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Spatial distribution of microsatellite and MHC-DRB exon 2 gene variability in the Jamaican fruit bat (Artibeus jamaicensis) in Mexico. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2016.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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2
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Tentelier C, Barroso-Gomila O, Lepais O, Manicki A, Romero-Garmendia I, Jugo BM. Testing mate choice and overdominance at MH in natural families of Atlantic salmon Salmo salar. JOURNAL OF FISH BIOLOGY 2017; 90:1644-1659. [PMID: 28097664 DOI: 10.1111/jfb.13260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
This study aimed to test mate choice and selection during early life stages on major histocompatibility (MH) genotype in natural families of Atlantic salmon Salmo salar spawners and juveniles, using nine microsatellites to reconstruct families, one microsatellite linked to an MH class I gene and one minisatellite linked to an MH class II gene. MH-based mate choice was only detected for the class I locus on the first year, with lower expected heterozygosity in the offspring of actually mated pairs than predicted under random mating. The genotype frequencies of MH-linked loci observed in the juveniles were compared with frequencies expected from Mendelian inheritance of parental alleles to detect selection during early life stages. No selection was detected on the locus linked to class I gene. For the locus linked to class II gene, observed heterozygosity was higher than expected in the first year and lower in the second year, suggesting overdominance and underdominance, respectively. Within family, juveniles' body size was linked to heterozygosity at the same locus, with longer heterozygotes in the first year and longer homozygotes in the second year. Selection therefore seems to differ from one locus to the other and from year to year.
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Affiliation(s)
- C Tentelier
- ECOBIOP, INRA, Univ. Pau & Pays Adour, 64310, Saint-Pée-sur-Nivelle, France
| | - O Barroso-Gomila
- Euskal Herriko Unibertsitatea UPV EHU, Zientzia & Teknol Fak, Genet Antropol Fis & Animalien Fisiol Saila, E-48080, Bilbao, Spain
| | - O Lepais
- ECOBIOP, INRA, Univ. Pau & Pays Adour, 64310, Saint-Pée-sur-Nivelle, France
| | - A Manicki
- ECOBIOP, INRA, Univ. Pau & Pays Adour, 64310, Saint-Pée-sur-Nivelle, France
| | - I Romero-Garmendia
- Euskal Herriko Unibertsitatea UPV EHU, Zientzia & Teknol Fak, Genet Antropol Fis & Animalien Fisiol Saila, E-48080, Bilbao, Spain
| | - B M Jugo
- Euskal Herriko Unibertsitatea UPV EHU, Zientzia & Teknol Fak, Genet Antropol Fis & Animalien Fisiol Saila, E-48080, Bilbao, Spain
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Temporal and spatial instability in neutral and adaptive (MHC) genetic variation in marginal salmon populations. Sci Rep 2017; 7:42416. [PMID: 28186200 PMCID: PMC5301200 DOI: 10.1038/srep42416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/10/2017] [Indexed: 12/04/2022] Open
Abstract
The role of marginal populations for the long-term maintenance of species’ genetic diversity and evolutionary potential is particularly timely in view of the range shifts caused by climate change. The Centre-Periphery hypothesis predicts that marginal populations should bear reduced genetic diversity and have low evolutionary potential. We analysed temporal stability at neutral microsatellite and adaptive MHC genetic variation over five decades in four marginal Atlantic salmon populations located at the southern limit of the species’ distribution with a complicated demographic history, which includes stocking with foreign and native salmon for at least 2 decades. We found a temporal increase in neutral genetic variation, as well as temporal instability in population structuring, highlighting the importance of temporal analyses in studies that examine the genetic diversity of peripheral populations at the margins of the species’ range, particularly in face of climate change.
