1
|
Clarke SH, Lawrence ER, Matte JM, Gallagher BK, Salisbury SJ, Michaelides SN, Koumrouyan R, Ruzzante DE, Grant JWA, Fraser DJ. Global assessment of effective population sizes: Consistent taxonomic differences in meeting the 50/500 rule. Mol Ecol 2024:e17353. [PMID: 38613250 DOI: 10.1111/mec.17353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Effective population size (Ne) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum Ne of 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between Ne and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced Ne estimates from 3829 populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal and amphibian populations had a <54% probability of reachingN ̂ e $$ {\hat{N}}_e $$ = 50 and a <9% probability of reachingN ̂ e $$ {\hat{N}}_e $$ = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller medianN ̂ e $$ {\hat{N}}_e $$ than unlisted populations, and this was consistent across all taxonomic groups.N ̂ e $$ {\hat{N}}_e $$ was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation ofN ̂ e $$ {\hat{N}}_e $$ in wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on Ne and help prioritise assessment of populations from taxa most at risk of failing to meet conservation thresholds.
Collapse
Affiliation(s)
- Shannon H Clarke
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Jean-Michel Matte
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Brian K Gallagher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sarah J Salisbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Ramela Koumrouyan
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - James W A Grant
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Dylan J Fraser
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| |
Collapse
|
2
|
Fuentes‐Pardo AP, Stanley R, Bourne C, Singh R, Emond K, Pinkham L, McDermid JL, Andersson L, Ruzzante DE. Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow. Evol Appl 2024; 17:e13675. [PMID: 38495946 PMCID: PMC10940790 DOI: 10.1111/eva.13675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Understanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome-environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so-called 'islands of divergence' related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
Collapse
Affiliation(s)
- Angela P. Fuentes‐Pardo
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Ryan Stanley
- Fisheries and Oceans CanadaMaritimes RegionDartmouthNova ScotiaCanada
| | - Christina Bourne
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt John'sNewfoundland and LabradorCanada
| | - Rabindra Singh
- Fisheries and Oceans CanadaSt. Andrews Biological StationSt. AndrewsNew BrunswickCanada
| | - Kim Emond
- Fisheries and Oceans CanadaMaurice Lamontagne InstituteMont‐JoliQuebecCanada
| | - Lisa Pinkham
- Department of Marine ResourcesWest Boothbay HarborMaineUSA
| | - Jenni L. McDermid
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
| | | |
Collapse
|
3
|
Kho J, Delgado ML, McCracken GR, Munden J, Ruzzante DE. Epigenetic patterns in Atlantic herring (Clupea harengus): Temperature and photoperiod as environmental stressors during larval development. Mol Ecol 2024; 33:e17187. [PMID: 37909655 DOI: 10.1111/mec.17187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Understanding the molecular mechanisms underlying individual responses to environmental changes is crucial for species conservation and management. Pelagic fishes including Atlantic herring (Clupea harengus) are of particular interest because of their key ecological and economic roles and their susceptibility to a changing ocean from global warming. Temperature and photoperiod have been linked with spawning time and location in adult herring, but no study has thus far investigated the role of environmental factors on gene regulation during the vulnerable early developmental stages. Here, we examine DNA methylation patterns of larval herring bred under two temperatures (11°C and 13°C) and photoperiod (6 and 12 h) regimes in a 2 × 2 factorial design. We found consistently high levels of global methylation across all individuals and a decline in global methylation with increased developmental stage that was more pronounced at 13°C (p ≤ 0.007) than at 11°C (p ≥ 0.21). Most of the differentially methylated sites were in exon and promoter regions for genes linked to metabolism and development, some of which were hypermethylated at higher temperature. These results demonstrate the important role of DNA methylation during larval development and suggest that this molecular mechanism might be key in regulating early-stage responses to environmental stressors in Atlantic herring.
Collapse
Affiliation(s)
- J Kho
- Department of Biology, Dalhousie University, Halifax, Canada
| | - M L Delgado
- Department of Biology, Dalhousie University, Halifax, Canada
| | - G R McCracken
- Department of Biology, Dalhousie University, Halifax, Canada
| | - J Munden
- Herring Science Council, Halifax, Canada
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Canada
| |
Collapse
|
4
|
Weise EM, Van Wyngaarden M, Den Heyer C, Mills Flemming J, Kess T, Einfeldt AL, Fisher JAD, Ditta R, Pare G, Ruzzante DE. SNP Panel and Genomic Sex Identification in Atlantic Halibut (Hippoglossus hippoglossus). Mar Biotechnol (NY) 2023; 25:580-587. [PMID: 37351707 DOI: 10.1007/s10126-023-10227-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023]
Abstract
The ability to identify sex is necessary in population biology for a proper understanding of the dynamics of a population. In Atlantic halibut, phenotypic sex identification is not possible due to the lack of significant external morphological differences. We developed an Illumina SNP panel for Atlantic halibut with 4000 SNPs spread evenly throughout the genome with a minor allele frequency MAF ≥ 0.4, except for N = 249 SNPs located in a sex-determining region on chromosome 12, N = 176 of these SNPs were selected to genetically identify male and female individuals using a DAPC analysis. The genomic identification of sex allows for non-lethal sex determination and validation of sex identification in the field. The SNP panel is a new genomic resource for Atlantic halibut that will make it possible to generate the genotypic data for the large number of individuals needed to estimate population abundance using genomics and the Close Kin Mark Recapture (CKMR) approach, an emerging component of fisheries management and stock monitoring.
