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Ono H, Nagai K, Higuchi H. Dark Morph of the Oriental Honey-Buzzard ( Pernis ptilorhynchus orientalis) is Attributable to Specific MC1R Haplotypes. Zoolog Sci 2024; 41:342-350. [PMID: 39093280 DOI: 10.2108/zs230092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/21/2024] [Indexed: 08/04/2024]
Abstract
A thorough understanding of the development of complex plumages in birds necessitates the acquisition of genetic data pertaining to the mechanism underlying this phenomenon from various avian species. The oriental honey-buzzard (Pernis ptilorhynchus orientalis), a tropical summer migrant to Northeast Asia, including Japan, exemplifies this aspect owing to the diversity of its ventral coloration and intra-feather barring patterns. However, genetic polymorphism responsible for this diversity has not been identified yet. This study aimed to investigate the link between dark-plumed phenotypes of this subspecies and haplotypes of the melanocortin-1-receptor (MC1R) gene. A draft sequence of MC1R was constructed using next generation sequencing and subsequently amplified using designed polymerase chain reaction (PCR) primers. The genome sequences of 32 honey-buzzard individuals were determined using PCR, and 12 MC1R haplotype sequences were obtained. Among these haplotypes, we found that unique haplotypes with nine non-synonymous substitutions and four or five synonymous substitutions in the coding region had a perfect correlation with the dark-plumed phenotype. The lack of correlation between the genotype of ASIP coding region and plumage phenotype reiterated that the dark morph is attributable to specific MC1R haplotypes. The absence of a correlation between genetic polymorphisms of MC1R and the intra-feather barring patterns, as well as the diversity observed within lighter ground color classes (pale and intermediate), implies the involvement of alternative molecular mechanisms in the manifestation of the aforementioned phenotypes.
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Affiliation(s)
- Hirotake Ono
- Department of Biology, Keio University, Yokohama, Kanagawa 223-8521, Japan,
- Research and Education Center for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan
| | - Kazuya Nagai
- Research and Education Center for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Hiroyoshi Higuchi
- Research and Education Center for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan
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2
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Manlik O, Krützen M, Kopps AM, Mann J, Bejder L, Allen SJ, Frère C, Connor RC, Sherwin WB. Is MHC diversity a better marker for conservation than neutral genetic diversity? A case study of two contrasting dolphin populations. Ecol Evol 2019; 9:6986-6998. [PMID: 31380027 PMCID: PMC6662329 DOI: 10.1002/ece3.5265] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia-one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty-three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population-for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human-induced changes to the coastal ecosystem it inhabits.
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Affiliation(s)
- Oliver Manlik
- Biology Department, College of ScienceUnited Arab Emirates UniversityAl AinUnited Arab Emirates
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Michael Krützen
- Department of AnthropologyUniversity of ZurichZurichSwitzerland
| | - Anna M. Kopps
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Janet Mann
- Department of Biology and Department of PsychologyGeorgetown UniversityWashingtonDistrict of Columbia
| | - Lars Bejder
- Marine Mammal Research Program, Hawai'i Institute of Marine BiologyUniversity of Hawai'i at ManoaKaneoheHonolulu
- Aquatic Megafauna Research Unit, School of Veterinary and Life SciencesMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Simon J. Allen
- School of Biological SciencesUniversity of BristolBristolUnited Kingdom
| | - Celine Frère
- Faculty of Science, Health, Education and EngineeringUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
| | | | - William B. Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Aquatic Megafauna Research Unit, School of Veterinary and Life SciencesMurdoch UniversityMurdochWestern AustraliaAustralia
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3
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Vanessa Huml J, Taylor MI, Edwin Harris W, Sen R, Ellis JS. Neutral variation does not predict immunogenetic variation in the European grayling (Thymallus thymallus)-implications for management. Mol Ecol 2018; 27:4157-4173. [PMID: 30194888 DOI: 10.1111/mec.14864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/21/2018] [Accepted: 08/29/2018] [Indexed: 11/28/2022]
Abstract
Preservation of genetic diversity is critical to successful conservation, and there is increasing demand for the inclusion of ecologically meaningful genetic information in management decisions. Supportive breeding programmes are increasingly implemented to combat declines in many species, yet their effect on adaptive genetic variation is understudied. This is despite the fact that supportive breeding may interfere with natural evolutionary processes. Here, we assessed the performance of neutral and adaptive markers (major histocompatibility complex; MHC) to inform management of European grayling (Thymallus thymallus), which routinely involves supplementation of natural populations with hatchery-reared fish (stocking). This study is the first to characterize MH II DAA and DAB loci in grayling and to investigate immune genetic variation in relation to management practice in this species. High-throughput Illumina sequencing of "introduced," "stocked native" and "non-stocked native" populations revealed significantly higher levels of allelic richness and heterozygosity for MH markers than microsatellites exclusively in non-stocked native populations. Likewise, significantly lower differentiation at the MH II than for microsatellites was apparent when considering non-stocked native populations, but not stocked populations. We developed a simulation model to test the effects of relaxation of selection during the early life stage within captivity. Dependent on the census population size and stocking intensity, there may be long-term effects of stocking on MH II, but not neutral genetic diversity. This is consistent with our empirical results. This study highlights the necessity for considering adaptive genetic variation in conservation decisions and raises concerns about the efficiency of stocking as a management practice.
