1
|
Holmes IA, Durso AM, Myers CR, Hendry TA. Changes in capture availability due to infection can lead to detectable biases in population-level infectious disease parameters. PeerJ 2024; 12:e16910. [PMID: 38436008 PMCID: PMC10909344 DOI: 10.7717/peerj.16910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024] Open
Abstract
Correctly identifying the strength of selection that parasites impose on hosts is key to predicting epidemiological and evolutionary outcomes of host-parasite interactions. However, behavioral changes due to infection can alter the capture probability of infected hosts and thereby make selection difficult to estimate by standard sampling techniques. Mark-recapture approaches, which allow researchers to determine if some groups in a population are less likely to be captured than others, can be used to identify infection-driven capture biases. If a metric of interest directly compares infected and uninfected populations, calculated detection probabilities for both groups may be useful in identifying bias. Here, we use an individual-based simulation to test whether changes in capture rate due to infection can alter estimates of three key metrics: 1) reduction in the reproductive success of infected parents relative to uninfected parents, 2) the relative risk of infection for susceptible genotypes compared to resistant genotypes, and 3) changes in allele frequencies between generations. We explore the direction and underlying causes of the biases that emerge from these simulations. Finally, we argue that short series of mark-recapture sampling bouts, potentially implemented in under a week, can yield key data on detection bias due to infection while not adding a significantly higher burden to disease ecology studies.
Collapse
Affiliation(s)
- Iris A. Holmes
- Department of Microbiology, Cornell University, Ithaca, NY, United States
- Cornell Institute of Host Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States
| | - Andrew M. Durso
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL, USA
| | - Christopher R. Myers
- Center for Advanced Computing & Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, United States
| | - Tory A. Hendry
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| |
Collapse
|
2
|
Van Nynatten A, Duncan AT, Lauzon R, Sheldon TA, Chen SK, Lovejoy NR, Mandrak NE, Chang BSW. Adaptive Evolution of Nearctic Deepwater Fish Vision: Implications for Assessing Functional Variation for Conservation. Mol Biol Evol 2024; 41:msae024. [PMID: 38314890 PMCID: PMC10896662 DOI: 10.1093/molbev/msae024] [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: 11/07/2023] [Revised: 12/15/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Intraspecific functional variation is critical for adaptation to rapidly changing environments. For visual opsins, functional variation can be characterized in vitro and often reflects a species' ecological niche but is rarely considered in the context of intraspecific variation or the impact of recent environmental changes on species of cultural or commercial significance. Investigation of adaptation in postglacial lakes can provide key insight into how rapid environmental changes impact functional evolution. Here, we report evidence for molecular adaptation in vision in 2 lineages of Nearctic fishes that are deep lake specialists: ciscoes and deepwater sculpin. We found depth-related variation in the dim-light visual pigment rhodopsin that evolved convergently in these 2 lineages. In vitro characterization of spectral sensitivity of the convergent deepwater rhodopsin alleles revealed blue-shifts compared with other more widely distributed alleles. These blue-shifted rhodopsin alleles were only observed in deep clear postglacial lakes with underwater visual environments enriched in blue light. This provides evidence of remarkably rapid and convergent visual adaptation and intraspecific functional variation in rhodopsin. Intraspecific functional variation has important implications for conservation, and these fishes are of conservation concern and great cultural, commercial, and nutritional importance to Indigenous communities. We collaborated with the Saugeen Ojibway Nation to develop and test a metabarcoding approach that we show is efficient and accurate in recovering the ecological distribution of functionally relevant variation in rhodopsin. Our approach bridges experimental analyses of protein function and genetics-based tools used in large-scale surveys to better understand the ecological extent of adaptive functional variation.
Collapse
Affiliation(s)
- Alexander Van Nynatten
- Department of Biological Science, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Alexander T Duncan
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, Ontario, Canada
- Fisheries Assessment Program, Chippewas of Nawash Unceded First Nation, Neyaashiinigmiing, Ontario, Canada
| | - Ryan Lauzon
- Fisheries Assessment Program, Chippewas of Nawash Unceded First Nation, Neyaashiinigmiing, Ontario, Canada
| | | | - Steven K Chen
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nathan R Lovejoy
- Department of Biological Science, University of Toronto Scarborough, Scarborough, Ontario, Canada
- Department of Ecological and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas E Mandrak
- Department of Biological Science, University of Toronto Scarborough, Scarborough, Ontario, Canada
- Department of Ecological and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Ecological and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
3
|
Rondeau EB, Christensen KA, Johnson HA, Sakhrani D, Biagi CA, Wetklo M, Despins CA, Leggatt RA, Minkley DR, Withler RE, Beacham TD, Koop BF, Devlin RH. Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function. G3 (BETHESDA, MD.) 2023; 13:jkad127. [PMID: 37293843 PMCID: PMC10411575 DOI: 10.1093/g3journal/jkad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.
Collapse
Affiliation(s)
- Eric B Rondeau
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Kris A Christensen
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Hollie A Johnson
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Dionne Sakhrani
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - Carlo A Biagi
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - Mike Wetklo
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Cody A Despins
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Rosalind A Leggatt
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - David R Minkley
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Ruth E Withler
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Terry D Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| |
Collapse
|
4
|
Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
Collapse
Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
| | | | | |
Collapse
|
5
|
Wenne R. Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations. Genes (Basel) 2023; 14:genes14040808. [PMID: 37107566 PMCID: PMC10138012 DOI: 10.3390/genes14040808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.
Collapse
Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| |
Collapse
|
6
|
P SS, Chennuru S, Krovvidi S, Chitichoti J. Status of tick-borne haemoprotozoan infection in south Indian sheep in association with variation in Ovar-DRB1 gene. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
7
|
Migalska M, Przesmycka K, Alsarraf M, Bajer A, Behnke-Borowczyk J, Grzybek M, Behnke JM, Radwan J. Long term patterns of association between MHC and helminth burdens in the bank vole support Red Queen dynamics. Mol Ecol 2022; 31:3400-3415. [PMID: 35510766 PMCID: PMC9325469 DOI: 10.1111/mec.16486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/28/2022]
Abstract
Major histocompatibility complex (MHC) genes encode proteins crucial for adaptive immunity of vertebrates. Negative frequency-dependent selection (NFDS), resulting from adaptation of parasites to common MHC types, has been hypothesized to maintain high, functionally relevant polymorphism of MHC, but demonstration of this relationship has remained elusive. In particular, differentiation of NFDS from fluctuating selection, resulting from changes in parasite communities in time and space (FS), has proved difficult in short-term studies. Here, we used temporal data, accumulated through long-term monitoring of helminths infecting bank voles (Myodes glareolus), to test specific predictions of NFDS on MHC class II. Data were collected in three, moderately genetically differentiated subpopulations in Poland, which were characterized by some stable spatiotemporal helminth communities but also events indicating introduction of new species and loss of others. We found a complex association between individual MHC diversity and species richness, where intermediate numbers of DRB supertypes correlated with lowest species richness, but the opposite was true for DQB supertypes - arguing against universal selection for immunogenetic optimality. We also showed that particular MHC supertypes explain a portion of the variance in prevalence and abundance of helminths, but this effect was subpopulation-specific, which is consistent with both NFDS and FS. Finally, in line with NFDS, we found that certain helminths that have recently colonized or spread in a given subpopulation, more frequently or intensely infected voles with MHC supertypes that have been common in the recent past. Overall, our results highlight complex spatial and temporal patterns of MHC-parasite associations, the latter being consistent with Red Queen coevolutionary dynamics.