Collapse
Affiliation(s)
- Ellen M Weise
- Department of Biology, Dalhousie University, 1355 Oxford St, B3H 4R2, Halifax, NS, Canada.
| | - Mallory Van Wyngaarden
- Department of Biology, Dalhousie University, 1355 Oxford St, B3H 4R2, Halifax, NS, Canada
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Cornelia Den Heyer
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, B2Y 4A2, Dartmouth, NS, Canada
| | - Joanna Mills Flemming
- Department of Mathematics & Statistics, Dalhousie University, 6316 Coburg Rd, B3H 4R2, Halifax, NS, Canada
| | - Tony Kess
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, B2Y 4A2, Dartmouth, NS, Canada
| | - Anthony L Einfeldt
- Department of Biology, Dalhousie University, 1355 Oxford St, B3H 4R2, Halifax, NS, Canada
- Parks Canada, East Kootenay, BC, Canada
| | - Jonathan A D Fisher
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, 155 Ridge Rd, A1C 5R3, St. John's, NL, Canada
| | - Reina Ditta
- Population Health Research Institute, 237 Barton Street, East Hamilton, ON, L8L 2X2, Canada
| | - Guillaume Pare
- Population Health Research Institute, 237 Barton Street, East Hamilton, ON, L8L 2X2, Canada
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, 1355 Oxford St, B3H 4R2, Halifax, NS, Canada.
| |
Collapse
|
5
|
Salisbury SJ, Perry R, Keefe D, McCracken GR, Layton KKS, Kess T, Bradbury IR, Ruzzante DE. Geography, environment, and colonization history interact with morph type to shape genomic variation in an Arctic fish. Mol Ecol 2023. [PMID: 36869618 DOI: 10.1111/mec.16913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/12/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023]
Abstract
Polymorphic species are useful models for investigating the evolutionary processes driving diversification. Such processes include colonization history as well as contemporary selection, gene flow, and genetic drift, which can vary between intraspecific morphs as a function of their distinct life histories. The interactive and relative influence of such evolutionary processes on morph differentiation critically informs morph-specific management decisions and our understanding of incipient speciation. We therefore investigated how geographic distance, environmental conditions, and colonization history interacted with morph migratory capacity in the highly polymorphic fish species, Arctic Charr (Salvelinus alpinus). Using an 87k SNP chip we genetically characterized recently evolved anadromous, resident, and landlocked charr collected from 45 locations across a secondary contact zone of three charr glacial lineages in eastern Canada. A strong pattern of isolation by distance across all populations suggested geographic distance principally shaped genetic structure. Landlocked populations had lower genetic diversities and higher genetic differentiation than anadromous populations. However, effective population size was generally temporally stable in landlocked populations in comparison to anadromous populations. Genetic diversity positively correlated with latitude, potentially indicating southern anadromous populations' vulnerability to climate change and greater introgression between the Arctic and Atlantic glacial lineages in northern Labrador. Local adaptation was suggested by the observation of several environmental variables strongly associating with functionally relevant outlier genes including a region on chromosome AC21 potentially associated with anadromy. Our results demonstrate that gene flow, colonization history, and local adaptation uniquely interact to influence the genetic variation and evolutionary trajectory of populations.
Collapse
Affiliation(s)
- S J Salisbury
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - R Perry
- Department of Environment, Fish and Wildlife Division, Government of Yukon, Whitehorse, YT, Canada
| | - D Keefe
- Department of Fisheries, Forestry, and Agriculture, Government of Newfoundland and Labrador, Corner Brook, NL, Canada
| | - G R McCracken
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - K K S Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - T Kess
- Department of Fisheries and Oceans, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - I R Bradbury
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Department of Fisheries and Oceans, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| |
Collapse
|
6
|
Delgado ML, Manosalva A, Urbina MA, Dalziel AC, Habit E, Link O, Ruzzante DE. Does the loss of diadromy imply the loss of salinity tolerance? A gene expression study with replicate nondiadromous populations of Galaxias maculatus. Mol Ecol 2023; 32:2219-2233. [PMID: 36715263 DOI: 10.1111/mec.16866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
The recurrent colonization of freshwater habitats and subsequent loss of diadromy is a major ecological transition that has been reported in many ancestrally diadromous fishes. Such residency is often accompanied by a loss of tolerance to seawater. The amphidromous Galaxias maculatus has repeatedly colonized freshwater streams with evidence that freshwater-resident populations exhibit stark differences in their tolerance to higher salinities. Here, we used transcriptomics to gain insight into the mechanisms contributing to reduced tolerance to higher salinities in freshwater resident populations. We conducted an acute salinity challenge (0 ppt to 23-25 ppt) and measured osmoregulatory ability (muscle water content) over 48 h in three populations: diadromous, saltwater intolerant resident (Toltén), and saltwater tolerant resident (Valdivia). RNA sequencing of the gills identified genes that were differentially expressed in association with the salinity change and associated with the loss of saltwater tolerance in the Toltén population. Key genes associated with saltwater acclimation were characterized in diadromous G. maculatus individuals, some of which were also expressed in the saltwater tolerant resident population (Valdivia). We found that some of these "saltwater acclimation" genes, including the cystic fibrosis transmembrane conductance regulator gene (CFTR), were not significantly upregulated in the saltwater intolerant resident population (Toltén), suggesting a potential mechanism for the loss of tolerance to higher salinities. As the suite of differentially expressed genes in the diadromous-resident comparison differed between freshwater populations, we hypothesize that diadromy loss results in unique evolutionary trajectories due to drift, so the loss of diadromy does not necessarily lead to a loss in upper salinity tolerance.
Collapse
Affiliation(s)
- M Lisette Delgado
- Department of Biology, Dalhousie University, Nova Scotia, Halifax, Canada
| | - Aliro Manosalva
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Mauricio A Urbina
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Anne C Dalziel
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Oscar Link
- Departamento de Ingeniería Civil, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, Nova Scotia, Halifax, Canada
| |
Collapse
|
7
|
Durante CA, Loizaga R, McCracken GR, Crespo EA, Ruzzante DE. Commerson's dolphin population structure: evidence for female phylopatry and male dispersal. Sci Rep 2022; 12:22219. [PMID: 36564404 PMCID: PMC9789068 DOI: 10.1038/s41598-022-26192-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
A key in species conservation is understanding the amount and distribution of genetic diversity and how environmental changes that occurred in the recent past may have influenced current patterns of population structure. Commerson's dolphin, Cephalorhynchus commersonii, has two subspecies, one of which is endemic to South America (C. commersonii commersonii) and little is known about its population genetics. Our objective was to investigate the population genetics of this subspecies throughout its distribution. Using 70 skin samples and information available in GenBank, 308 mitochondrial DNA sequences and 28 species-specific microsatellites were analyzed. The species presented low genetic diversity when compared to other dolphin species, but was consistent with other species within the genus. Strong population structure based on mitochondrial DNA was exhibited throughout its entire distribution, a pattern consistent with female philopatry. However, this pattern was not detected when using microsatellites, suggesting male-mediated gene flow. Demographic tests suggested a population expansion beginning approximately 15,000 years ago, after the Last Glacial Maximum. In a climate change scenario, we recommended considering each sampling location as an independent population management unit in order to evaluate the impact of possible environmental changes on the distribution of genetic information within the species.