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Affiliation(s)
- J Vanessa Huml
- School of Science & Environment, Manchester Metropolitan University, Manchester, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - W Edwin Harris
- School of Science & Environment, Manchester Metropolitan University, Manchester, UK
| | - Robin Sen
- School of Science & Environment, Manchester Metropolitan University, Manchester, UK
| | - Jonathan S Ellis
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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4
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Gilroy DL, van Oosterhout C, Komdeur J, Richardson DS. Toll-like receptor variation in the bottlenecked population of the endangered Seychelles warbler. Anim Conserv 2016. [DOI: 10.1111/acv.12307] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- D. L. Gilroy
- School of Biological Sciences; Norwich Research Park; University of East Anglia; Norwich UK
| | - C. van Oosterhout
- School of Environmental Sciences; Norwich Research Park; University of East Anglia; Norwich UK
| | - J. Komdeur
- Behavioural Ecology and Self-Organization; Centre for Ecological and Evolutionary Studies; University of Groningen; Groningen The Netherlands
| | - D. S. Richardson
- School of Biological Sciences; Norwich Research Park; University of East Anglia; Norwich UK
- Nature Seychelles; Mahe Republic of Seychelles
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5
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Piertney SB. High-Throughput DNA Sequencing and the Next Generation of Molecular Markers in Wildlife Research. CURRENT TRENDS IN WILDLIFE RESEARCH 2016. [DOI: 10.1007/978-3-319-27912-1_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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6
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Wenzel MA, James MC, Douglas A, Piertney SB. Genome-wide association and genome partitioning reveal novel genomic regions underlying variation in gastrointestinal nematode burden in a wild bird. Mol Ecol 2015; 24:4175-92. [PMID: 26179597 DOI: 10.1111/mec.13313] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 06/23/2015] [Accepted: 07/03/2015] [Indexed: 02/06/2023]
Abstract
Identifying the genetic architecture underlying complex phenotypes is a notoriously difficult problem that often impedes progress in understanding adaptive eco-evolutionary processes in natural populations. Host-parasite interactions are fundamentally important drivers of evolutionary processes, but a lack of understanding of the genes involved in the host's response to chronic parasite insult makes it particularly difficult to understand the mechanisms of host life history trade-offs and the adaptive dynamics involved. Here, we examine the genetic basis of gastrointestinal nematode (Trichostrongylus tenuis) burden in 695 red grouse (Lagopus lagopus scotica) individuals genotyped at 384 genome-wide SNPs. We first use genome-wide association to identify individual SNPs associated with nematode burden. We then partition genome-wide heritability to identify chromosomes with greater heritability than expected from gene content, due to harbouring a multitude of additive SNPs with individually undetectable effects. We identified five SNPs on five chromosomes that accounted for differences of up to 556 worms per bird, but together explained at best 4.9% of the phenotypic variance. These SNPs were closely linked to genes representing a range of physiological processes including the immune system, protein degradation and energy metabolism. Genome partitioning indicated genome-wide heritability of up to 29% and three chromosomes with excess heritability of up to 4.3% (total 8.9%). These results implicate SNPs and novel genomic regions underlying nematode burden in this system and suggest that this phenotype is somewhere between being based on few large-effect genes (oligogenic) and based on a large number of genes with small individual but large combined effects (polygenic).