Collapse
Affiliation(s)
- Magdalena Migalska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Karolina Przesmycka
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Mohammed Alsarraf
- Department of Eco-epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Anna Bajer
- Department of Eco-epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jolanta Behnke-Borowczyk
- Department of Forest Entomology and Pathology, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625, Poznań, Poland
| | - Maciej Grzybek
- Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Powstania Styczniowego 9B, 81-429, Gdynia, Poland
| | - Jerzy M Behnke
- School of Life Science, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jacek Radwan
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| |
Collapse
|
8
|
Bass AL, Bateman AW, Connors BM, Staton BA, Rondeau EB, Mordecai GJ, Teffer AK, Kaukinen KH, Li S, Tabata AM, Patterson DA, Hinch SG, Miller KM. Identification of infectious agents in early marine Chinook and Coho salmon associated with cohort survival. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Recent decades have seen an increased appreciation for the role infectious diseases can play in mass mortality events across a diversity of marine taxa. At the same time many Pacific salmon populations have declined in abundance as a result of reduced marine survival. However, few studies have explicitly considered the potential role pathogens could play in these declines. Using a multi-year dataset spanning 59 pathogen taxa in Chinook and Coho salmon sampled along the British Columbia coast, we carried out an exploratory analysis to quantify evidence for associations between pathogen prevalence and cohort survival and between pathogen load and body condition. While a variety of pathogens had moderate to strong negative correlations with body condition or survival for one host species in one season, we found that Tenacibaculum maritimum and Piscine orthoreovirus had consistently negative associations with body condition in both host species and seasons and were negatively associated with survival for Chinook salmon collected in the fall and winter. Our analyses, which offer the most comprehensive examination of associations between pathogen prevalence and Pacific salmon survival to date, suggest that pathogens in Pacific salmon warrant further attention, especially those whose distribution and abundance may be influenced by anthropogenic stressors.
Collapse
Affiliation(s)
- Arthur L. Bass
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew W. Bateman
- Pacific Salmon Foundation, Vancouver, BC V6J 4S6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Brendan M. Connors
- Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, BC V8L 5T5, Canada
| | - Benjamin A. Staton
- Fisheries Science Department, Columbia River Inter-Tribal Fish Commission, Portland, OR 97232, USA
| | - Eric B. Rondeau
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Gideon J. Mordecai
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC V9T 6N7, Canada
| | - Amy K. Teffer
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Karia H. Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Amy M. Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - David A. Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Science Branch, Burnaby, BC V5A 1S6, Canada
| | - Scott G. Hinch
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kristina M. Miller
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| |
Collapse
|
9
|
Christensen KA, Rondeau EB, Sakhrani D, Biagi CA, Johnson H, Joshi J, Flores AM, Leelakumari S, Moore R, Pandoh PK, Withler RE, Beacham TD, Leggatt RA, Tarpey CM, Seeb LW, Seeb JE, Jones SJM, Devlin RH, Koop BF. The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle. PLoS One 2021; 16:e0255752. [PMID: 34919547 PMCID: PMC8682878 DOI: 10.1371/journal.pone.0255752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.
Collapse
Affiliation(s)
- Kris A. Christensen
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail: (KAC); (BFK)
| | - Eric B. Rondeau
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Dionne Sakhrani
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
| | - Carlo A. Biagi
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
| | - Hollie Johnson
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Jay Joshi
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Sreeja Leelakumari
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pawan K. Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Ruth E. Withler
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Terry D. Beacham
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | | | - Carolyn M. Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - James E. Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Steven J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Robert H. Devlin
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
| | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail: (KAC); (BFK)
| |
Collapse
|
10
|
Watson KB, Lehnert SJ, Bentzen P, Kess T, Einfeldt A, Duffy S, Perriman B, Lien S, Kent M, Bradbury IR. Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon (Salmo salar). Mol Ecol 2021; 31:1057-1075. [PMID: 34862998 DOI: 10.1111/mec.16307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/25/2021] [Accepted: 11/19/2021] [Indexed: 01/17/2023]
Abstract
Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non-model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans-Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine-scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence.
Collapse
Affiliation(s)
- K Beth Watson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Sarah J Lehnert
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Antony Einfeldt
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Steven Duffy
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Ben Perriman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Matthew Kent
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ian R Bradbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| |
Collapse
|
11
|
Gibson AK, Nguyen AE. Does genetic diversity protect host populations from parasites? A meta-analysis across natural and agricultural systems. Evol Lett 2020; 5:16-32. [PMID: 33552533 PMCID: PMC7857278 DOI: 10.1002/evl3.206] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 11/24/2022] Open
Abstract
If parasites transmit more readily between closely related hosts, then parasite burdens should decrease with increased genetic diversity of host populations. This important hypothesis is often accepted at face value—notorious epidemics of crop monocultures testify to the vulnerability of host populations that have been purged of diversity. Yet the relationship between genetic diversity and parasitism likely varies across contexts, differing between crop and noncrop hosts and between experimental and natural host populations. Here, we used a meta‐analytic approach to ask if host diversity confers protection against parasites over the range of contexts in which it has been tested. We synthesized the results of 102 studies, comprising 2004 effect sizes representing a diversity of approaches and host‐parasite systems. Our results validate a protective effect of genetic diversity, while revealing significant variation in its strength across biological and empirical contexts. In experimental host populations, genetic diversity reduces parasitism by ∼20% for noncrop hosts and by ∼50% for crop hosts. In contrast, observational studies of natural host populations show no consistent relationship between genetic diversity and parasitism, with both strong negative and positive correlations reported. This result supports the idea that, if parasites preferentially attack close relatives, the correlation of genetic diversity with parasitism could be positive or negative depending upon the potential for host populations to evolve in response to parasite selection. Taken together, these results reinforce genetic diversity as a priority for both conservation and agriculture and emphasize the challenges inherent to drawing comparisons between controlled experimental populations and dynamic natural populations.
Collapse
Affiliation(s)
- Amanda Kyle Gibson
- Department of Biology University of Virginia Charlottesville Virginia 22904
| | - Anna E Nguyen
- Department of Biology University of Virginia Charlottesville Virginia 22904
| |
Collapse
|
12
|
STAT3/SOCS3 axis contributes to the outcome of salmonid whirling disease. PLoS One 2020; 15:e0234479. [PMID: 32542025 PMCID: PMC7295227 DOI: 10.1371/journal.pone.0234479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
There are differences in disease susceptibility to whirling disease (WD) among strains of rainbow trout. The North American strain Trout Lodge (TL) is highly susceptible, whereas the German Hofer (HO) strain is more resistant. The suppressor of cytokine signaling (SOCS) proteins are key in inhibiting cytokine signaling. Their role in modulating the immune response against whirling disease is not completely clear. This study aimed at investigating the transcriptional response of SOCS1 and SOCS3 genes to Myxobolus cerebralis along with that of several upstream regulators and immune response genes. M. cerebralis induced the expression of SOCS1, the IL-6-dependent SOCS3, the anti-inflammatory cytokine IL-10 and the Treg associated transcription factor FOXP3 in TL fish at multiple time points, which likely caused a restricted STAT1 and STAT3 activity affecting the Th17/Treg17 balance. The expression of SOCS1 and the IL-6-dependent SOCS3 was induced constraining the activation of STAT1 and STAT3 in TL fish, thereby causing Th17/Treg17 imbalance and leaving the fish unable to establish a protective immune response against M. cerebralis or control inflammatory reactions increasing susceptibility to WD. Conversely, in HO fish, the expression of SOCS1 and SOCS3 was restrained, whereas the expression of STAT1 and IL-23-mediated STAT3 was induced potentially enabling more controlled immune responses, accelerating parasite clearance and elevating resistance. The induced expression of STAT1 and IL-23-mediated STAT3 likely maintained a successful Th17/Treg17 balance and enabled fish to promote effective immune responses favouring resistance against WD. The results provide insights into the role of SOCS1 and SOCS3 in regulating the activation and magnitude of host immunity in rainbow trout, which may help us understand the mechanisms that underlie the variation in resistance to WD.