Collapse
Affiliation(s)
- Cristian Alberto Durante
- Laboratorio de Mamíferos Marinos, Centro Para El Estudio de Sistemas Marinos (CESIMAR) - CONICET, Bv. Brown 2915, U9120ACD Puerto Madryn, Chubut, Argentina.
- Universidad Nacional del Comahue, San Carlos de Bariloche, Rio Negro, Argentina.
| | - Rocio Loizaga
- Laboratorio de Mamíferos Marinos, Centro Para El Estudio de Sistemas Marinos (CESIMAR) - CONICET, Bv. Brown 2915, U9120ACD Puerto Madryn, Chubut, Argentina
| | | | - Enrique Alberto Crespo
- Laboratorio de Mamíferos Marinos, Centro Para El Estudio de Sistemas Marinos (CESIMAR) - CONICET, Bv. Brown 2915, U9120ACD Puerto Madryn, Chubut, Argentina
| | | |
Collapse
|
8
|
Wolfenson LI, McCracken GR, Ruzzante DE, Mirol P, Solé-Cava A. Low STR variability in the threatened marsh deer, Blastocerus dichotomus, detected through amplicon sequencing in non-invasive samples. Genet Mol Biol 2022; 45:e20220105. [PMID: 36288451 PMCID: PMC9601240 DOI: 10.1590/1678-4685-gmb-2022-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/24/2022] [Indexed: 11/04/2022] Open
Abstract
Blastocerus dichotomus is the largest deer in South America. We have used 25 microsatellite markers detected and genotyped by Next Generation Sequencing to estimate the genetic variability of B. dichotomus in Argentina, where most of its populations are threatened. Primer design was based on the sequence of a shallow partial genome (15,967,456 reads; 16.66% genome coverage, mean depth 1.64) of a single individual. From the thousands of microsatellite loci found, even under high stringency selection, we chose and tested a set of 80 markers on 30 DNA samples extracted from tissue and feces from three Argentinean populations. Heterozygosity levels were low across all loci in all populations (H=0.31 to 0.40). Amplicon sequencing is a fast, easy, and affordable technique that can be very useful for the characterization of microsatellite marker sets for the conservation genetics of non-model organisms. This work is also one of the first ones to use amplicon sequencing in non-invasive samples and represents an important development for the study of threatened species.
Collapse
Affiliation(s)
- Laura Irene Wolfenson
- Museo Argentino de Ciencias Naturales, "Bernardino Rivadavia", División de Mastozoología, Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Daniel E Ruzzante
- Dalhousie University, Department of Biology, Halifax, Nova Scotia, Canada
| | - Patricia Mirol
- Museo Argentino de Ciencias Naturales, "Bernardino Rivadavia", División de Mastozoología, Ciudad Autónoma de Buenos Aires, Argentina
| | - Antonio Solé-Cava
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genetica, Centro Nacional para a Identificação Molecular do Pescado (CENIMP), Rio de Janeiro, RJ, Brazil
| |
Collapse
|
9
|
Salisbury S, McCracken GR, Perry R, Keefe D, Layton KKS, Kess T, Nugent CM, Leong JS, Bradbury IR, Koop BF, Ferguson MM, Ruzzante DE. The Genomic Consistency of the Loss of Anadromy in an Arctic Fish (Salvelinus alpinus). Am Nat 2022; 199:617-635. [DOI: 10.1086/719122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
10
|
Abstract
Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- S J Salisbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| |
Collapse
|
11
|
Valenzuela-Aguayo F, McCracken GR, Diaz G, Manosalva A, Habit E, Ruzzante DE. Connectivity, diversity, and hybridization between two endemic fish species (Percilia spp.) in a complex temperate landscape. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01400-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
12
|
Kess T, Dempson JB, Lehnert SJ, Layton KKS, Einfeldt A, Bentzen P, Salisbury SJ, Messmer AM, Duffy S, Ruzzante DE, Nugent CM, Ferguson MM, Leong JS, Koop BF, O'Connell MF, Bradbury IR. Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs. Mol Ecol 2021; 30:4415-4432. [PMID: 34152667 DOI: 10.1111/mec.16033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/30/2022]
Abstract
The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (FST = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.
Collapse
Affiliation(s)
- Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - J Brian Dempson
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Sarah J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Kara K S Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Anthony Einfeldt
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | | | - Amber M Messmer
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Steven Duffy
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | | | - Cameron M Nugent
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Moira M Ferguson
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Michael F O'Connell
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Ian R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| |
Collapse
|
13
|
Prystupa S, McCracken GR, Perry R, Ruzzante DE. Population abundance in arctic grayling using genetics and close-kin mark-recapture. Ecol Evol 2021; 11:4763-4773. [PMID: 33976846 PMCID: PMC8093667 DOI: 10.1002/ece3.7378] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/29/2021] [Accepted: 02/16/2021] [Indexed: 11/10/2022] Open
Abstract
Arctic Grayling (Thymallus arcticus) are among the most widely distributed and abundant freshwater fish in the Yukon Territory of Canada, yet little information exists regarding their broad and fine-scale population structures or the number and size of these populations. The estimation of population abundance is fundamental for robust management and conservation, yet estimating abundance in the wild is often difficult. Here, we estimated abundance of an Arctic Grayling population using multiple genetic markers and the close-kin mark-recapture (CKMR) method. A total of N = 1,104 Arctic Grayling collected from two systems in Yukon were genotyped at 38 sequenced microsatellites. We first identified structure and assessed genetic diversity (effective population size,N ^ e ). Collections from one of the systems (Lubbock River) comprised adults and young-of-the-year sampled independently allowing the identification of parent-offspring pairs (POPs), and thus, the estimation of abundance using CKMR. We used COLONY and CKMRsim to identify POPs and both provided similar results leading to indistinguishable estimates (95% CI) of census size, that is,N ^ c ( C O L O N Y ) = 1858 (1259-2457) andN ^ c ( C K M R s i m ) = 1812 (1229-2389). The accuracy of the population abundance estimates can in the future be improved with temporal sampling and more precise age or size-specific fecundity estimates for Arctic Grayling. Our study demonstrates that the method can be used to inform management and conservation policy for Arctic Grayling and likely also for other fish species for which the assumption of random and independent sampling of adults and offspring can be assured.