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Affiliation(s)
- Marius A Wenzel
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Marianne C James
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Stuart B Piertney
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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7
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Bono JM, Olesnicky EC, Matzkin LM. Connecting genotypes, phenotypes and fitness: harnessing the power of CRISPR/Cas9 genome editing. Mol Ecol 2015; 24:3810-22. [PMID: 26033315 DOI: 10.1111/mec.13252] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/20/2015] [Accepted: 05/26/2015] [Indexed: 12/26/2022]
Abstract
One of the fundamental goals in evolution and ecology is to identify the genetic basis of adaptive phenotypes. Unfortunately, progress towards this goal has been hampered by a lack of genetic tools available for nonmodel organisms. The exciting new development of the CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 (CRISPR-associated nuclease 9) genome-editing system now promises to transform the field of molecular ecology by providing a versatile toolkit for manipulating the genome of a wide variety of organisms. Here, we review the numerous applications of this groundbreaking technology and provide a practical guide to the creation of genetic knockouts, transgenics and other related forms of gene manipulation in nonmodel organisms. We also specifically discuss the potential uses of the CRISPR/Cas9 system in ecological and evolutionary studies, which will further advance the field towards the long-standing goal of connecting genotypes, phenotypes and fitness.
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Affiliation(s)
- Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Luciano M Matzkin
- Department of Biological Sciences, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL, 35899, USA.,HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
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8
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Gene dynamics of toll-like receptor 4 through a population bottleneck in an insular population of water voles (Arvicola amphibius). CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0731-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Wenzel MA, Piertney SB. Digging for gold nuggets: uncovering novel candidate genes for variation in gastrointestinal nematode burden in a wild bird species. J Evol Biol 2015; 28:807-25. [DOI: 10.1111/jeb.12614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/13/2015] [Accepted: 02/16/2015] [Indexed: 12/16/2022]
Affiliation(s)
- M. A. Wenzel
- Institute of Biological and Environmental Sciences; University of Aberdeen; Aberdeen UK
| | - S. B. Piertney
- Institute of Biological and Environmental Sciences; University of Aberdeen; Aberdeen UK
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10
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Anthony NM, Atteke C, Bruford MW, Dallmeier F, Freedman A, Hardy O, Ibrahim B, Jeffery KJ, Johnson M, Lahm SA, Lepengue N, Lowenstein JH, Maisels F, Mboumba JF, Mickala P, Morgan K, Ntie S, Smith TB, Sullivan JP, Verheyen E, Gonder MK. Evolution and Conservation of Central African Biodiversity: Priorities for Future Research and Education in the Congo Basin and Gulf of Guinea. Biotropica 2014. [DOI: 10.1111/btp.12188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicola M. Anthony
- Department of Biological Sciences; University of New Orleans; New Orleans Louisiana 70148 U.S.A
| | - Christiane Atteke
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Michael W. Bruford
- Organisms and Environment Division; School of Biosciences; Cardiff University; Cardiff CF10 3TL U.K
| | - Francisco Dallmeier
- Smithsonian Conservation Biology Institute; Center for Conservation Education and Sustainability; Box 37012 MRC 705 Washington DC 20013-7012 U.S.A
| | - Adam Freedman
- Department of Ecology and Evolutionary Biology and Center for Tropical Research; Institute of Environment and Sustainability; University of California Los Angeles; Los Angeles California 90092 U.S.A
- Department of Organismic and Evolutionary Biology; Harvard University; Boston Massachusetts U.S.A
| | - Olivier Hardy
- Evolutionary Biology and Ecology; Université Libre de Bruxelles; CP 160/12 1050 Brussels Belgium
| | - Brama Ibrahim
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs Nationaux; Libreville BP 20379 Gabon
- School of Natural Sciences; University of Stirling; Stirling FK9 4LA U.K
- Institut de Recherche en Écologie Tropicale; BP13354 Libreville Gabon
| | - Mireille Johnson
- Gabon Biodiversity Program; Center for Conservation Education and Sustainability; Smithsonian Conservation Biology Institute; B.P. 48 Gamba Gabon
| | - Sally A. Lahm