Collapse
|
13
|
Genome-Wide Association Study Confirms Previous Findings of Major Loci Affecting Resistance to Piscine myocarditis virus in Atlantic Salmon ( Salmo salar L.). Genes (Basel) 2020; 11:genes11060608. [PMID: 32486315 PMCID: PMC7349847 DOI: 10.3390/genes11060608] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/16/2022] Open
Abstract
Cardiomyopathy syndrome is a viral disease of Atlantic salmon, mostly affecting fish during the late stages of production, resulting in significant losses to the industry. It has been shown that resistance to this disease has a strong genetic component, with quantitative trait loci (QTL) on chromosomes 27 (Ssa27) and Ssa12 to explain most of the additive genetic variance. Here, by analysing animals from a different year-class and a different population, we further aimed to confirm and narrow down the locations of these QTL. The data support the existence of the two QTL and suggest that the causative mutation on Ssa27 is most likely within the 10–10.5 Mbp segment of this chromosome. This region contains a cluster of major histocompatibility complex class I (MHC I) genes with the most strongly associated marker mapped to one of these loci. On Ssa12, the data confirmed the previous finding that the location of the causative mutation is within the 61.3 to 61.7 Mbp region. This segment contains several immune-related genes, but of particular interest are genes related to MHC II. Together, these findings highlight the likely key role of MHC genes in Atlantic salmon following infection with Piscine myocarditis virus (PMCV) and their potential impact on influencing the trajectory of this disease.
Collapse
|
14
|
Meron D, Davidovich N, Ofek‐Lalzar M, Berzak R, Scheinin A, Regev Y, Diga R, Tchernov D, Morick D. Specific pathogens and microbial abundance within liver and kidney tissues of wild marine fish from the Eastern Mediterranean Sea. Microb Biotechnol 2020; 13:770-780. [PMID: 32059079 PMCID: PMC7111072 DOI: 10.1111/1751-7915.13537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 11/26/2022] Open
Abstract
This study is an initial description and discussion of the kidney and liver microbial communities of five common fish species sampled from four sites along the Eastern Mediterranean Sea shoreline. The goals of the present study were to establish a baseline dataset of microbial communities associated with the tissues of wild marine fish, in order to examine species-specific microbial characteristics and to screen for candidate pathogens. This issue is especially relevant due to the development of mariculture farms and the possible transmission of pathogens from wild to farmed fish and vice versa. Although fish were apparently healthy, 16S rRNA NGS screening identified three potential fish bacterial pathogens: Photobacterium damselae, Vibrio harveyi and Streptococcus iniae. Based on the distribution patterns and relative abundance, 16 samples were classified as potential pathogenic bacteria-infected samples (PPBIS). Hence, PPBIS prevalence was significantly higher in kidneys than in liver samples and variation was found between the fish species. Significant differences were observed between fish species, organs and sites, indicating the importance of the environmental conditions on the fish microbiome. We applied a consistent sampling and analytical method for monitoring in long-term surveys which may be incorporated within other marine fish pathogens surveys around the world.
Collapse
Affiliation(s)
- Dalit Meron
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | | | | | - Ran Berzak
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Aviad Scheinin
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Yael Regev
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Rei Diga
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Dan Tchernov
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Danny Morick
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| |
Collapse
|
15
|
Stefan T, Matthews L, Prada JM, Mair C, Reeve R, Stear MJ. Divergent Allele Advantage Provides a Quantitative Model for Maintaining Alleles with a Wide Range of Intrinsic Merits. Genetics 2019; 212:553-564. [PMID: 30952668 PMCID: PMC6553829 DOI: 10.1534/genetics.119.302022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/30/2019] [Indexed: 01/28/2023] Open
Abstract
The Major Histocompatibility Complex (MHC) is the most genetically diverse region of the genome in most vertebrates. Some form of balancing selection is necessary to account for the extreme diversity, but the precise mechanism of balancing selection is unknown. Due to the way MHC molecules determine immune recognition, overdominance (also referred to as heterozygote advantage) has been suggested as the main driving force behind this unrivalled diversity. However, both theoretical results and simulation models have shown that overdominance in its classical form cannot maintain large numbers of alleles unless all alleles confer unrealistically similar levels of fitness. There is increasing evidence that heterozygotes containing genetically divergent alleles allow for broader antigen presentation to immune cells, providing a selective mechanism for MHC polymorphism. By framing competing models of overdominance within a general framework, we show that a model based on Divergent Allele Advantage (DAA) provides a superior mechanism for maintaining alleles with a wide range of intrinsic merits, as intrinsically less-fit MHC alleles that are more divergent can survive under DAA. Specifically, our results demonstrate that a quantitative mechanism built from the DAA hypothesis is able to maintain polymorphism in the MHC. Applying such a model to both livestock breeding and conservation could provide a better way of identifying superior heterozygotes, and quantifying the advantages of genetic diversity at the MHC.
Collapse
Affiliation(s)
- Thorsten Stefan
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
- Institute of Applied Mathematics and Statistics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Louise Matthews
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
| | - Joaquin M Prada
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
| | - Colette Mair
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
| | - Michael J Stear
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
| |
Collapse
|
16
|
Khrustaleva AM. Inferring Adaptive Nature of Major Histocompatibility Complex (MHC) Polymorphism from Single Nucleotide Substitutions in Asian Sockeye Salmon Populations: II. Factors Determining Onne-DAB Gene Variability in the Kamchatka River Basin. RUSS J GENET+ 2018. [DOI: 10.1134/s102279541811008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
17
|
Sylvester EVA, Beiko RG, Bentzen P, Paterson I, Horne JB, Watson B, Lehnert S, Duffy S, Clément M, Robertson MJ, Bradbury IR. Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America. Mol Ecol 2018; 27:4026-4040. [PMID: 30152128 DOI: 10.1111/mec.14849] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 12/18/2022]
Abstract
Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon-based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed clear differentiation between populations spawning in rivers flowing into a large marine embayment (Lake Melville) compared to coastal populations. The mechanisms influencing the differentiation of embayment populations were investigated using both multivariate and machine-learning landscape genetic approaches. We identified temperature as the strongest correlate with genetic structure, particularly warm temperature extremes and wider annual temperature ranges. The genomic basis of this divergence was further explored using a subset of locations (n = 17) and a 220K SNP array. SNPs associated with spatial structuring and temperature mapped to a diverse set of genes and molecular pathways, including regulation of gene expression, immune response, and cell development and differentiation. The results spanning molecular marker types and both novel and established methods clearly show climate-associated, fine-scale population structure across an environmental gradient in Atlantic salmon near its range limit in North America, highlighting valuable approaches for predicting population responses to climate change and managing species sustainability.
