, adapted to different habitats (beach, estuary, spring), are genetically differentiated and result from parallel ecotypic divergence in two distinct geographical regions. We obtained genetic data from thousands of single nucleotide polymorphisms (SNPs) from restriction-site associated DNA sequencing (RADseq) and from six microsatellite markers for 12 populations to assess genetic divergence at ecotypic, geographic and population level. The genetic patterns support differentiation among ecotypes as suggested by morphology and ecology. The data fit a scenario where the ancestral beach ecotype has recurrently and polytopically given rise to the estuary and spring ecotypes. Several ecologically-relevant loci with consistent non-random segregating patterns are identified across the recurrent origins, in particular around genes related to salt stress. Despite being ecologically distinct, the Cochlearia ecotypes still represent an early stage in the process of speciation, as reproductive isolation has not (yet) developed. A sequenced annotated genome is needed to specifically target candidate genes underlying local adaptation.
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Plenk K, Bardy K, Höhn M, Thiv M, Kropf M. No obvious genetic erosion, but evident relict status at the westernmost range edge of the Pontic-Pannonian steppe plant Linum flavum L. (Linaceae) in Central Europe. Ecol Evol 2017; 7:6527-6539. [PMID: 28861254 PMCID: PMC5574788 DOI: 10.1002/ece3.2990] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 11/08/2022] Open
Abstract
We investigate patterns of genetic variation along an east–west transect of Central European populations of Linum flavum and interpret the Quaternary history of its peripheral populations, especially those at the westernmost isolated range edge, discussing their migrations and possible relict status. We defined our peripheral transect across three study regions from Central Hungary, eastern Austria to southwestern Germany. Using AFLP fingerprinting and cpDNA sequence variation (rpL16 intron, atpI‐H), we analyzed 267 and 95 individuals, respectively, representing each study region by four populations. Hierarchical AMOVA (AFLPs) indicated significant variation among study regions (12% of total variance) and moderate differentiation between populations (10%). Population differentiation was high at the westernmost range edge (11.5%, Germany), but also in the east (13.4%, Hungary), compared to the Austrian study region (8.6%). Correspondingly, AFLP diversity was highest in the center of the study transect in eastern Austria. CpDNA haplotypes support a pattern of regional structuring with the strongest separation of the westernmost range edge, and some haplotype sharing among Austrian and Hungarian individuals. Equilibrating nucleotide versus haplotype diversity patterns, the highly diverse populations at the Pannonian range edge (Austria) indicate long‐term persistence, while Central Pannonian populations are obviously effected by recent bottlenecks. Intermediate nucleotide, but high haplotype diversity within the westernmost exclave (Swabian Alb), is indicative of a founder bottleneck during its pre‐LGM or early postglacial migration history, followed by sufficient time to accumulate cpDNA variation. The not obviously reduced genetic diversity and distinctiveness of L. flavum at the westernmost range edge suggest a long‐term persistence (relict status) of populations in this region, where the species has survived probably even the Würm glaciation in extra‐Mediterranean refugia. This genetic relict variation represents an important part of the overall genetic diversity found in the western periphery of this steppe plant and highlights the high conservation priority of respective gene pools.