- Department of Global Health; George Washington University; Washington DC 20037 U.S.A
| | - Nicaise Lepengue
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Jacob H. Lowenstein
- Department of Ecology Evolution and Environmental Biology; Columbia University; New York New York 10027 U.S.A
- Division of Vertebrate Zoology; American Museum of Natural History; New York New York 10024 U.S.A
| | - Fiona Maisels
- School of Natural Sciences; University of Stirling; Stirling FK9 4LA U.K
- Wildlife Conservation Society; 2300 Southern Boulevard New York New York 10460 U.S.A
| | - Jean-François Mboumba
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
- Equipe Biodiversité et Gestion des Territoires; UMR 7204 Muséum National d'Histoire Naturelle; Université de Rennes 1; Rennes France
| | - Patrick Mickala
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Katy Morgan
- Department of Biological Sciences; University of New Orleans; New Orleans Louisiana 70148 U.S.A
| | - Stephan Ntie
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology and Center for Tropical Research; Institute of Environment and Sustainability; University of California Los Angeles; Los Angeles California 90092 U.S.A
| | - John P. Sullivan
- Cornell University Museum of Vertebrates; Ithaca New York 14850 U.S.A
| | - Erik Verheyen
- OD Taxonomy and Phylogeny; Vertebrates; Royal Belgian Institute of Natural Sciences; Vautierstraat 29 1000 Brussels Belgium
- Evolutionary Biology Group; Department of Biology; University of Antwerp; Groenenborgerlaan 171 2020 Antwerpen Belgium
| | - Mary K. Gonder
- Department of Biology; Drexel University; Philadelphia Pennsylvannia 19104 U.S.A
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11
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Identification and characterisation of 17 polymorphic candidate genes for response to parasitic nematode (Trichostrongylus tenuis) infection in red grouse (Lagopus lagopus scotica). CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0323-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Shen H, Xiong H, Guo X, Wang P, Duan P, Zhang L, Zhang F, Zuo Y. AhDMT1, a Fe(2+) transporter, is involved in improving iron nutrition and N2 fixation in nodules of peanut intercropped with maize in calcareous soils. PLANTA 2014; 239:1065-77. [PMID: 24519544 DOI: 10.1007/s00425-014-2033-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 01/20/2014] [Indexed: 05/10/2023]
Abstract
Peanut (Arachis hypogaea L.) is an important legume providing edible proteins and N2 fixation. However, iron deficiency severely reduces peanut growth in calcareous soils. The maize/peanut intercropping effectively improves iron nutrition and N2 fixation of peanut under pot and field conditions on calcareous soils. However, little was known of how intercropping regulates iron transporters in peanut. We identified AhDMT1 as a Fe(2+) transporter which was highly expressed in mature nodules with stronger N2 fixation capacity. Promoter expression analysis indicated that AhDMT1 was localized in the vascular tissues of both roots and nodules in peanut. Short-term Fe-deficiency temporarily induced an AhDmt1 expression in mature nodules in contrast to roots. However, analysis of the correlation between the complex regulation pattern of AhDmt1 expression and iron nutrition status indicated that sufficient iron supply for long term was a prerequisite for keeping AhDmt1 at a high expression level in both, peanut roots and mature nodules. The AhDmt1 expression in peanut intercropped with maize under 3 years greenhouse experiments was similar to that of peanut supplied with sufficient iron in laboratory experiments. Thus, the positive interspecific effect of intercropping may supply sufficient iron to enhance the expression of AhDmt1 in peanut roots and mature nodules to improve the iron nutrition and N2 fixation in nodules. This study may also serve as a paradigm in which functionally important genes and their ecological significance in intercropping were characterized using a candidate gene approach.
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Affiliation(s)
- Hongyun Shen
- Key Laboratory of Plant-Soil Interactions, MOE, Centre for Resource, Environment and Food Surity, College of Resources and Environmental Sciences, China Agricultural University, No. 2, Yuanmingyuan West Road, Beijing, 100193, China
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13
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Zueva KJ, Lumme J, Veselov AE, Kent MP, Lien S, Primmer CR. Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution? PLoS One 2014; 9:e91672. [PMID: 24670947 PMCID: PMC3966780 DOI: 10.1371/journal.pone.0091672] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 02/14/2014] [Indexed: 12/15/2022] Open
Abstract
Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved.