Collapse
Affiliation(s)
- Samuel Prystupa
- Department of BiologyDalhousie UniversityHalifaxNSCanada
- Present address:
Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | | | - Robert Perry
- Fish and Wildlife DivisionDepartment of EnvironmentWhitehorse, YukonCanada
| | | |
Collapse
|
14
|
Einfeldt AL, Kess T, Messmer A, Duffy S, Wringe BF, Fisher J, den Heyer C, Bradbury IR, Ruzzante DE, Bentzen P. Chromosome level reference of Atlantic halibut Hippoglossus hippoglossus provides insight into the evolution of sexual determination systems. Mol Ecol Resour 2021; 21:1686-1696. [PMID: 33655659 DOI: 10.1111/1755-0998.13369] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 02/24/2021] [Indexed: 12/22/2022]
Abstract
Changes in the genetic mechanisms that control sexual determination have occurred independently across the tree of life, and with exceptional frequency in teleost fishes. To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome-level genome, multitissue transcriptomes, and reduced representation population data for the Atlantic halibut (Hippoglossus hippoglossus), which has an XY/XX sex determination mechanism and has recently diverged (0.9-3.8 Ma) from the Pacific halibut (Hippoglossus stenolepis), which has a ZZ/ZW system. We used frequency and coverage-based population approaches to identify a putative sex-determining factor, GSDF. We characterized regions with elevated heterozygosity and linkage disequilibrium indicating suppression of recombination across a nascent sex chromosome. We detected testis-specific expression of GSDF, the sequence of which is highly conserved across flatfishes. Based on evidence from genome-wide association, coverage, linkage disequilibrium, testis and brain transcriptomes, and sequence conservation with other flatfishes, we propose a mechanism for the recent evolution of an XY sex-determination mechanism in Atlantic halibut. Changes to the ancestral sex-determining gene DMRT1 in regulating the downstream gene GSDF probably coincided with GSDF, or a proximal regulatory element of it, becoming the primary sex-determining factor. Our results suggest changes to a small number of elements can have drastic repercussions for the genomic substrate available to sex-specific evolutionary forces, providing insight into how certain elements repeatedly evolve to control sex across taxa. Our chromosome-level assembly, multitissue transcriptomes, and population genomic data provide a valuable resource and understanding of the evolution of sexual systems in fishes.
Collapse
Affiliation(s)
| | - Tony Kess
- Fisheries and Oceans Canada, Dartmouth, NS, Canada
| | | | - Steven Duffy
- Fisheries and Oceans Canada, St. John's, NL, Canada
| | | | - Jonathan Fisher
- Fisheries and Marine Institute of Memorial University, St. John's, NL, Canada
| | | | | | | | - Paul Bentzen
- Biology Department, Dalhousie University, Halifax, NS, Canada
| |
Collapse
|
15
|
Petrou EL, Fuentes-Pardo AP, Rogers LA, Orobko M, Tarpey C, Jiménez-Hidalgo I, Moss ML, Yang D, Pitcher TJ, Sandell T, Lowry D, Ruzzante DE, Hauser L. Functional genetic diversity in an exploited marine species and its relevance to fisheries management. Proc Biol Sci 2021; 288:20202398. [PMID: 33622133 PMCID: PMC7934995 DOI: 10.1098/rspb.2020.2398] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/28/2021] [Indexed: 01/02/2023] Open
Abstract
The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring (Clupea pallasii) across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particular SYNE2, which influences the development of retinal photoreceptors in vertebrates. SYNE2 is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (Clupea harengus). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.
Collapse
Affiliation(s)
- Eleni L. Petrou
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA
| | | | - Luke A. Rogers
- Fisheries and Oceans Canada, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Melissa Orobko
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA
| | - Isadora Jiménez-Hidalgo
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA
| | - Madonna L. Moss
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | - Dongya Yang
- Department of Archaeology, Simon Fraser University, Education Building 9635, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Tony J. Pitcher
- University of British Columbia, Institute for the Oceans and Fisheries, Vancouver, British Columbia, Canada
| | - Todd Sandell
- Washington Department of Fish and Wildlife, 16018 Mill Creek Boulevard, Mill Creek, WA 98012-1541, USA
| | - Dayv Lowry
- Washington Department of Fish and Wildlife, 1111 Washington Street SE, 6th Floor, Olympia, WA 98504-3150, USA
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA
| |
Collapse
|
16
|
Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
Collapse
Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| |
Collapse
|
17
|
Delgado ML, Manosalva A, Urbina MA, Habit E, Link O, Ruzzante DE. Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments. Mol Ecol 2020; 29:4857-4870. [PMID: 33048403 DOI: 10.1111/mec.15686] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022]
Abstract
Diadromy is known for having major effects on the distribution and richness of aquatic species, and so does its loss. The loss of diadromy has led to the diversification of many species, yet research focusing on understanding its molecular basis and consequences are limited. This is particularly true for amphidromous species despite being the most abundant group of diadromous species. Galaxias maculatus, an amphidromous species and one of the most widely distributed fishes in the Southern Hemisphere, exhibits many instances of nonmigratory or resident populations. The existence of naturally replicated resident populations in Patagonia can serve as an ideal system for the study of the mechanisms that lead to the loss of the diadromy and its ecological and evolutionary consequences. Here, we studied two adjacent river systems in which resident populations are genetically differentiated yet derived from the same diadromous population. By combining a reciprocal transplant experiment with genomic data, we showed that the two resident populations followed different evolutionary pathways by exhibiting a differential response in their capacity to survive in salt water. While one resident population was able to survive salt water, the other was not. Genomic analyses provided insights into the genes that distinguished (a) migratory from nonmigratory populations; (b) populations that can vs those that cannot survive a saltwater environment; and (c) between these resident populations. This study demonstrates that the loss of diadromy can be achieved by different pathways and that environmental (selection) and random (genetic drift) forces shape this dynamic evolutionary process.