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Affiliation(s)
- Kristina Plenk
- Institute for Integrative Nature Conservation Research University of Natural Resources and Life Sciences (BOKU) Vienna Austria
| | - Katharina Bardy
- Institute for Integrative Nature Conservation Research University of Natural Resources and Life Sciences (BOKU) Vienna Austria
| | - Maria Höhn
- Department of Botany and Botanical Garden of Soroksár Faculty of Horticultural Science Szent István University Budapest Hungary
| | - Mike Thiv
- Botany Department Stuttgart State Museum of Natural History Stuttgart Germany
| | - Matthias Kropf
- Institute for Integrative Nature Conservation Research University of Natural Resources and Life Sciences (BOKU) Vienna Austria
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39
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Beltrán DM, Schizas NV, Appeldoorn RS, Prada C. Effective Dispersal of Caribbean Reef Fish is Smaller than Current Spacing Among Marine Protected Areas. Sci Rep 2017; 7:4689. [PMID: 28680075 PMCID: PMC5498645 DOI: 10.1038/s41598-017-04849-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/18/2017] [Indexed: 11/09/2022] Open
Abstract
The oceans are deteriorating at a fast pace. Conservation measures, such as Marine Protected Areas, are being implemented to relieve areas from local stressors and allow populations to restore to natural levels. Successful networks of MPAs operate if the space among MPAs is smaller than the dispersal capacity of the species under protection. We studied connectivity patterns across populations in a series of MPAs in the common yellowhead Jawfish, Opistognathus aurifrons. Using the power of genome-wide variation, we estimated that the maximum effective dispersal is 8.3 km. We found that MPAs exchange migrants likely via intermediate unprotected habitats through stepping stone dispersal. At scales >50 km such connectivity is decreased, particularly across the Mona Passage. The MPA network studied would be unable to maintain connectivity of these small benthic fishes if habitat in between them is extirpated. Our study highlights the power of SNPs to derive effective dispersal distance and the ability of SNPs to make inferences from single individuals. Given that overall reef fish diversity is driven by species with life histories similar to that of the yellowhead jawfish, managers face a challenge to develop strategies that allow connectivity and avoid isolation of populations and their possible extinction.
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Affiliation(s)
- Diana M Beltrán
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico, USA
| | - Nikolaos V Schizas
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico, USA
| | - Richard S Appeldoorn
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico, USA
| | - Carlos Prada
- Smithsonian Tropical Research Institute, Box 2072, Balboa, Panama.
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40
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Sikkink KL, Kobiela ME, Snell-Rood EC. Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. BMC Genomics 2017; 18:412. [PMID: 28549454 PMCID: PMC5446745 DOI: 10.1186/s12864-017-3787-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/11/2017] [Indexed: 12/30/2022] Open
Abstract
Background Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades. Results First, we show that the agricultural population has diverged phenotypically relative to a nonagricultural population: when reared on a host plant distantly related to canola, the agricultural population is smaller and more likely to go into diapause than the nonagricultural population. Second, drawing from deep sequencing runs from six individuals from the agricultural population, we assembled the gut transcriptome of this population. Then, we sequenced RNA transcripts from the midguts of 96 individuals from this canola agricultural population and the nonagricultural population in order to describe patterns of genomic divergence between the two. While population divergence is low, 235 genes show evidence of significant differentiation between populations. These genes are significantly enriched for cofactor and small molecule metabolic processes, and many genes also have transporter or catalytic activity. Analyses of population structure suggest the agricultural population contains a subset of the genetic variation in the nonagricultural population. Conclusions Taken together, our results suggest that adaptation of cabbage whites to an agricultural environment occurred at least in part through selection on standing genetic variation. Both the phenotypic and genetic data are consistent with the idea that this pest has adapted to an abundant and predictable agricultural resource through a narrowing of niche breadth and loss of genetic variants rather than de novo gain of adaptive alleles. The present research develops genomic resources to pave the way for future studies using cabbage whites as a model contributing to our understanding of adaptation to agricultural environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3787-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kristin L Sikkink
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA.