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Affiliation(s)
- Ksenia J. Zueva
- Department of Biology, University of Turku, Turku, Finland
- * E-mail:
| | - Jaakko Lumme
- Department of Biology, University of Oulu, Oulu, Finland
| | - Alexey E. Veselov
- Institute of Biology, Karelian Research Centre of RAS, Petrozavodsk, Russia
| | - Matthew P. Kent
- Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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14
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Zhigileva ON, Sheykina ZV, Malkova NA. Allozyme variability in common shrew Sorex araneus of Western Siberia. CONTEMP PROBL ECOL+ 2013. [DOI: 10.1134/s1995425513060140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Lack of variation at phosphoglucose isomerase (pgi) in bumblebees: implications for conservation genetics studies. PLoS One 2013; 8:e65600. [PMID: 23750269 PMCID: PMC3672202 DOI: 10.1371/journal.pone.0065600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/29/2013] [Indexed: 11/30/2022] Open
Abstract
Assessing genetic variation underlying ecologically important traits is increasingly of interest and importance in population and conservation genetics. For some groups generally useful markers exist for examining the relative role of selection and drift in shaping genetic diversity e.g. the major histocompatibility complex in vertebrates and self-incompatibility loci in plants. For invertebrates there is no such generally useful locus. However, phosphoglucose isomerase (Pgi) has been proposed as a useful functional marker in the conservation genetics of invertebrates. Where thermal microclimate varies, balanced polymorphisms may be maintained due to trade-offs between thermally stable and kinetically advantageous allelic forms. We here report very low levels of Pgi variation in bumblebees rendering this locus to be of little use as an adaptive marker in a conservation genetics context in this group. Potential explanations for this lack of variation are considered.
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16
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Diopere E, Hellemans B, Volckaert FA, Maes GE. Identification and validation of single nucleotide polymorphisms in growth- and maturation-related candidate genes in sole (Solea solea L.). Mar Genomics 2013; 9:33-8. [DOI: 10.1016/j.margen.2012.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/27/2012] [Accepted: 09/28/2012] [Indexed: 11/29/2022]
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17
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Backström N, Shipilina D, Blom MPK, Edwards SV. Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus). Ecol Evol 2013; 3:655-66. [PMID: 23532859 PMCID: PMC3605853 DOI: 10.1002/ece3.484] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/17/2012] [Accepted: 12/24/2012] [Indexed: 01/19/2023] Open
Abstract
Characterization of the genetic basis of fitness traits in natural populations is important for understanding how organisms adapt to the changing environment and to novel events, such as epizootics. However, candidate fitness-influencing loci, such as regulatory regions, are usually unavailable in nonmodel species. Here, we analyze sequence data from targeted resequencing of the cis-regulatory regions of three candidate genes for disease resistance (CD74, HSP90α, and LCP1) in populations of the house finch (Carpodacus mexicanus) historically exposed (Alabama) and naïve (Arizona) to Mycoplasma gallisepticum. Our study, the first to quantify variation in regulatory regions in wild birds, reveals that the upstream regions of CD74 and HSP90α are GC-rich, with the former exhibiting unusually low sequence variation for this species. We identified two SNPs, located in a GC-rich region immediately upstream of an inferred promoter site in the gene HSP90α, that were significantly associated with Mycoplasma pathogen load in the two populations. The SNPs are closely linked and situated in potential regulatory sequences: one in a binding site for the transcription factor nuclear NFYα and the other in a dinucleotide microsatellite ((GC)6). The genotype associated with pathogen load in the putative NFYα binding site was significantly overrepresented in the Alabama birds. However, we did not see strong effects of selection at this SNP, perhaps because selection has acted on standing genetic variation over an extremely short time in a highly recombining region. Our study is a useful starting point to explore functional relationships between sequence polymorphisms, gene expression, and phenotypic traits, such as pathogen resistance that affect fitness in the wild.