Collapse
Affiliation(s)
| | - Aliro Manosalva
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Mauricio A Urbina
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Oscar Link
- Departamento de Ingeniería Civil, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
| | | |
Collapse
|
18
|
Salisbury SJ, McCracken GR, Perry R, Keefe D, Layton KK, Kess T, Nugent CM, Leong JS, Bradbury IR, Koop BF, Ferguson MM, Ruzzante DE. Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (
Salvelinus alpinus
). Mol Ecol 2020; 29:4280-4294. [DOI: 10.1111/mec.15634] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Robert Perry
- Department of Environment Fish and Wildlife Division Government of Yukon Whitehorse YT Canada
| | - Donald Keefe
- Department of Environment and Conservation Wildlife Division Government of Newfoundland and Labrador Corner Brook NL Canada
| | - Kara K.S. Layton
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Tony Kess
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
| | - Cameron M. Nugent
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | - Jong S. Leong
- Department of Biology University of Victoria Victoria BC Canada
| | - Ian R. Bradbury
- Department of Biology Dalhousie University Halifax NS Canada
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Ben F. Koop
- Department of Biology University of Victoria Victoria BC Canada
- Centre for Biomedical Research University of Victoria Victoria BC Canada
| | - Moira M. Ferguson
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | | |
Collapse
|
19
|
Ruzzante DE, Simons AP, McCracken GR, Habit E, Walde SJ. Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites. Proc Biol Sci 2020; 287:20200468. [PMID: 32486985 PMCID: PMC7341911 DOI: 10.1098/rspb.2020.0468] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here, we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers. Fish (n= 835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean (headwaters east of Andes). The remaining five drainages empty into the Atlantic. Three analytical approaches (neighbour-joining tree, hierarchical AMOVAs, Structure) revealed evidence of historic drainage reversals: fish from four of the five trans-Andean systems (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic similarity with Atlantic draining systems than with Pacific systems with headwaters west of Andes. Present-day drainage (Pacific versus Atlantic) explained only 5% of total genetic variance, while ancestral drainage explained nearly 27% of total variance. Thus, the phylogeographic structure of P. trucha is consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographical distribution of P. trucha in Patagonia. The study emphasizes the significant role of historical processes in the current pattern of genetic diversity and differentiation in a fish from a southern temperate region.
Collapse
Affiliation(s)
- Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Annie P Simons
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Sandra J Walde
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
20
|
Layton KKS, Dempson B, Snelgrove PVR, Duffy SJ, Messmer AM, Paterson IG, Jeffery NW, Kess T, Horne JB, Salisbury SJ, Ruzzante DE, Bentzen P, Côté D, Nugent CM, Ferguson MM, Leong JS, Koop BF, Bradbury IR. Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish. Evol Appl 2020; 13:1055-1068. [PMID: 32431752 PMCID: PMC7232759 DOI: 10.1111/eva.12922] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022] Open
Abstract
The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here, we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine-scale population structure in a critically important salmonid in north eastern Canada, Arctic Charr (Salvelinus alpinus). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29-year tagging dataset. Self-assignment and simulation-based analyses of 111 genome-wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic Charr in north-eastern Canada identified largely river-specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self-assignment accuracy was similar with the microsatellite loci and the SNP panel (>90%). Subsequent analysis of 996 fishery-collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence-based microsatellite genotyping to advance understanding of fine-scale population structure and harvest composition in northern and understudied species.
Collapse
Affiliation(s)
- Kara K. S. Layton
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Brian Dempson
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Paul V. R. Snelgrove
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
| | - Steven J. Duffy
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Amber M. Messmer
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | | | - Nicholas W. Jeffery
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | - Tony Kess
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - John B. Horne
- National Oceanic and Atmospheric AdministrationSouthwest Fisheries Science CenterLa JollaCAUSA
| | | | | | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - David Côté
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | | | | | - Jong S. Leong
- Department of BiologyUniversity of VictoriaVictoriaBCCanada
| | - Ben F. Koop
- Department of BiologyUniversity of VictoriaVictoriaBCCanada
- Centre for Biomedical ResearchUniversity of VictoriaVictoriaBCCanada
| | - Ian R. Bradbury
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| |
Collapse
|
21
|
Valenzuela‐Aguayo F, McCracken GR, Manosalva A, Habit E, Ruzzante DE. Human-induced habitat fragmentation effects on connectivity, diversity, and population persistence of an endemic fish, Percilia irwini, in the Biobío River basin (Chile). Evol Appl 2020; 13:794-807. [PMID: 32211068 PMCID: PMC7086057 DOI: 10.1111/eva.12901] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/14/2019] [Accepted: 11/05/2019] [Indexed: 01/15/2023] Open
Abstract
An understanding of how genetic variability is distributed in space is fundamental for the conservation and maintenance of diversity in spatially fragmented and vulnerable populations. While fragmentation can occur from natural barriers, it can also be exacerbated by anthropogenic activities such as hydroelectric power plant development. Whatever the source, fragmentation can have significant ecological effects, including disruptions of migratory processes and gene flow among populations. In Chile, the Biobío River basin exhibits a high degree of habitat fragmentation due to the numerous hydroelectric power plants in operation, the number of which is expected to increase following new renewable energy use strategies. Here, we assessed the effects of different kinds of barriers on the genetic structure of the endemic freshwater fish Percilia irwini, knowledge that is critically needed to inform conservation strategies in light of current and anticipated further fragmentation initiatives in the system. We identified eight genetic units throughout the entire Biobío system with high effective sizes. A reduced effective size estimate was, however, observed in a single population located between two impassable barriers. Both natural waterfalls and human-made dams were important drivers of population differentiation in this system; however, dams affect genetic diversity differentially depending on their mode of operation. Evidence of population extirpation was found in two river stretches limited by upstream and downstream dams. Significant gene flow in both directions was found among populations not separated by natural or anthropogenic barriers. Our results suggest a significant vulnerability of P. irwini populations to future dam development and demonstrate the importance of studying basin-wide data sets with genetic metrics to understand the strength and direction of anthropogenic impacts on fish populations.