| | - Megan E Kobiela
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA
| | - Emilie C Snell-Rood
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul, MN, 55108, USA
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41
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Andersson A, Jansson E, Wennerström L, Chiriboga F, Arnyasi M, Kent MP, Ryman N, Laikre L. Complex genetic diversity patterns of cryptic, sympatric brown trout (Salmo trutta) populations in tiny mountain lakes. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0972-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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An M, Deng M, Zheng SS, Jiang XL, Song YG. Introgression Threatens the Genetic Diversity of Quercus austrocochinchinensis (Fagaceae), an Endangered Oak: A Case Inferred by Molecular Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:229. [PMID: 28270827 PMCID: PMC5318416 DOI: 10.3389/fpls.2017.00229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/06/2017] [Indexed: 05/25/2023]
Abstract
Natural introgression can cause negative effects where rare species experience genetic assimilation and invade by their abundant congeners. Quercus austrocochinchinensis and Q. kerrii (subgenus Cyclobalanopsis) are a pair of closely related species in the Indo-China area. Morphological intermediates of the two species have been reported in this region. In this study, we used AFLP, SSR and two key leaf morphological diagnostic traits to study the two Q. austrocochinchinensis populations, two pure Q. kerrii and two putative hybrid populations in China. Rates of individual admixture were examined using the Bayesian clustering programs STRUCTURE and NewHybrids, with no a priori species assignment. In total, we obtained 151 SSR alleles and 781 polymorphic loci of AFLP markers. Population differentiation inferred by SSR and AFLP was incoherent with recognized species boundaries. Bayesian admixture analyses and principal coordinate analysis identified more hybrids and backcrossed individuals than morphological intermediates in the populations. SSR inferred a wide genetic assimilation in Q. austrocochinchinensis, except for subpopulation D2 in the core area of Xi-Shuang-Ban-Na Nature Reserve (XSBN). However, AFLP recognized more Q. austrocochinchinensis purebreds than SSR. Analysis using NewHybrids on AFLP data indicated that these hybridized individuals were few F2 and predominantly backcrosses with both parental species. All these evidences indicate the formation of a hybrid swarm at XSBN where the two species co-exist. Both AFLP and SSR recognized that the core protected area of XSBN (D2) has a high percentage of Q. austrocochinchinensis purebreds and a unique germplasm. The Hainan population and the other subpopulations of XSBN of the species might have lost their genetic integrity. Our results revealed a clear genetic differentiation in the populations and subpopulations of Q. austrocochinchinensis and ongoing introgression between Q. austrocochinchinensis and Q. kerrii at the disturbed contact areas. Combining the results from genetic and morphological analyses, the conservation of subpopulation D2 should be prioritized. Conservation and restoration of the integrity of tropical ravine rainforest is an important long-term goal for the successful conservation of Q. austrocochinchinensis. The fine-scale landscape might play an essential role in shaping the spatial patterns of hybridization. Further studies are needed to evaluate these patterns and dynamics.
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Affiliation(s)
- Miao An
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
| | - Min Deng
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
| | - Si-Si Zheng
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
| | - Xiao-Long Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
| | - Yi-Gang Song
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
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43
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Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour 2016; 17:142-152. [PMID: 27860289 DOI: 10.1111/1755-0998.12635] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 12/26/2022]
Abstract
Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.
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Affiliation(s)
- David B Lowry
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Sean Hoban
- The Morton Arboretum, Lisle, IL, USA.,National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA, 01908, USA
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35406, USA
| | - Michael F Antolin
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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Larsson J, Lönn M, Lind EE, Świeżak J, Smolarz K, Grahn M. Sewage treatment plant associated genetic differentiation in the blue mussel from the Baltic Sea and Swedish west coast. PeerJ 2016; 4:e2628. [PMID: 27812424 PMCID: PMC5088577 DOI: 10.7717/peerj.2628] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 09/29/2016] [Indexed: 12/31/2022] Open
Abstract
Human-derived environmental pollutants and nutrients that reach the aquatic environment through sewage effluents, agricultural and industrial processes are constantly contributing to environmental changes that serve as drivers for adaptive responses and evolutionary changes in many taxa. In this study, we examined how two types of point sources of aquatic environmental pollution, harbors and sewage treatment plants, affect gene diversity and genetic differentiation in the blue mussel in the Baltic Sea area and off the Swedish west coast (Skagerrak). Reference sites (REF) were geographically paired with sites from sewage treatments plant (STP) and harbors (HAR) with a nested sampling scheme, and genetic differentiation was evaluated using a high-resolution marker amplified fragment length polymorphism (AFLP). This study showed that genetic composition in the Baltic Sea blue mussel was associated with exposure to sewage treatment plant effluents. In addition, mussel populations from harbors were genetically divergent, in contrast to the sewage treatment plant populations, suggesting that there is an effect of pollution from harbors but that the direction is divergent and site specific, while the pollution effect from sewage treatment plants on the genetic composition of blue mussel populations acts in the same direction in the investigated sites.