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Affiliation(s)
- Niclas Backström
- Department of Organismic and Evolutionary Biology (OEB), Museum of Comparative Zoology (MCZ), Harvard University26 Oxford Street, Cambridge, MA, 02138
| | - Daria Shipilina
- Department of Organismic and Evolutionary Biology (OEB), Museum of Comparative Zoology (MCZ), Harvard University26 Oxford Street, Cambridge, MA, 02138
| | - Mozes P K Blom
- Department of Organismic and Evolutionary Biology (OEB), Museum of Comparative Zoology (MCZ), Harvard University26 Oxford Street, Cambridge, MA, 02138
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology (OEB), Museum of Comparative Zoology (MCZ), Harvard University26 Oxford Street, Cambridge, MA, 02138
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Liberman SA, Mashoodh R, Thompson RC, Dolinoy DC, Champagne FA. Concordance in hippocampal and fecal Nr3c1 methylation is moderated by maternal behavior in the mouse. Ecol Evol 2012; 2:3123-31. [PMID: 23301177 PMCID: PMC3539005 DOI: 10.1002/ece3.416] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/25/2012] [Accepted: 10/03/2012] [Indexed: 12/11/2022] Open
Abstract
Recent advances in genomic technologies now enable a reunion of molecular and evolutionary biology. Researchers investigating naturally living animal populations are thus increasingly able to capitalize upon genomic technologies to connect molecular findings with multiple levels of biological organization. Using this vertical approach in the laboratory, epigenetic gene regulation has emerged as an important mechanism integrating genotype and phenotype. To connect phenotype to population fitness, however, this same vertical approach must now be applied to naturally living populations. A major obstacle to studying epigenetics in noninvasive samples is tissue specificity of epigenetic marks. Here, using the mouse as a proof-of-principle model, we present the first known attempt to validate an epigenetic assay for use in noninvasive samples. Specifically, we compare DNA methylation of the NGFI-A (nerve growth factor-inducible protein A) binding site in the promoter of the glucocorticoid receptor (Nr3c1) gene between central (hippocampal) and peripheral noninvasive (fecal) tissues in juvenile Balb/c mice that had received varying levels of postnatal maternal care. Our results indicate that while hippocampal DNA methylation profiles correspond to maternal behavior, fecal DNA methylation levels do not. Moreover, concordance in methylation levels between these tissues within individuals only emerges after accounting for the effects of postnatal maternal care. Thus, although these findings may be specific to the Nr3c1 gene, we urge caution when interpreting DNA methylation patterns from noninvasive tissues, and offer suggestions for further research in this field.
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Affiliation(s)
- Shayna A Liberman
- Department of Environmental Health Sciences, University of Michigan School of Public Health Ann Arbor, Michigan, 48109
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Dobson AE, Schmidt DJ, Hughes JM. Sequence Variation in the Melanocortin-1 Receptor (MC1R) Does Not Explain Continent-wide Plumage Color Differences in the Australian Magpie (Cracticus tibicen). J Hered 2012; 103:769-80. [DOI: 10.1093/jhered/ess053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Ellis JS, Turner LM, Knight ME. Patterns of selection and polymorphism of innate immunity genes in bumblebees (Hymenoptera: Apidae). Genetica 2012; 140:205-17. [PMID: 22899493 DOI: 10.1007/s10709-012-9672-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/07/2012] [Indexed: 01/22/2023]
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Oppenheim SJ, Gould F, Hopper KR. The genetic architecture of a complex ecological trait: host plant use in the specialist moth, Heliothis subflexa. Evolution 2012; 66:3336-51. [PMID: 23106701 DOI: 10.1111/j.1558-5646.2012.01712.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We used genetic mapping to examine the genetic architecture of differences in host plant use between two species of noctuid moths, Heliothis subflexa, a specialist on Physalis spp., and its close relative, the broad generalist H. virescens. We introgressed H. subflexa chromosomes into the H. virescens background and analyzed 1462 backcross insects. The effects of H. subflexa-origin chromosomes were small when measured as the percent variation explained in backcross populations (0.2-5%), but were larger when considered in relation to the interspecific difference explained (1.5-165%). Most significant chromosomes had effects on more than one trait, and their effects varied between years, sexes, and genetic backgrounds. Different chromosomes could produce similar phenotypes, suggesting that the same trait might be controlled by different chromosomes in different backcross populations. It appears that many loci of small effect contribute to the use of Physalis by H. subflexa. We hypothesize that behavioral changes may have paved the way for physiological adaptation to Physalis by the generalist ancestor of H. subflexa and H. virescens.
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Affiliation(s)
- Sara J Oppenheim
- Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA.
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23
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Liedvogel M, Cornwallis CK, Sheldon BC. Integrating candidate gene and quantitative genetic approaches to understand variation in timing of breeding in wild tit populations. J Evol Biol 2012; 25:813-23. [PMID: 22409177 DOI: 10.1111/j.1420-9101.2012.02480.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two commonly used techniques for estimating the effect of genes on traits in wild populations are the candidate gene approach and quantitative genetic analyses. However, whether these two approaches measure the same underlying processes remains unresolved. Here, we use these two methods to test whether they are alternative or complementary approaches to understanding genetic variation in the timing of reproduction - a key trait involved in adaptation to climate change - in wild tit populations. Our analyses of the candidate gene Clock show weak correlates with timing variables in blue tits, but no association in great tits, confirming earlier results. Quantitative genetic analyses revealed very low levels of both direct (female) and indirect (male) additive genetic variation in timing traits for both species, in contrast to previous studies on these traits, and much lower than generally assumed. Hence, neither method suggests strong genetic effects on the timing of breeding in birds, and further work should seek to assess the generality of these conclusions. We discuss how differences in the genetic control of traits, species life-history and confounding environmental variables may determine how useful integrating these two techniques is to understand the phenotypic variation in wild populations.