Collapse
Affiliation(s)
- Francisca Valenzuela‐Aguayo
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | | | - Aliro Manosalva
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
| | - Evelyn Habit
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
| | | |
Collapse
|
22
|
Delgado ML, Górski K, Habit E, Ruzzante DE. The effects of diadromy and its loss on genomic divergence: The case of amphidromous
Galaxias maculatus
populations. Mol Ecol 2019; 28:5217-5231. [DOI: 10.1111/mec.15290] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/16/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Konrad Górski
- Departamento de Ecología Facultad de Ciencias y Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS) Universidad Católica de la Santísima Concepción Concepción Chile
| | - Evelyn Habit
- Centro de Ciencias Ambientales EULA Universidad de Concepción Concepción Chile
| | | |
Collapse
|
23
|
Ruzzante DE, McCracken GR, Førland B, MacMillan J, Notte D, Buhariwalla C, Mills Flemming J, Skaug H. Validation of close‐kin mark–recapture (CKMR) methods for estimating population abundance. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13243] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - Brage Førland
- Department of Mathematics University of Bergen Bergen Norway
| | - John MacMillan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture Halifax Nova Scotia Canada
| | - Daniela Notte
- Department of Biology Dalhousie University Halifax Nova Scotia Canada
| | - Colin Buhariwalla
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture Halifax Nova Scotia Canada
| | - Joanna Mills Flemming
- Department of Mathematics and Statistics Dalhousie University Halifax Nova Scotia Canada
| | - Hans Skaug
- Department of Mathematics University of Bergen Bergen Norway
| |
Collapse
|
24
|
Vera-Escalona I, Habit E, Ruzzante DE. Invasive species and postglacial colonization: their effects on the genetic diversity of a Patagonian fish. Proc Biol Sci 2019; 286:20182567. [PMID: 30963839 PMCID: PMC6408905 DOI: 10.1098/rspb.2018.2567] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/01/2019] [Indexed: 01/18/2023] Open
Abstract
The present distribution of Patagonian species is the result of a complex history involving Quaternary refugial populations, Holocene range expansions and demographic changes occurring during the Anthropocene. Invasive salmonids were introduced in Patagonia during the last century, occupying most rivers and lakes, preying on and competing with native species, including the fish Galaxias platei. Here, we used G. platei as a case study to understand how long-term (i.e. population differentiation during the Holocene) and short-term historical processes (salmonid introductions) affect genetic diversity. Using a suite of microsatellite markers, we found that the number of alleles is negatively correlated with the presence of salmonids (short-term processes), with G. platei populations from lakes with salmonids exhibiting significantly lower genetic diversity than populations from lakes without salmonids. Simulations (100 years backwards) showed that this difference in genetic diversity can be explained by a 99% reduction in population size. Allelic richness and observed heterozygosities were also negatively correlated with the presence of salmonids, but also positively correlated with long-term processes linked to Quaternary glaciations. Our results show how different genetic parameters can help identify processes taking place at different scales and their importance in terms of conservation.
Collapse
Affiliation(s)
- Iván Vera-Escalona
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada B3H 4R2
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Alonso de Ribera 2850, Concepción, Chile
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Barrio Universitario s/n. Concepción, Casilla 160-C, Chile
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada B3H 4R2
| |
Collapse
|
25
|
Salisbury SJ, McCracken GR, Keefe D, Perry R, Ruzzante DE. Extensive secondary contact among three glacial lineages of Arctic Char ( Salvelinus alpinus) in Labrador and Newfoundland. Ecol Evol 2019; 9:2031-2045. [PMID: 30847090 PMCID: PMC6392391 DOI: 10.1002/ece3.4893] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/26/2018] [Accepted: 12/07/2018] [Indexed: 01/20/2023] Open
Abstract
AIM The Pleistocene glaciation event prompted the allopatric divergence of multiple glacial lineages of Arctic char (Salvelinus alpinus), some of which have come into secondary contact upon their recolonization of the Holarctic. While three glacial lineages (Arctic, Atlantic, and Acadian) are known to have recolonized the western Atlantic, the degree of overlap of these three lineages is largely unknown. We sought to determine the distribution of these three glacial lineages in Labrador and Newfoundland at a fine spatial scale to assess their potential for introgression and their relative contribution to local fisheries. LOCATION Labrador and Newfoundland, Canada. METHODS We sequenced a portion of the D-loop region in over 1,000 Arctic char (S. alpinus) samples from 67 locations across Labrador and Newfoundland. RESULTS Within Labrador, the Arctic and Atlantic lineages were widespread. Two locations (one landlocked and one with access to the sea) also contained individuals of the Acadian lineage, constituting the first record of this lineage in Labrador. Atlantic and Acadian lineage individuals were found in both eastern and western Newfoundland. Multiple sampling locations in Labrador and Newfoundland contained fish of two or more different glacial lineages, implying their introgression. Glacial lineage did not appear to dictate contemporary genetic divergence between the pale and dark morph of char present in Gander Lake, Newfoundland. Both were predominately of the Atlantic lineage, suggesting the potential for their divergence in sympatry. MAIN CONCLUSIONS Our study reveals Labrador and Newfoundland to be a unique junction of three glacial lineages which have likely hybridized extensively in this region.