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Egernia stokesii (gidgee skink) MHC I positively selected sites lack concordance with HLA peptide binding regions. Immunogenetics 2016; 69:49-61. [PMID: 27517292 DOI: 10.1007/s00251-016-0947-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Genes of the major histocompatibility complex (MHC) play an important role in vertebrate disease resistance, kin recognition and mate choice. Mammalian MHC is the most widely characterised of all vertebrates, and attention is often given to the peptide binding regions of the MHC because they are presumed to be under stronger selection than non-peptide binding regions. For vertebrates where the MHC is less well understood, researchers commonly use the amino acid positions of the peptide binding regions of the human leukocyte antigen (HLA) to infer the peptide binding regions within the MHC sequences of their taxon of interest. However, positively selected sites within MHC have been reported to lack correspondence with the HLA in fish, frogs, birds and reptiles including squamates. Despite squamate diversity, the MHC has been characterised in few snakes and lizards. The Egernia group of scincid lizards is appropriate for investigating mechanisms generating MHC variation, as their inclusion will add a new lineage (i.e. Scincidae) to studies of selection on the MHC. We aimed to identify positively selected sites within the MHC of Egernia stokesii and then determine if these sites corresponded with the peptide binding regions of the HLA. Six positively selected sites were identified within E. stokesii MHC I, only two were homologous with the HLA. E. stokesii positively selected sites corresponded more closely to non-lizard than other lizard taxa. The characterisation of the MHC of more intermediate taxa within the squamate order is necessary to understand the evolution of the MHC across all vertebrates.
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Miller KM, Teffer A, Tucker S, Li S, Schulze AD, Trudel M, Juanes F, Tabata A, Kaukinen KH, Ginther NG, Ming TJ, Cooke SJ, Hipfner JM, Patterson DA, Hinch SG. Infectious disease, shifting climates, and opportunistic predators: cumulative factors potentially impacting wild salmon declines. Evol Appl 2014; 7:812-55. [PMID: 25469162 PMCID: PMC4227861 DOI: 10.1111/eva.12164] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 03/06/2014] [Indexed: 12/23/2022] Open
Abstract
Emerging diseases are impacting animals under high-density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.
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Affiliation(s)
- Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
- Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
| | - Amy Teffer
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Strahan Tucker
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Marc Trudel
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Francis Juanes
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Norma G Ginther
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton UniverisyOttawa, ON, Canada
| | - J Mark Hipfner
- Environment Canada, Wildlife Research DivisionDelta, BC, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Science BranchBurnaby, BC, Canada
| | - Scott G Hinch
- Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
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Kapralova KH, Gudbrandsson J, Reynisdottir S, Santos CB, Baltanás VC, Maier VH, Snorrason SS, Palsson A. Differentiation at the MHCIIα and Cath2 loci in sympatric Salvelinus alpinus resource morphs in Lake Thingvallavatn. PLoS One 2013; 8:e69402. [PMID: 23894470 PMCID: PMC3722248 DOI: 10.1371/journal.pone.0069402] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 06/09/2013] [Indexed: 11/19/2022] Open
Abstract
Northern freshwater fish may be suitable for the genetic dissection of ecological traits because they invaded new habitats after the last ice age (∼10.000 years ago). Arctic charr (Salvelinus alpinus) colonizing streams and lakes in Iceland gave rise to multiple populations of small benthic morphotypes, often in sympatry with a pelagic morphotype. Earlier studies have revealed significant, but subtle, genetic differentiation between the three most common morphs in Lake Thingvallavatn. We conducted a population genetic screen on four immunological candidate genes Cathelicidin 2 (Cath2), Hepcidin (Hamp), Liver expressed antimicrobial peptide 2a (Leap-2a), and Major Histocompatibility Complex IIα (MHCIIα) and a mitochondrial marker (D-loop) among the three most common Lake Thingvallavatn charr morphs. Significant differences in allele frequencies were found between morphs at the Cath2 and MHCIIα loci. No such signal was detected in the D-loop nor in the other two immunological genes. In Cath2 the small benthic morph deviated from the other two (FST = 0.13), one of the substitutions detected constituting an amino acid replacement polymorphism in the antimicrobial peptide. A more striking difference was found in the MHCIIα. Two haplotypes were very common in the lake, and their frequency differed greatly between the morphotypes (from 22% to 93.5%, FST = 0.67). We then expanded our study by surveying the variation in Cath2 and MHCIIα in 9 Arctic charr populations from around Iceland. The populations varied greatly in terms of allele frequencies at Cath2, but the variation did not correlate with morphotype. At the MHCIIα locus, the variation was nearly identical to the variation in the two benthic morphs of Lake Thingvallavatn. The results are consistent with a scenario where parts of the immune systems have diverged substantially among Arctic charr populations in Iceland, after colonizing the island ∼10.000 years ago.