Collapse
Affiliation(s)
- Emma V A Sylvester
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Ian Paterson
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - John B Horne
- University of Southern Mississippi Gulf Coast Research Laboratory, Ocean Springs, MS, Canada
| | - Beth Watson
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Sarah Lehnert
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Steven Duffy
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St. John's, NL, Canada.,Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Martha J Robertson
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Ian R Bradbury
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada.,Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada.,Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, Canada
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Pritchard VL, Mäkinen H, Vähä JP, Erkinaro J, Orell P, Primmer CR. Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes. Mol Ecol 2018; 27:2560-2575. [DOI: 10.1111/mec.14705] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Hannu Mäkinen
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute; University of Turku; Turku Finland
| | | | - Panu Orell
- Natural Resources Institute Finland (LUKE); Oulu Finland
| | - Craig R. Primmer
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
| |
Collapse
|
20
|
Gordeeva NV, Salmenkova EA. Genetic markers of adaptive processes in the Far Eastern pink salmon Oncorhynchus gorbuscha: Allelic diversity at the locus of major histocompatibility complex MHC I-A1. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417110035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
21
|
Jeffery NW, Stanley RRE, Wringe BF, Guijarro-Sabaniel J, Bourret V, Bernatchez L, Bentzen P, Beiko RG, Gilbey J, Clément M, Bradbury IR. Range-wide parallel climate-associated genomic clines in Atlantic salmon. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171394. [PMID: 29291123 PMCID: PMC5717698 DOI: 10.1098/rsos.171394] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/13/2017] [Indexed: 05/02/2023]
Abstract
Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.
Collapse
Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland and Labrador, CanadaA1C 5X1
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
- Author for correspondence: Nicholas W. Jeffery e-mail:
| | - Ryan R. E. Stanley
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, CanadaB2Y 4A2
| | - Brendan F. Wringe
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland and Labrador, CanadaA1C 5X1
| | - Javier Guijarro-Sabaniel
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, CanadaB2Y 4A2
| | - Vincent Bourret
- Laboratoire d'expertise biolégale, MFFP, Québec, Québec, CanadaG1P 3W8
| | - Louis Bernatchez
- Department of Biology, Université Laval, Québec, Québec, CanadaG1 V 0A6
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
| | - John Gilbey
- Marine Scotland, Freshwater Fisheries Laboratory, Faskally, Pitlochry PH16 5LB, UK
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St John's, NL, Canada
- Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Ian R. Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland and Labrador, CanadaA1C 5X1
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
| |
Collapse
|
22
|
Perrier C, Ferchaud AL, Sirois P, Thibault I, Bernatchez L. Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish. Mol Ecol 2017; 26:6317-6335. [PMID: 29024140 DOI: 10.1111/mec.14361] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 01/01/2023]
Abstract
Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.
Collapse
Affiliation(s)
- Charles Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Pascal Sirois
- Chaire de Recherche sur les Espèces Aquatiques Exploitées, Laboratoire des Sciences Aquatiques, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Isabel Thibault
- Direction de l'expertise sur la Faune Aquatique, Ministère des Forêts de la Faune et des Parcs du Québec, Québec, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| |
Collapse
|
23
|
Cortázar-Chinarro M, Lattenkamp EZ, Meyer-Lucht Y, Luquet E, Laurila A, Höglund J. Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian. BMC Evol Biol 2017; 17:189. [PMID: 28806900 PMCID: PMC5557520 DOI: 10.1186/s12862-017-1022-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/26/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. RESULTS Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. CONCLUSION Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.
Collapse
Affiliation(s)
- Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
| | - Ella Z Lattenkamp
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Present address: Department of Neurogenetics of Vocal Communication, Max Planck Institute of Psycholinguistics, Box 310, 6500, Nijmegen, Netherlands
| | - Yvonne Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Emilien Luquet
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Present address: Université Claude Bernard - Lyon I, CNRS, UMR 5023 - LEHNA, 3-6, rue Raphaël Dubois - Bâtiments Darwin C and Forel, 69622 Villeurbanne Cedex 43, Boulevard du 11 novembre, 1918, Lyon, France
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| |
Collapse
|
24
|
Slade JWG, Sarquis-Adamson Y, Gloor GB, Lachance MA, MacDougall-Shackleton EA. Population Differences at MHC Do Not Explain Enhanced Resistance of Song Sparrows to Local Parasites. J Hered 2017; 108:127-134. [PMID: 27940472 DOI: 10.1093/jhered/esw082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023] Open
Abstract
Infectious disease represents an emerging threat to natural populations, particularly when hosts are more susceptible to novel parasites (allopatric) than to parasites from the local area (sympatric). This pattern could arise through evolutionary processes (host populations become adapted to their local parasites and genetically differentiated from other populations at immune-related loci) and/or through ecological interactions (host individuals develop resistance to local parasites through previous exposure). The relative importance of these candidate mechanisms remains unclear. In jawed vertebrates, genes of the major histocompatibility complex (MHC) play a fundamental role in immunity and are compelling candidates for spatially varying selection. We recently showed that song sparrows (Melospiza melodia) are more susceptible to allopatric than to sympatric strains of malaria (Plasmodium). In the current study, to determine whether population differences at MHC explain this pattern, we characterized the peptide-binding regions of MHC (classes I and II) of birds that did or did not become infected in the previous experiment. We recovered up to 4 alleles per individual at class I, implying at least 2 loci, and up to 26 alleles per individual at class II, implying at least 13 loci. Individuals with more class I alleles were less likely to become infected by Plasmodium, consistent with parasite-mediated balancing selection. However, we found no evidence for population genetic differentiation at either class of MHC, based on 36 individuals sequenced. Resistance to sympatric parasites previously described for this system likely stems from individuals' prior immune experience, not from population differentiation and locally protective alleles at MHC.
Collapse
Affiliation(s)
- Joel W G Slade
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | | | - Gregory B Gloor
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | | |
Collapse
|
25
|
Small-scale intraspecific patterns of adaptive immunogenetic polymorphisms and neutral variation in Lake Superior lake trout. Immunogenetics 2017; 70:53-66. [PMID: 28547520 DOI: 10.1007/s00251-017-0996-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
Abstract
Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species' evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake. To investigate patterns of adaptive immunogenetic variation among lake trout ecomorphs, we used Illumina high-throughput sequencing. The population's genetic structure of the major histocompatibility complex (MHC Class IIβ exon 2) and 18 microsatellite loci were compared to disentangle neutral and selective processes at a small geographic scale. Both MHC and microsatellite variation were partitioned more by water depth stratum than by ecomorph. Several metrics showed strong clustering by water depth in MHC alleles, but not microsatellites. We report a 75% increase in the number of MHC alleles shared between the predominant shallow and deep water ecomorphs since a previous lake trout MHC study at the same locale (c. 1990s data). This result is consistent with the reverse speciation hypothesis, although adaptive MHC polymorphisms persist along an ecological gradient. Finally, results suggested that the lake trout have multiple copies of the MHC II locus consistent with a historic genomic duplication event. Our findings indicated that conservation approaches for this species could focus on managing various ecological habitats by depth, in addition to regulating the fisheries specific to ecomorphs.
Collapse
|
26
|
Heinrich SK, Hofer H, Courtiol A, Melzheimer J, Dehnhard M, Czirják GÁ, Wachter B. Cheetahs have a stronger constitutive innate immunity than leopards. Sci Rep 2017; 7:44837. [PMID: 28333126 PMCID: PMC5363065 DOI: 10.1038/srep44837] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 02/14/2017] [Indexed: 11/21/2022] Open
Abstract
As a textbook case for the importance of genetics in conservation, absence of genetic variability at the major histocompatibility complex (MHC) is thought to endanger species viability, since it is considered crucial for pathogen resistance. An alternative view of the immune system inspired by life history theory posits that a strong response should evolve in other components of the immune system if there is little variation in the MHC. In contrast to the leopard (Panthera pardus), the cheetah (Acinonyx jubatus) has a relatively low genetic variability at the MHC, yet free-ranging cheetahs are healthy. By comparing the functional competence of the humoral immune system of both species in sympatric populations in Namibia, we demonstrate that cheetahs have a higher constitutive innate but lower induced innate and adaptive immunity than leopards. We conclude (1) immunocompetence of cheetahs is higher than previously thought; (2) studying both innate and adaptive components of immune systems will enrich conservation science.