Collapse
Affiliation(s)
| | | | - Donald Keefe
- Department of Environment and ConservationCorner BrookNewfoundland and LabradorCanada
| | - Robert Perry
- Department of Environment and ConservationCorner BrookNewfoundland and LabradorCanada
| | | |
Collapse
|
26
|
Kerr Q, Fuentes‐Pardo AP, Kho J, McDermid JL, Ruzzante DE. Temporal stability and assignment power of adaptively divergent genomic regions between herring ( Clupea harengus) seasonal spawning aggregations. Ecol Evol 2019; 9:500-510. [PMID: 30680131 PMCID: PMC6342187 DOI: 10.1002/ece3.4768] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/07/2018] [Accepted: 11/12/2018] [Indexed: 11/07/2022] Open
Abstract
Atlantic herring (Clupea harengus), a vital ecosystem component and target of the largest Northwest Atlantic pelagic fishery, undergo seasonal spawning migrations that result in elusive sympatric population structure. Herring spawn mostly in fall or spring, and genomic differentiation was recently detected between these groups. Here we used a subset of this differentiation, 66 single nucleotide polymorphisms (SNPs) to analyze the temporal dynamics of this local adaptation and the applicability of SNP subsets in stock assessment. We showed remarkable temporal stability of genomic differentiation corresponding to spawning season, between samples taken a decade apart (2005 N = 90 vs. 2014 N = 71) in the Gulf of St. Lawrence, and new evidence of limited interbreeding between spawning components. We also examined an understudied and overexploited herring population in Bras d'Or lake (N = 97); using highly reduced SNP panels (N SNPs > 6), we verified little-known sympatric spawning populations within this unique inland sea. These results describe consistent local adaptation, arising from asynchronous reproduction in a migratory and dynamic marine species. Our research demonstrates the efficiency and precision of SNP-based assessments of sympatric subpopulations; and indeed, this temporally stable local adaptation underlines the importance of such fine-scale management practices.
Collapse
Affiliation(s)
- Quentin Kerr
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | | | - James Kho
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jenni L. McDermid
- Marine Fish and Mammals Section, Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | | |
Collapse
|
27
|
Vera-Escalona I, Senthivasan S, Habit E, Ruzzante DE. Past, present, and future of a freshwater fish metapopulation in a threatened landscape. Conserv Biol 2018; 32:849-859. [PMID: 29431232 DOI: 10.1111/cobi.13093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 02/02/2018] [Indexed: 05/22/2023]
Abstract
It is well documented that hydropower plants can affect the dynamics of fish populations through landscape alterations and the creation of new barriers. Less emphasis has been placed on the examination of the genetic consequences for fish populations of the construction of dams. The relatively few studies that focus on genetics often do not consider colonization history and even fewer tend to use this information for conservation purposes. As a case study, we used a 3-pronged approach to study the influence of historical processes, contemporary landscape features, and potential future anthropogenic changes in landscape on the genetic diversity of a fish metapopulation. Our goal was to identify the metapopulation's main attributes, detect priority areas for conservation, and assess the consequences of the construction of hydropower plants for the persistence of the metapopulation. We used microsatellite markers and coalescent approaches to examine historical colonization processes, traditional population genetics, and simulations of future populations under alternate scenarios of population size reduction and gene flow. Historical gene flow appeared to have declined relatively recently and contemporary populations appeared highly susceptible to changes in landscape. Gene flow is critical for population persistence. We found that hydropower plants could lead to a rapid reduction in number of alleles and to population extirpation 50-80 years after their construction. More generally, our 3-pronged approach for the analyses of empirical genetic data can provide policy makers with information on the potential impacts of landscape changes and thus lead to more robust conservation efforts.
Collapse
Affiliation(s)
- Iván Vera-Escalona
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4R2, Canada
| | - Shreeram Senthivasan
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4R2, Canada
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Barrio Universitario s/n, Concepción, Casilla, 160-C, Chile
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4R2, Canada
| |
Collapse
|
28
|
Yu D, Ding X, Zhang Z, Zeng Y, Liu H, Wang L, Gong Y, Liu X, Lyu X, McCracken GR, Valenzuela-Aguayo FV, Habit EM, Ruzzante DE, Du M, Wang W, Song T, Niu B, Zhang Q, Simmons CL, Taylor TK, Zalucki JM, Hoebee SE, Fernando DR, Holmes GD, Shapcott A, Zhang Z, Yan X, Zhang Q. Correction to: Microsatellite records for volume 10, issue 2. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1056-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
29
|
Fuentes-Pardo AP, Ruzzante DE. Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations. Mol Ecol 2017; 26:5369-5406. [PMID: 28746784 DOI: 10.1111/mec.14264] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
Collapse
|
30
|
Ruzzante DE, Doyle RW. EVOLUTION OF SOCIAL BEHAVIOR IN A RESOURCE-RICH, STRUCTURED ENVIRONMENT: SELECTION EXPERIMENTS WITH MEDAKA (ORYZIAS LATIPES). Evolution 2017; 47:456-470. [DOI: 10.1111/j.1558-5646.1993.tb02106.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/1992] [Accepted: 07/27/1992] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel E. Ruzzante
- Department of Biology; Dalhousie University; Halifax Nova Scotia B3H 4J1 CANADA
| | - Roger W. Doyle
- Department of Biology; Dalhousie University; Halifax Nova Scotia B3H 4J1 CANADA
| |
Collapse
|
31
|
Ruzzante DE, Doyle RW. RAPID BEHAVIORAL CHANGES IN MEDAKA (ORYZIAS LATIPES) CAUSED BY SELECTION FOR COMPETITIVE AND NONCOMPETITIVE GROWTH. Evolution 2017; 45:1936-1946. [PMID: 28563972 DOI: 10.1111/j.1558-5646.1991.tb02698.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/1990] [Accepted: 05/20/1991] [Indexed: 11/28/2022]
Abstract
Behavior is a major component of growth rate variation in fish, but the genetic relationship between behavior and growth is largely unknown. In particular, it is not known how behavior responds to natural or artificial selection on growth. It has been argued that artificial selection for fast growth in competitive environments might lead to higher levels of overall aggression, and therefore there would be no net gain in assimilation efficiency or growth. The contrary has also been argued. It is not immediately obvious, therefore, whether fish that avoid interacting with conspecifics should grow faster, or whether more aggressive, dominant individuals should grow faster. In the present study, we artificially selected fish on the basis of growth in two environments that differed in the intensity of social interactions. In the high interaction environment (HI), food was provided to excess inside a floating cork ring, which limited access to the food and allowed fish to attempt to monopolize the food supply. In the low interaction environment (LI), an equivalent amount of food was spread over the container's surface. In each social environment, fish were selected within family for fast and for slow growth rate during two generations (G1 and G2 ). The response was measured in the third generation (G3 ) on the directly selected trait (growth) and on a correlated trait (agonistic behavior). The magnitude of the direct response to selection on growth in medaka was directly related to population density, i.e., selection was most effective at high densities. Agonistic behavior was inversely related to growth when individuals were raised and selected in an environment where enforced social interaction took place, so long as food was not limited in quantity.