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Affiliation(s)
- Kalina H. Kapralova
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Johannes Gudbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Sigrun Reynisdottir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Cristina B. Santos
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Vanessa C. Baltanás
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Valerie H. Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Sigurdur S. Snorrason
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Arnar Palsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
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O'Farrell B, Dennis C, Benzie JA, McGinnity P, Carlsson J, de Eyto E, Coughlan JP, Igoe F, Meehan R, Cross TF. Balancing selection on MHC class I in wild brown trout Salmo trutta. JOURNAL OF FISH BIOLOGY 2012; 81:1357-1374. [PMID: 22957875 DOI: 10.1111/j.1095-8649.2012.03421.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Evidence is reported for balancing selection acting on variation at major histocompatibility complex (MHC) in wild populations of brown trout Salmo trutta. First, variation at an MHC class I (satr-uba)-linked microsatellite locus (mhc1) is retained in small S. trutta populations isolated above waterfalls although variation is lost at neutral microsatellite markers. Second, populations across several catchments are less differentiated at mhc1 than at neutral markers, as predicted by theory. The population structure of these fish was also elucidated.
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Affiliation(s)
- B O'Farrell
- Environmental Research Institute, University College Cork, Cork, Ireland.
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O'Farrell B, Benzie JAH, McGinnity P, Carlsson J, Eyto ED, Dillane E, Graham C, Coughlan J, Cross T. MHC-mediated spatial distribution in brown trout (Salmo trutta) fry. Heredity (Edinb) 2012; 108:403-9. [PMID: 21934705 PMCID: PMC3313050 DOI: 10.1038/hdy.2011.87] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 07/19/2011] [Accepted: 08/18/2011] [Indexed: 11/08/2022] Open
Abstract
Major histocompatibility complex (MHC) class I-linked microsatellite data and parental assignment data for a group of wild brown trout (Salmo trutta L.) provide evidence of closer spatial aggregation among fry sharing greater numbers of MHC class I alleles under natural conditions. This result confirms predictions from laboratory experiments demonstrating a hierarchical preference for association of fry sharing MHC alleles. Full-siblings emerge from the same nest (redd), and a passive kin association pattern arising from limited dispersal from the nest (redd effect) would predict that all such pairs would have a similar distribution. However, this study demonstrates a strong, significant trend for reduced distance between pairs of full-sibling fry sharing more MHC class I alleles reflecting their closer aggregation (no alleles shared, 311.5 ± (s.e.)21.03 m; one allele shared, 222.2 ± 14.49 m; two alleles shared, 124.9 ± 23.88 m; P<0.0001). A significant trend for closer aggregation among fry sharing more MHC class I alleles was also observed in fry pairs, which were known to have different mothers and were otherwise unrelated (ML-r = 0) (no alleles: 457.6 ± 3.58 m; one allele (422.4 ± 3.86 m); two alleles (381.7 ± 10.72 m); P<0.0001). These pairs are expected to have emerged from different redds and a passive association would then be unlikely. These data suggest that sharing MHC class I alleles has a role in maintaining kin association among full-siblings after emergence. This study demonstrates a pattern consistent with MHC-mediated kin association in the wild for the first time.
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Affiliation(s)
- B O'Farrell
- Microbial Phylogeography, Department of Microbiology, Environmental Research Institute, University College Cork, Cork, Ireland
| | - J A H Benzie
- School of Biological, Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Cork, Ireland
| | - P McGinnity
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
- Marine Institute, Newport, Co. Mayo, Ireland
| | - J Carlsson
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - E de Eyto
- Marine Institute, Newport, Co. Mayo, Ireland
| | - E Dillane
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - C Graham
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - J Coughlan
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - T Cross
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
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Marsden CD, Woodroffe R, Mills MGL, McNutt JW, Creel S, Groom R, Emmanuel M, Cleaveland S, Kat P, Rasmussen GSA, Ginsberg J, Lines R, André JM, Begg C, Wayne RK, Mable BK. Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus). Mol Ecol 2012; 21:1379-93. [PMID: 22320891 DOI: 10.1111/j.1365-294x.2012.05477.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e) < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.
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Affiliation(s)
- Clare D Marsden
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, UK.
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Garcia de Leaniz C. William Crozier Jordan (Bill) 1962–2011 [corrected]. JOURNAL OF FISH BIOLOGY 2011; 79:1089-1093. [PMID: 22026594 DOI: 10.1111/j.1095-8649.2011.03119.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- C Garcia de Leaniz
- Swansea University Department of BioSciences Singleton Park Swansea SA2 8PP U.K
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