Collapse
Affiliation(s)
- Sonja K. Heinrich
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Heribert Hofer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Alexandre Courtiol
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Jörg Melzheimer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Martin Dehnhard
- Department of Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Gábor Á. Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Bettina Wachter
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| |
Collapse
|
27
|
Hansen MM, Rogers SM. Recipient of the 2016 Molecular Ecology Prize: Louis Bernatchez - advancing the conservation of aquatic resources with his contributions on the ecological genomics of adaptation and speciation. Mol Ecol 2017; 26:413-419. [PMID: 28130941 DOI: 10.1111/mec.13941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 116., DK-8000, Aarhus C, Denmark
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, 2500 University Dr., NW, Calgary, AB, T2N 1N4, Canada
| |
Collapse
|
28
|
Osborne MJ, Pilger TJ, Lusk JD, Turner TF. Spatio-temporal variation in parasite communities maintains diversity at the major histocompatibility complex class IIβ in the endangered Rio Grande silvery minnow. Mol Ecol 2016; 26:471-489. [PMID: 27864911 DOI: 10.1111/mec.13936] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/02/2016] [Accepted: 11/14/2016] [Indexed: 01/30/2023]
Abstract
Climate change will strongly impact aquatic ecosystems particularly in arid and semi-arid regions. Fish-parasite interactions will also be affected by predicted altered flow and temperature regimes, and other environmental stressors. Hence, identifying environmental and genetic factors associated with maintaining diversity at immune genes is critical for understanding species' adaptive capacity. Here, we combine genetic (MHC class IIβ and microsatellites), parasitological and ecological data to explore the relationship between these factors in the remnant wild Rio Grande silvery minnow (Hybognathus amarus) population, an endangered species found in the southwestern United States. Infections with multiple parasites on the gills were observed and there was spatio-temporal variation in parasite communities and patterns of infection among individuals. Despite its highly endangered status and chronically low genetic effective size, Rio Grande silvery minnow had high allelic diversity at MHC class IIβ with more alleles recognized at the presumptive DAB1 locus compared to the DAB3 locus. We identified significant associations between specific parasites and MHC alleles against a backdrop of generalist parasite prevalence. We also found that individuals with higher individual neutral heterozygosity and higher amino acid divergence between MHC alleles had lower parasite abundance and diversity. Taken together, these results suggest a role for fluctuating selection imposed by spatio-temporal variation in pathogen communities and divergent allele advantage in maintenance of high MHC polymorphism. Understanding the complex interaction of habitat, pathogens and immunity in protected species will require integrated experimental, genetic and field studies.
Collapse
Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, Albuquerque, NM, 87131, USA
| | - Tyler J Pilger
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, Albuquerque, NM, 87131, USA
| | - Joel D Lusk
- U.S. Fish and Wildlife Service, New Mexico Ecological Services, Albuquerque, NM, 87113, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, Albuquerque, NM, 87131, USA
| |
Collapse
|
29
|
Lewnard JA, Townsend JP. Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India. Proc Natl Acad Sci U S A 2016; 113:14601-14608. [PMID: 27791071 PMCID: PMC5187705 DOI: 10.1073/pnas.1604985113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Immune heterogeneity in wild host populations indicates that disease-mediated selection is common in nature. However, the underlying dynamic feedbacks involving the ecology of disease transmission, evolutionary processes, and their interaction with environmental drivers have proven challenging to characterize. Plague presents an optimal system for interrogating such couplings: Yersinia pestis transmission exerts intense selective pressure driving the local persistence of disease resistance among its wildlife hosts in endemic areas. Investigations undertaken in colonial India after the introduction of plague in 1896 suggest that, only a decade after plague arrived, a heritable, plague-resistant phenotype had become prevalent among commensal rats of cities undergoing severe plague epidemics. To understand the possible evolutionary basis of these observations, we developed a mathematical model coupling environmentally forced plague dynamics with evolutionary selection of rats, capitalizing on extensive archival data from Indian Plague Commission investigations. Incorporating increased plague resistance among rats as a consequence of intense natural selection permits the model to reproduce observed changes in seasonal epidemic patterns in several cities and capture experimentally observed associations between climate and flea population dynamics in India. Our model results substantiate Victorian era claims of host evolution based on experimental observations of plague resistance and reveal the buffering effect of such evolution against environmental drivers of transmission. Our analysis shows that historical datasets can yield powerful insights into the transmission dynamics of reemerging disease agents with which we have limited contemporary experience to guide quantitative modeling and inference.
Collapse
Affiliation(s)
- Joseph A Lewnard
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510;
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520
| |
Collapse
|
30
|
Rico Y, Ethier DM, Davy CM, Sayers J, Weir RD, Swanson BJ, Nocera JJ, Kyle CJ. Spatial patterns of immunogenetic and neutral variation underscore the conservation value of small, isolated American badger populations. Evol Appl 2016; 9:1271-1284. [PMID: 27877205 PMCID: PMC5108218 DOI: 10.1111/eva.12410] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/14/2016] [Indexed: 12/29/2022] Open
Abstract
Small and isolated populations often exhibit low genetic diversity due to drift and inbreeding, but may simultaneously harbour adaptive variation. We investigate spatial distributions of immunogenetic variation in American badger subspecies (Taxidea taxus), as a proxy for evaluating their evolutionary potential across the northern extent of the species' range. We compared genetic structure of 20 microsatellites and the major histocompatibility complex (MHC DRB exon 2) to evaluate whether small, isolated populations show low adaptive polymorphism relative to large and well-connected populations. Our results suggest that gene flow plays a prominent role in shaping MHC polymorphism across large spatial scales, while the interplay between gene flow and selection was stronger towards the northern peripheries. The similarity of MHC alleles within subspecies relative to their neutral genetic differentiation suggests that adaptive divergence among subspecies can be maintained despite ongoing gene flow along subspecies boundaries. Neutral genetic diversity was low in small relative to large populations, but MHC diversity within individuals was high in small populations. Despite reduced neutral genetic variation, small and isolated populations harbour functional variation that likely contribute to the species evolutionary potential at the northern range. Our findings suggest that conservation approaches should focus on managing adaptive variation across the species range rather than protecting subspecies per se.