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Affiliation(s)
- Miriam Liedvogel
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK.
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24
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Balenger SL, McClure CJW, Hill GE. Primer design and transcript quantification of a highly multiplexed RT-PCR for a nonmodel avian species. Mol Ecol Resour 2011; 12:116-22. [PMID: 21848525 DOI: 10.1111/j.1755-0998.2011.03058.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Multiplexed qRT-PCR assays are currently lacking for nearly all species without genome or transcriptome resources. Here, we present a strategy for primer design of highly multiplexed qRT-PCR assays, evaluate Beckman Coulter's Quant Tool gene expression quantification software and provide details of our assay for the North American songbird Carpodacus mexicanus (house finch), for which only small sections of genome sequence are available. We combined Beckman Coulter's eXpress Designer module for creating custom multiplex primers with the free, online program Amplify 3 to design and evaluate primers computationally before testing them empirically. We also generated a standard curve for each gene included in the final multiplex. We compared models using cubic and quadratic polynomial estimators that did and did not force the intercept through zero. Ultimately, we used the sequences available for 316 clones differentially expressed in cDNA macroarray and microarray comparisons, and from these sequences, we were able to generate a set of transcript-specific primers for use with the GeXP analyser for 20 house finch genes.
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Affiliation(s)
- Susan L Balenger
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
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25
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Kirk H, Freeland JR. Applications and implications of neutral versus non-neutral markers in molecular ecology. Int J Mol Sci 2011; 12:3966-88. [PMID: 21747718 PMCID: PMC3131602 DOI: 10.3390/ijms12063966] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/06/2011] [Accepted: 06/07/2011] [Indexed: 11/17/2022] Open
Abstract
The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection.
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Affiliation(s)
- Heather Kirk
- Department of Biology, Trent University, Peterborough, Ontario K9J 7B8, Canada; E-Mail:
| | - Joanna R. Freeland
- Department of Biology, Trent University, Peterborough, Ontario K9J 7B8, Canada; E-Mail:
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26
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Ekblom R, French L, Slate J, Burke T. Evolutionary analysis and expression profiling of zebra finch immune genes. Genome Biol Evol 2010; 2:781-90. [PMID: 20884724 PMCID: PMC2975445 DOI: 10.1093/gbe/evq061] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Genes of the immune system are generally considered to evolve rapidly due to host-parasite coevolution. They are therefore of great interest in evolutionary biology and molecular ecology. In this study, we manually annotated 144 avian immune genes from the zebra finch (Taeniopygia guttata) genome and conducted evolutionary analyses of these by comparing them with their orthologs in the chicken (Gallus gallus). Genes classified as immune receptors showed elevated d(N)/d(S) ratios compared with other classes of immune genes. Immune genes in general also appear to be evolving more rapidly than other genes, as inferred from a higher d(N)/d(S) ratio compared with the rest of the genome. Furthermore, ten genes (of 27) for which sequence data were available from at least three bird species showed evidence of positive selection acting on specific codons. From transcriptome data of eight different tissues, we found evidence for expression of 106 of the studied immune genes, with primary expression of most of these in bursa, blood, and spleen. These immune-related genes showed a more tissue-specific expression pattern than other genes in the zebra finch genome. Several of the avian immune genes investigated here provide strong candidates for in-depth studies of molecular adaptation in birds.
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Affiliation(s)
- Robert Ekblom
- University of Sheffield, Department of Animal and Plant Sciences, Sheffield, UK.