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Affiliation(s)
- Josefine Larsson
- School of Natural Science, Technology and Environmental Studies, Södertörn University, Huddinge, Stockholm, Sweden
| | - Mikael Lönn
- School of Natural Science, Technology and Environmental Studies, Södertörn University, Huddinge, Stockholm, Sweden
| | - Emma E. Lind
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Stockholm, Stockholm, Sweden
| | - Justyna Świeżak
- Department of Marine Ecosystem Functioning, University of Gdansk, Institute of Oceanography, Gdynia, Poland
| | - Katarzyna Smolarz
- Department of Marine Ecosystem Functioning, University of Gdansk, Institute of Oceanography, Gdynia, Poland
| | - Mats Grahn
- School of Natural Science, Technology and Environmental Studies, Södertörn University, Huddinge, Stockholm, Sweden
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45
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Maroso F, Franch R, Dalla Rovere G, Arculeo M, Bargelloni L. RAD SNP markers as a tool for conservation of dolphinfish Coryphaena hippurus in the Mediterranean Sea: Identification of subtle genetic structure and assessment of populations sex-ratios. Mar Genomics 2016; 28:57-62. [PMID: 27450636 DOI: 10.1016/j.margen.2016.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 01/10/2023]
Abstract
Dolphinfish is an important fish species for both commercial and sport fishing, but so far limited information is available on genetic variability and pattern of differentiation of dolphinfish populations in the Mediterranean basin. Recently developed techniques allow genome-wide identification of genetic markers for better understanding of population structure in species with limited genome information. Using restriction-site associated DNA analysis we successfully genotyped 140 individuals of dolphinfish from eight locations in the Mediterranean Sea at 3324 SNP loci. We identified 311 sex-related loci that were used to assess sex-ratio in dolphinfish populations. In addition, we identified a weak signature of genetic differentiation of the population closer to Gibraltar Strait in comparison to other Mediterranean populations, which might be related to introgression of individuals from Atlantic. No further genetic differentiation could be detected in the other populations sampled, as expected considering the known highly mobility of the species. The results obtained improve our knowledge of the species and can help managing dolphinfish stock in the future.
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Affiliation(s)
- Francesco Maroso
- Department of Compared Biomedicine and Food Science, University of Padova, viale dell'Università, 16, 35020 Legnaro, Italy.
| | - Rafaella Franch
- Department of Compared Biomedicine and Food Science, University of Padova, viale dell'Università, 16, 35020 Legnaro, Italy
| | - Giulia Dalla Rovere
- Department of Compared Biomedicine and Food Science, University of Padova, viale dell'Università, 16, 35020 Legnaro, Italy
| | - Marco Arculeo
- Department STEBICEF, University of Palermo, CoNISMa, via Archirafi, 18, 90123 Palermo, Italy
| | - Luca Bargelloni
- Department of Compared Biomedicine and Food Science, University of Padova, viale dell'Università, 16, 35020 Legnaro, Italy
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46
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Guo B, Lu D, Liao WB, Merilä J. Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toadBufo andrewsi. Mol Ecol 2016; 25:3884-900. [PMID: 27289071 DOI: 10.1111/mec.13722] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 06/02/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Baocheng Guo
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| | - Di Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Juha Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
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47
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Muñoz J, Chaturvedi A, De Meester L, Weider LJ. Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS). Sci Rep 2016; 6:28569. [PMID: 27346179 PMCID: PMC4921830 DOI: 10.1038/srep28569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/01/2016] [Indexed: 12/01/2022] Open
Abstract
The keystone aquatic herbivore Daphnia has been studied for more than 150 years in the context of evolution, ecology and ecotoxicology. Although it is rapidly becoming an emergent model for environmental and population genomics, there have been limited genome-wide level studies in natural populations. We report a unique resource of novel Single Nucleotide Polymorphic (SNP) markers for Daphnia pulicaria using the reduction in genomic complexity with the restriction enzymes approach, genotyping-by-sequencing. Using the genome of D. pulex as a reference, SNPs were scored for 53 clones from five natural populations that varied in lake trophic status. Our analyses resulted in 32,313 highly confident and bi-allelic SNP markers. 1,364 outlier SNPs were mapped on the annotated D. pulex genome, which identified 2,335 genes, including 565 within functional genes. Out of 885 EuKaryotic Orthologous Groups that we found from outlier SNPs, 294 were involved in three metabolic and four regulatory pathways. Bayesian-clustering analyses showed two distinct population clusters representing the possible combined effects of geography and lake trophic status. Our results provide an invaluable tool for future population genomics surveys in Daphnia targeting informative regions related to physiological processes that can be linked to the ecology of this emerging eco-responsive taxon.