Collapse
Affiliation(s)
- Yessica Rico
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
- Present address: CONACYTInstituto de Ecología A.C.Centro Regional del BajíoAvenida Lázaro Cárdenas 253PátzcuaroMichoacán61600México
| | - Danielle M. Ethier
- Ontario Badger ProjectGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Christina M. Davy
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
| | | | - Richard D. Weir
- Ecosystems Protection & Sustainability BranchMinistry of EnvironmentVictoriaBCCanada
| | | | - Joseph J. Nocera
- Wildlife Research and Monitoring SectionMinistry of Natural Resources & ForestryPeterboroughONCanada
| | - Christopher J. Kyle
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
| |
Collapse
|
31
|
Hoover B, Nevitt G. Modeling the Importance of Sample Size in Relation to Error in MHC-Based Mate-Choice Studies on Natural Populations. Integr Comp Biol 2016; 56:925-933. [DOI: 10.1093/icb/icw105] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
32
|
Kjærner-Semb E, Ayllon F, Furmanek T, Wennevik V, Dahle G, Niemelä E, Ozerov M, Vähä JP, Glover KA, Rubin CJ, Wargelius A, Edvardsen RB. Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection. BMC Genomics 2016; 17:610. [PMID: 27515098 PMCID: PMC4982270 DOI: 10.1186/s12864-016-2867-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/30/2016] [Indexed: 12/31/2022] Open
Abstract
Background Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplication in the salmonid lineage which resulted in a partly tetraploid species with duplicated genes and regions. Results In order to elucidate the genes and genomic regions underlying the genetic differences, we conducted a genome wide association study using whole genome resequencing data from eight populations from Northern and Southern Norway. From a total of ~4.5 million sequencing-derived SNPs, more than 10 % showed significant differentiation between populations from these two regions and ten selective sweeps on chromosomes 5, 10, 11, 13–15, 21, 24 and 25 were identified. These comprised 59 genes, of which 15 had one or more differentiated missense mutation. Our analysis showed that most sweeps have paralogous regions in the partially tetraploid genome, each lacking the high number of significant SNPs found in the sweeps. The most significant sweep was found on Chr 25 and carried several missense mutations in the antiviral mx genes, suggesting that these populations have experienced differing viral pressures. Interestingly the second most significant sweep, found on Chr 5, contains two genes involved in the NF-KB pathway (nkap and nkrf), which is also a known pathogen target that controls a large number of processes in animals. Conclusion Our results show that natural selection acting on immune related genes has contributed to genetic divergence between salmon populations in Norway. The differences between populations may have been facilitated by the plasticity of the salmon genome. The observed signatures of selection in duplicated genomic regions suggest that the recently duplicated genome has provided raw material for evolutionary adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2867-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Erik Kjærner-Semb
- Institute of Marine Research, Bergen, Norway. .,Department of Biology, University of Bergen, Bergen, Norway.
| | | | | | | | - Geir Dahle
- Institute of Marine Research, Bergen, Norway
| | - Eero Niemelä
- Natural Resources Institute Finland, Helsinki, Finland
| | - Mikhail Ozerov
- Kevo Subarctic Research Institute, University of Turku, Turku, Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute, University of Turku, Turku, Finland.,Association for Water and Environment of Western Uusimaa, Uusimaa, Finland
| | - Kevin A Glover
- Institute of Marine Research, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Carl J Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | |
Collapse
|
33
|
Rosengrave P, Montgomerie R, Gemmell N. Cryptic female choice enhances fertilization success and embryo survival in chinook salmon. Proc Biol Sci 2016; 283:20160001. [PMID: 27009221 PMCID: PMC4822462 DOI: 10.1098/rspb.2016.0001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 02/24/2016] [Indexed: 12/27/2022] Open
Abstract
In this study, we investigated two potentially important intersexual postcopulatory gametic interactions in a population of chinook salmon (Oncorhynchus tshawytscha): (i) the effect of female ovarian fluid (OF) on the behaviour of spermatozoa during fertilization and (ii) the effects of multilocus heterozygosity (MLH) (as an index of male quality) and female-male genetic relatedness on sperm behaviour and male fertilization success when there is sperm competition in the presence of that OF. To do this, we conducted a series of in vitro competitive fertilization experiments and found that, when ejaculates from two males are competing for access to a single female's unfertilized eggs, fertilization success was significantly biased towards the male whose sperm swam fastest in the female's OF. Embryo survival--a measure of fitness--was also positively correlated with both sperm swimming speed in OF and male MLH, providing novel evidence that cryptic female choice is adaptive for the female, enhancing the early survival of her offspring and potentially influencing her fitness.
Collapse
Affiliation(s)
- Patrice Rosengrave
- Department of Anatomy, University of Otago, Dunedin, New Zealand Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy University of Otago, Dunedin, New Zealand
| | - Robert Montgomerie
- Department of Biology, Queen's University, Kingston, Ontario, Canada K7 L 3N6
| | - Neil Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy University of Otago, Dunedin, New Zealand
| |
Collapse
|
34
|
Kennedy DA, Kurath G, Brito IL, Purcell MK, Read AF, Winton JR, Wargo AR. Potential drivers of virulence evolution in aquaculture. Evol Appl 2016; 9:344-54. [PMID: 26834829 PMCID: PMC4721074 DOI: 10.1111/eva.12342] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/06/2015] [Indexed: 01/24/2023] Open
Abstract
Infectious diseases are economically detrimental to aquaculture, and with continued expansion and intensification of aquaculture, the importance of managing infectious diseases will likely increase in the future. Here, we use evolution of virulence theory, along with examples, to identify aquaculture practices that might lead to the evolution of increased pathogen virulence. We identify eight practices common in aquaculture that theory predicts may favor evolution toward higher pathogen virulence. Four are related to intensive aquaculture operations, and four others are related specifically to infectious disease control. Our intention is to make aquaculture managers aware of these risks, such that with increased vigilance, they might be able to detect and prevent the emergence and spread of increasingly troublesome pathogen strains in the future.
Collapse
Affiliation(s)
- David A Kennedy
- Center for Infectious Disease Dynamics Departments of Biology and Entomology The Pennsylvania State University University Park PA USA; Fogarty International Center National Institutes of Health Bethesda MD USA
| | - Gael Kurath
- U.S. Geological Survey Western Fisheries Research Center Seattle WA USA
| | - Ilana L Brito
- Massachusetts Institute of Technology Cambridge MA USA
| | - Maureen K Purcell
- U.S. Geological Survey Western Fisheries Research Center Seattle WA USA
| | - Andrew F Read
- Center for Infectious Disease Dynamics Departments of Biology and Entomology The Pennsylvania State University University Park PA USA; Fogarty International Center National Institutes of Health Bethesda MD USA
| | - James R Winton
- U.S. Geological Survey Western Fisheries Research Center Seattle WA USA
| | - Andrew R Wargo
- Virginia Institute of Marine Science College of William and Mary Gloucester Point VA USA
| |
Collapse
|
35
|
|
36
|
Seifertová M, Jarkovský J, Šimková A. Does the parasite-mediated selection drive the MHC class IIB diversity in wild populations of European chub (Squalius cephalus)? Parasitol Res 2015; 115:1401-15. [PMID: 26693717 DOI: 10.1007/s00436-015-4874-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/07/2015] [Indexed: 11/29/2022]
Abstract
The genes of major histocompatibility complex (MHC) provide an excellent opportunity to study host-parasite relationships because they are expected to evolve in response to parasites and variation in parasite communities. In this study, we investigated the potential role of parasite-mediated selection acting on MHC class IIB (DAB) genes in European chub (Squalius cephalus) natural populations. We found significant differences between populations in metazoan parasites, neutral and adaptive genetic diversities. The analyses based on pairwise data revealed that populations with dissimilar MHC allelic profiles were geographically distant populations with significantly different diversity in microsatellites and a dissimilar composition of parasite communities. The results from the generalized estimating equations method (GEE) on the level of individuals revealed that metazoan parasite load in European chub was influenced by the diversity of DAB alleles as well as by the diversity of neutral genetic markers and host traits reflecting condition and immunocompetence. The multivariate co-inertia analysis showed specific associations between DAB alleles and parasite species. DAB1-like alleles were more involved in associations with ectoparasites, while DAB3-like alleles were positively associated with endoparasites which could suggest potential differences between DAB genes caused by different selection pressure. Our study revealed that parasite-mediated selection is not the only variable affecting MHC diversity in European chub; however, we strongly support the role of neutral processes as the main driver of DAB diversity across populations. In addition, our study contributes to the understanding of the evolution of MHC genes in wild living fish.