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Webster LMI, Mello LV, Mougeot F, Martinez-Padilla J, Paterson S, Piertney SB. Identification of genes responding to nematode infection in red grouse. Mol Ecol Resour 2010; 11:305-13. [PMID: 21429137 DOI: 10.1111/j.1755-0998.2010.02912.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The identification of genes involved in a host's response to parasite infection provides both a means for understanding the pathways involved in immune defence and a target for examining host-parasite co-evolution. Most studies rely on a candidate gene approach derived from model systems to identify gene targets of interest, and there have been a dearth of studies geared towards providing a holistic overview of immune response from natural populations. We carried out an experiment in a natural population of red grouse (Lagopus lagopus scoticus) to manipulate levels of Trichostrongylus tenuis parasite infection. The transcriptomic response of individuals was examined from standard cDNA and suppressive subtractive hybridization (SSH) libraries produced from gut, liver and spleen, enriching for genes expressed in response to T. tenuis infection. A total of 2209 and 3716 unique transcript sequences were identified from the cDNA and SSH libraries, respectively. Forty-five of these had Gene Ontology annotation associated with immune response. Some of these genes have previously been reported from laboratory-based studies of model species as important in immune response to gastrointestinal parasite infection; however, multiple novel genes were also identified. These may reveal novel pathways involved in the host response of grouse to T. tenuis and provide a resource that can be utilized as candidate genes in other species. All sequences described have been deposited in GenBank (accession numbers GW698221-GW706922)
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Affiliation(s)
- L M I Webster
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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Shikano T, Ramadevi J, Merilä J. Identification of local- and habitat-dependent selection: scanning functionally important genes in nine-spined sticklebacks (Pungitius pungitius). Mol Biol Evol 2010; 27:2775-89. [PMID: 20591843 DOI: 10.1093/molbev/msq167] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Understanding the selective forces promoting adaptive population divergence is a central issue in evolutionary biology. The role of environmental salinity in driving adaptation and evolution in aquatic organisms is still poorly understood. We investigated the relative impacts of habitat type (cf. saltwater vs. freshwater) and geographic area in shaping adaptive population divergence, as well as genes responsible for adaptation to different salinities in nine-spined sticklebacks (Pungitius pungitius). To this end, we employed a hitchhiking mapping approach with 111 microsatellite loci and one insertion/deletion locus including 63 loci situated within or close to genes with important physiological functions such as osmoregulation, growth, and thermal response. Using three pairs of marine and freshwater populations from different geographic areas, we identified several loci showing consistent evidence of being under directional selection in different outlier tests. Analyses of molecular variance at the loci under selection indicated that geographic area rather than habitat type has been acting as a central force in shaping adaptive population divergence. Nevertheless, both outlier tests and a spatial analysis method indicated that two loci (growth hormone receptor 2 and DEAD box polypeptide 56) are involved in adaptation to different habitats, implying that environmental salinity has been affecting them as a selective force. These loci are promising candidates for further investigations focusing on the molecular mechanisms of adaptation to marine and freshwater environments.
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Affiliation(s)
- Takahito Shikano
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland.
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Skoglund P, Höglund J. Sequence polymorphism in candidate genes for differences in winter plumage between Scottish and Scandinavian Willow Grouse (Lagopus lagopus). PLoS One 2010; 5:e10334. [PMID: 20428241 PMCID: PMC2859059 DOI: 10.1371/journal.pone.0010334] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Accepted: 03/30/2010] [Indexed: 11/18/2022] Open
Abstract
Background Population variation in the degree of seasonal polymorphism is rare in birds, and the genetic basis of this phenomenon remains largely undescribed. Both sexes of Scandinavian and Scottish Willow grouse (Lagopus lagopus) display marked differences in their winter phenotypes, with Scottish grouse retaining a pigmented plumage year-round and Scandinavian Willow grouse molting to a white morph during winter. A widely studied pathway implicated in vertebrate pigmentation is the melanin system, for which functional variation has been characterised in many taxa. Methodology/Principal Findings We sequenced coding regions from four genes involved in melanin pigmentation (DCT, MC1R, TYR and TYRP1), and an additional control involved in the melanocortin pathway (AGRP), to investigate the genetic basis of winter plumage in Lagopus. Despite the well documented role of the melanin system in animal coloration, we found no plumage-associated polymorphism or evidence for selection in a total of ∼2.6 kb analysed sequence. Conclusions/Significance Our results indicate that the genetic basis of alternating between pigmented and unpigmented seasonal phenotypes is more likely explained by regulatory changes controlling the expression of these or other loci in the physiological pathway leading to pigmentation.
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Affiliation(s)
- Pontus Skoglund
- Department of Population Biology and Conservation Biology, Uppsala University, Uppsala, Sweden.
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30
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Ekblom R, Balakrishnan CN, Burke T, Slate J. Digital gene expression analysis of the zebra finch genome. BMC Genomics 2010; 11:219. [PMID: 20359325 PMCID: PMC2996964 DOI: 10.1186/1471-2164-11-219] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 04/01/2010] [Indexed: 11/10/2022] Open
Abstract
Background In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates.
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Affiliation(s)
- Robert Ekblom
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK.
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