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Affiliation(s)
- Joaquín Muñoz
- Doñana Biological Station (CSIC), Isla de La Cartuja, Av. Américo Vespucio S/N, 41092-Seville, Spain.,Department of Biology, Program in Ecology and Evolutionary Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Anurag Chaturvedi
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda. G3-GENES GENOMES GENETICS 2016; 6:1573-84. [PMID: 27172181 PMCID: PMC4889654 DOI: 10.1534/g3.116.027235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The tsetse fly Glossina fuscipes fuscipes (Gff) is the insect vector of the two forms of Human African Trypanosomiasis (HAT) that exist in Uganda. Understanding Gff population dynamics, and the underlying genetics of epidemiologically relevant phenotypes is key to reducing disease transmission. Using ddRAD sequence technology, complemented with whole-genome sequencing, we developed a panel of ∼73,000 single-nucleotide polymorphisms (SNPs) distributed across the Gff genome that can be used for population genomics and to perform genome-wide-association studies. We used these markers to estimate genomic patterns of linkage disequilibrium (LD) in Gff, and used the information, in combination with outlier-locus detection tests, to identify candidate regions of the genome under selection. LD in individual populations decays to half of its maximum value (r(2) max/2) between 1359 and 2429 bp. The overall LD estimated for the species reaches r(2) max/2 at 708 bp, an order of magnitude slower than in Drosophila Using 53 infected (Trypanosoma spp.) and uninfected flies from four genetically distinct Ugandan populations adapted to different environmental conditions, we were able to identify SNPs associated with the infection status of the fly and local environmental adaptation. The extent of LD in Gff likely facilitated the detection of loci under selection, despite the small sample size. Furthermore, it is probable that LD in the regions identified is much higher than the average genomic LD due to strong selection. Our results show that even modest sample sizes can reveal significant genetic associations in this species, which has implications for future studies given the difficulties of collecting field specimens with contrasting phenotypes for association analysis.
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Yang AH, Wei N, Fritsch PW, Yao XH. AFLP Genome Scanning Reveals Divergent Selection in Natural Populations of Liriodendron chinense (Magnoliaceae) along a Latitudinal Transect. FRONTIERS IN PLANT SCIENCE 2016; 7:698. [PMID: 27303414 PMCID: PMC4880593 DOI: 10.3389/fpls.2016.00698] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/06/2016] [Indexed: 05/27/2023]
Abstract
Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci) provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae) along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Both frequency-based (Dfdist and BayeScan) and correlation-based (MLM) methods were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity toward the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation, and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies.
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Affiliation(s)
- Ai-Hong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Na Wei
- Department of Ecology and Evolutionary Biology, University of MichiganAnn Arbor, MI, USA
| | | | - Xiao-Hong Yao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
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Wang T, Wang Z, Xia F, Su Y. Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China. Sci Rep 2016; 6:25031. [PMID: 27113970 PMCID: PMC4844950 DOI: 10.1038/srep25031] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/04/2016] [Indexed: 01/02/2023] Open
Abstract
Cephalotaxus oliveri is an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution of C. oliveri. In order to comprehend the mechanism of adaptive evolution to climate variation, we employed ISSR markers to detect adaptive evolution loci, to identify the association between variation in temperature and precipitation and adaptive loci, and to investigate the genetic structure for 22 C. oliveri natural populations. In total, 14 outlier loci were identified, of which five were associated with temperature and precipitation. Among outlier loci, linkage disequilibrium (LD) was high (42.86%), which also provided strong evidence for selection. In addition, C. oliveri possessed high genetic variation (93.31%) and population differentiation, which may provide raw material to evolution and accelerate local adaptation, respectively. Ecological niche modeling showed that global warming will cause a shift for populations of C. oliveri from south to north with a shrinkage of southern areas. Our results contribute to understand the potential response of conifers to climatic changes, and provide new insights for conifer resource management and conservation strategies.
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Affiliation(s)
- Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhen Wang
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fan Xia
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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