Collapse
Affiliation(s)
- Mária Seifertová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic.
| | - Jiří Jarkovský
- Institute of Biostatistics and Analyses, Faculty of Medicine and Faculty of Science, Masaryk University, Kamenice 126/3, 625 00, Brno, Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| |
Collapse
|
37
|
Talbot B, Garant D, Rioux Paquette S, Mainguy J, Pelletier F. Genetic structure and diversity among rabid and nonrabid raccoons. ECOSCIENCE 2015. [DOI: 10.2980/20-4-3633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
38
|
O'Malley KG, Perales B, Whitcomb AC. Influence of immune-relevant genotype on the reproductive success of a salmonid alternative mating strategy. JOURNAL OF FISH BIOLOGY 2015; 86:871-881. [PMID: 25643937 DOI: 10.1111/jfb.12597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 10/09/2014] [Indexed: 06/04/2023]
Abstract
Major histocompatibility complex (MHC) and immune-relevant gene markers were used to evaluate differences in reproductive success (RS) among naturally spawning coho salmon Oncorhynchus kisutch mate pairs involving an alternative male reproductive phenotype, known as jacks. These mate pairs included both hatchery-reared and wild origin fish such that three classes were evaluated in two consecutive years (2005 and 2006) using a previously constructed multigenerational genetic pedigree: wild × wild (W × W), hatchery × hatchery (H × H) and wild × hatchery (W × H). Oncorhynchus kisutch jack mate pairs mated randomly based on immune-relevant genotype in both years; a result consistent with the opportunistic mating strategy of jacks. An association between greater number of alleles shared at three immune-relevant gene markers and increased RS was found for: W × H mate pairs in 2005 (BHMS429), W × H pairs in 2006 (SsalR016TKU) and W × W pairs in 2006 (OMM3085). No correlation between immune gene diversity and RS was found for H × H pairs in either year. The results suggest that the influence of immune-relevant genotype on mating success may be different for jacks when compared with previous studies of large adult male O. kisutch.
Collapse
Affiliation(s)
- K G O'Malley
- Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Department of Fisheries and Wildlife, Oregon State University, 2030 SE Marine Science Drive, Newport, OR 97365, U.S.A
| | | | | |
Collapse
|
39
|
Lemay MA, Russello MA. Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon. BMC Res Notes 2014; 7:778. [PMID: 25367228 PMCID: PMC4228061 DOI: 10.1186/1756-0500-7-778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/24/2014] [Indexed: 11/28/2022] Open
Abstract
Background Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit (AtpA) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat. Results We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats. Conclusions We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with environmental sampling to better understand the ecology of pathogen infection in this species. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-778) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Matthew A Lemay
- University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada.
| | | |
Collapse
|
40
|
Role of selection versus neutral processes determining genetic variation in a small mammal along a climatic gradient in southern Africa. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9731-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Boutin S, Sauvage C, Bernatchez L, Audet C, Derome N. Inter individual variations of the fish skin microbiota: host genetics basis of mutualism? PLoS One 2014; 9:e102649. [PMID: 25068850 PMCID: PMC4113282 DOI: 10.1371/journal.pone.0102649] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 06/20/2014] [Indexed: 11/19/2022] Open
Abstract
The commensal microbiota of fish skin is suspected to provide a protection against opportunist infections. The skin of fish harbors a complex and diverse microbiota that closely interacts with the surrounding water microbial communities. Up to now there is no clear evidence as to whether the host regulates the recruitment of environmental bacteria to build a specific skin microbiota. To address this question, we detected Quantitative Trait Loci (QTL) associated with the abundance of specific skin microbiota bacterial strains in brook charr (Salvelinus fontinalis), combining 16S RNA tagged-amplicon 454 pyrosequencing with genetic linkage analysis. Skin microbiota analysis revealed high inter-individual variation among 86 F2 fish progeny based upon the relative abundance of bacterial operational taxonomic units (OTUs). Out of those OTUs, the pathogenic strain Flavobacterium psychrophilum and the non-pathogenic strain Methylobacterium rhodesianum explained the majority of inter-individual distances. Furthermore, a strong negative correlation was found between Flavobacterium and Methylobacterium, suggesting a mutually competitive relationship. Finally, after considering a total of 266 markers, genetic linkage analysis highlighted three major QTL associated with the abundance of Lysobacter, Rheinheimera and Methylobacterium. All these three genera are known for their beneficial antibacterial activity. Overall, our results provide evidence that host genotype may regulate the abundance of specific genera among their surface microbiota. They also indicate that Lysobacter, Rheinheimera and Methylobacterium are potentially important genera in providing protection against pathogens.
Collapse
Affiliation(s)
- Sébastien Boutin
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, Québec, Canada
| | - Christopher Sauvage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, Québec, Canada
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - Allée des Chênes, Montfavet, France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, Québec, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski, Québec, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, Québec, Canada
- * E-mail:
| |
Collapse
|
43
|
Lamaze FC, Pavey SA, Normandeau E, Roy G, Garant D, Bernatchez L. Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis). Mol Ecol 2014; 23:1730-48. [PMID: 24795997 DOI: 10.1111/mec.12684] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The capacity of an individual to battle infection is an important fitness determinant in wild vertebrate populations. The major histocompatibility complex (MHC) genes are crucial for a host's adaptive immune system to detect pathogens. However, anthropogenic activities may disrupt natural cycles of co-evolution between hosts and pathogens. In this study, we investigated the dynamic sequence and expression variation of host parasite interactions in brook charr (Salvelinus fontinalis) in a context of past human disturbance via population supplementation from domestic individuals. To do so, we developed a new method to examine selection shaping MHC diversity within and between populations and found a complex interplay between neutral and selective processes that varied between lakes that were investigated. We provided evidence for a lower introgression rate of domestic alleles and found that parasite infection increased with domestic genomic background of individuals. We also documented an association between individual MHC alleles and parasite taxa. Finally, longer cis-regulatory minisatellites were positively correlated with MHC II down-regulation and domestic admixture, suggesting that inadvertent selection during domestication resulted in a lower immune response capacity, through a trade-off between growth and immunity, which explained the negative selection of domestic alleles at least under certain circumstances.
Collapse
|
44
|
O'Donnell DR, Parigi A, Fish JA, Dworkin I, Wagner AP. The roles of standing genetic variation and evolutionary history in determining the evolvability of anti-predator strategies. PLoS One 2014; 9:e100163. [PMID: 24955847 PMCID: PMC4067307 DOI: 10.1371/journal.pone.0100163] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/22/2014] [Indexed: 11/19/2022] Open
Abstract
Standing genetic variation and the historical environment in which that variation arises (evolutionary history) are both potentially significant determinants of a population's capacity for evolutionary response to a changing environment. Using the open-ended digital evolution software Avida, we evaluated the relative importance of these two factors in influencing evolutionary trajectories in the face of sudden environmental change. We examined how historical exposure to predation pressures, different levels of genetic variation, and combinations of the two, affected the evolvability of anti-predator strategies and competitive abilities in the presence or absence of threats from new, invasive predator populations. We show that while standing genetic variation plays some role in determining evolutionary responses, evolutionary history has the greater influence on a population's capacity to evolve anti-predator traits, i.e. traits effective against novel predators. This adaptability likely reflects the relative ease of repurposing existing, relevant genes and traits, and the broader potential value of the generation and maintenance of adaptively flexible traits in evolving populations.
Collapse
Affiliation(s)
- Daniel R. O'Donnell
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan, United States of America
- Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
| | - Abhijna Parigi
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan, United States of America
- Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jordan A. Fish
- Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Ian Dworkin
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan, United States of America
- Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
| | - Aaron P. Wagner
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
| |
Collapse
|
45
|
Llewellyn MS, Boutin S, Hoseinifar SH, Derome N. Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front Microbiol 2014; 5:207. [PMID: 24917852 PMCID: PMC4040438 DOI: 10.3389/fmicb.2014.00207] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/18/2014] [Indexed: 01/10/2023] Open
Abstract
Indigenous microbiota play a critical role in the lives of their vertebrate hosts. In human and mouse models it is increasingly clear that innate and adaptive immunity develop in close concert with the commensal microbiome. Furthermore, several aspects of digestion and nutrient metabolism are governed by intestinal microbiota. Research on teleosts has responded relatively slowly to the introduction of massively parallel sequencing procedures in microbiomics. Nonetheless, progress has been made in biotic and gnotobiotic zebrafish models, defining a core microbiome and describing its role in development. However, microbiome research in other teleost species, especially those important from an aquaculture perspective, has been relatively slow. In this review, we examine progress in teleost microbiome research to date. We discuss teleost microbiomes in health and disease, microbiome ontogeny, prospects for successful microbiome manipulation (especially in an aquaculture setting) and attempt to identify important future research themes. We predict an explosion in research in this sector in line with the increasing global demand for fish protein, and the need to find sustainable approaches to improve aquaculture yield. The reduced cost and increasing ease of next generation sequencing technologies provides the technological backing, and the next 10 years will be an exciting time for teleost microbiome research.
Collapse
Affiliation(s)
- Martin S Llewellyn
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada ; Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Wales Bangor, UK
| | - Sébastien Boutin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada
| | - Seyed Hossein Hoseinifar
- Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources Gorgan, Iran
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada
| |
Collapse
|
46
|
Sevellec M, Pavey SA, Boutin S, Filteau M, Derome N, Bernatchez L. Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis
) using next-generation sequencing. J Evol Biol 2014; 27:1029-46. [DOI: 10.1111/jeb.12374] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 03/16/2014] [Indexed: 12/21/2022]
Affiliation(s)
- M. Sevellec
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - S. A. Pavey
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - S. Boutin
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - M. Filteau
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - N. Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - L. Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| |
Collapse
|
47
|
Kamath PL, Turner WC, Küsters M, Getz WM. Parasite-mediated selection drives an immunogenetic trade-off in plains zebras (Equus quagga). Proc Biol Sci 2014; 281:20140077. [PMID: 24718761 DOI: 10.1098/rspb.2014.0077] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Pathogen evasion of the host immune system is a key force driving extreme polymorphism in genes of the major histocompatibility complex (MHC). Although this gene family is well characterized in structure and function, there is still much debate surrounding the mechanisms by which MHC diversity is selectively maintained. Many studies have investigated relationships between MHC variation and specific pathogens, and have found mixed support for and against the hypotheses of heterozygote advantage, frequency-dependent or fluctuating selection. Few, however, have focused on the selective effects of multiple parasite types on host immunogenetic patterns. Here, we examined relationships between variation in the equine MHC gene, ELA-DRA, and both gastrointestinal (GI) and ectoparasitism in plains zebras (Equus quagga). Specific alleles present at opposing population frequencies had antagonistic effects, with rare alleles associated with increased GI parasitism and common alleles with increased tick burdens. These results support a frequency-dependent mechanism, but are also consistent with fluctuating selection. Maladaptive GI parasite 'susceptibility alleles' were reduced in frequency, suggesting that these parasites may play a greater selective role at this locus. Heterozygote advantage, in terms of allele mutational divergence, also predicted decreased GI parasite burden in genotypes with a common allele. We conclude that an immunogenetic trade-off affects resistance/susceptibility to parasites in this system. Because GI and ectoparasites do not directly interact within hosts, our results uniquely show that antagonistic parasite interactions can be indirectly modulated through the host immune system. This study highlights the importance of investigating the role of multiple parasites in shaping patterns of host immunogenetic variation.
Collapse
Affiliation(s)
- Pauline L Kamath
- US Geological Survey, Northern Rocky Mountain Science Center, , 2327 University Way, Bozeman, MT 59715, USA, Department of Environmental Science, Policy, and Management, University of California, , 130 Mulford Hall No. 3114, Berkeley, CA 94720, USA, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, , PO Box 1066 Blindern, Oslo 0361, Norway, Berkeley Etosha Anthrax Research Project, , Swakopmund, Namibia, School of Mathematical Sciences, University of KwaZulu-Natal, , Private Bag X54001, 14, Durban 4000, South Africa
| | | | | | | |
Collapse
|
48
|
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.
Collapse
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
| | | |
Collapse
|
49
|
Khrustaleva AM, Gritsenko OF, Klovach NV. Single-nucleotide polymorphism in populations of sockeye salmon Oncorhynchus nerka from Kamchatka Peninsula. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413110094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
50
|
Collin H, Burri R, Comtesse F, Fumagalli L. Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (Phoxinus phoxinus). Ecol Evol 2013; 3:2568-85. [PMID: 24567825 PMCID: PMC3930049 DOI: 10.1002/ece3.650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 11/10/2022] Open
Abstract
Host-pathogen interactions are a major evolutionary force promoting local adaptation. Genes of the major histocompatibility complex (MHC) represent unique candidates to investigate evolutionary processes driving local adaptation to parasite communities. The present study aimed at identifying the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of European minnows (Phoxinus phoxinus). To this end, we isolated and genotyped exon 2 of two MHCIIB gene duplicates (DAB1 and DAB3) and 1'665 amplified fragment length polymorphism (AFLP) markers in nine populations, and characterized local bacterial communities by 16S rDNA barcoding using 454 amplicon sequencing. Both MHCIIB loci exhibited signs of historical balancing selection. Whereas genetic differentiation exceeded that of neutral markers at both loci, the populations' genetic diversities were positively correlated with local pathogen diversities only at DAB3. Overall, our results suggest pathogen-mediated local adaptation in European minnows at both MHCIIB loci. While at DAB1 selection appears to favor different alleles among populations, this is only partially the case in DAB3, which appears to be locally adapted to pathogen communities in terms of genetic diversity. These results provide new insights into the importance of host-pathogen interactions in driving local adaptation in the European minnow, and highlight that the importance of adaptive processes driving MHCIIB gene evolution may differ among duplicates within species, presumably as a consequence of alternative selective regimes or different genomic context. Using next-generation sequencing, the present manuscript identifies the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of a cyprinid fish: the European minnow (Phoxinus phoxinus). We highlight that the relative importance of neutral versus adaptive processes in shaping immune competence may differ between duplicates as a consequence of alternative selective regimes or different genomic contexts.
Collapse
Affiliation(s)
- Helene Collin
- Department of Ecology and Evolution Laboratory for Conservation Biology, University of Lausanne Biophore, 1015, Lausanne, Switzerland ; Institute of Integrative Biology, University of Liverpool Biosciences Building, Crown St., Liverpool L69 7ZB, U.K
| | - Reto Burri
- Department of Ecology and Evolution Laboratory for Conservation Biology, University of Lausanne Biophore, 1015, Lausanne, Switzerland ; Department of Evolutionary Biology Evolutionary Biology Centre, Uppsala University Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Fabien Comtesse
- Department of Ecology and Evolution Laboratory for Conservation Biology, University of Lausanne Biophore, 1015, Lausanne, Switzerland
| | - Luca Fumagalli
- Department of Ecology and Evolution Laboratory for Conservation Biology, University of Lausanne Biophore, 1015, Lausanne, Switzerland
| |
Collapse
|