Collapse
Affiliation(s)
- Daniel E Ruzzante
- Biology Department, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, CANADA
| | - Roger W Doyle
- Biology Department, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, CANADA
| |
Collapse
|
32
|
Lamichhaney S, Fuentes-Pardo AP, Rafati N, Ryman N, McCracken GR, Bourne C, Singh R, Ruzzante DE, Andersson L. Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean. Proc Natl Acad Sci U S A 2017; 114:E3452-E3461. [PMID: 28389569 PMCID: PMC5410801 DOI: 10.1073/pnas.1617728114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean. This feature of the Atlantic herring facilitates the detection of genetic factors affecting adaptation because of the sharp contrast between loci showing genetic differentiation resulting from natural selection and the low background noise resulting from genetic drift. We show that genetic factors associated with timing of reproduction are shared between genetically distinct and geographically distant populations. The genes for thyroid-stimulating hormone receptor (TSHR), the SOX11 transcription factor (SOX11), calmodulin (CALM), and estrogen receptor 2 (ESR2A), all with a significant role in reproductive biology, were among the loci that showed the most consistent association with spawning time throughout the species range. In fact, the same two SNPs located at the 5' end of TSHR showed the most significant association with spawning time in both the east and west Atlantic. We also identified unexpected haplotype sharing between spring-spawning oceanic herring and autumn-spawning populations across the Atlantic Ocean and the Baltic Sea. The genomic regions showing this pattern are unlikely to control spawning time but may be involved in adaptation to ecological factor(s) shared among these populations.
Collapse
Affiliation(s)
- Sangeet Lamichhaney
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | | | - Nima Rafati
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Nils Ryman
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Gregory R McCracken
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Christina Bourne
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland A1C 5X1, Canada
| | - Rabindra Singh
- Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, New Brunswick E5B 2L9, Canada
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden;
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843
| |
Collapse
|
33
|
Salisbury SJ, McCracken GR, Keefe D, Perry R, Ruzzante DE. A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation. Mol Ecol 2016; 25:4126-45. [PMID: 27393723 DOI: 10.1111/mec.13757] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/28/2016] [Accepted: 06/28/2016] [Indexed: 01/19/2023]
Abstract
Dendritic metapopulations have been attributed unique properties by in silico studies, including an elevated genetic diversity relative to a panmictic population of equal total size. These predictions have not been rigorously tested in nature, nor has there been full consideration of the interacting effects among contemporary landscape features, colonization history and life history traits of the target species. We tested for the effects of dendritic structure as well as the relative importance of life history, environmental barriers and historical colonization on the neutral genetic structure of a longnose sucker (Catostomus catostomus) metapopulation in the Kogaluk watershed of northern Labrador, Canada. Samples were collected from eight lakes, genotyped with 17 microsatellites, and aged using opercula. Lakes varied in differentiation, historical and contemporary connectivity, and life history traits. Isolation by distance was detected only by removing two highly genetically differentiated lakes, suggesting a lack of migration-drift equilibrium and the lingering influence of historical factors on genetic structure. Bayesian analyses supported colonization via the Kogaluk's headwaters. The historical concentration of genetic diversity in headwaters inferred by this result was supported by high historical and contemporary effective sizes of the headwater lake, T-Bone. Alternatively, reduced allelic richness in headwaters confirmed the dendritic structure's influence on gene flow, but this did not translate to an elevated metapopulation effective size. A lack of equilibrium and upstream migration may have dampened the effects of dendritic structure. We suggest that interacting historical and contemporary factors prevent the achievement of the idealized traits of a dendritic metapopulation in nature.
Collapse
Affiliation(s)
- Sarah J Salisbury
- Department of Biology, Dalhousie University, Halifax, NS, B3H4R2, Canada
| | | | - Donald Keefe
- Department of Environment and Conservation, Newfoundland and Labrador, Corner Brook, NL, Canada
| | - Robert Perry
- Department of Environment and Conservation, Newfoundland and Labrador, Corner Brook, NL, Canada
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, NS, B3H4R2, Canada
| |
Collapse
|
34
|
Trovant B, Basso NG, Orensanz JM, Lessa EP, Dincao F, Ruzzante DE. Scorched mussels (Brachidontes spp., Bivalvia: Mytilidae) from the tropical and warm-temperate southwestern Atlantic: the role of the Amazon River in their speciation. Ecol Evol 2016; 6:1778-98. [PMID: 26929816 PMCID: PMC4758806 DOI: 10.1002/ece3.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 11/16/2022] Open
Abstract
Antitropicality is a distribution pattern where closely related taxa are separated by an intertropical latitudinal gap. Two potential examples include Brachidontes darwinianus (south eastern Brazil to Uruguay), considered by some authors as a synonym of B. exustus (Gulf of Mexico and the Caribbean), and B. solisianus, distributed along the Brazilian coast with dubious records north of the intertropical zone. Using two nuclear (18S and 28S rDNA) and one mitochondrial gene (mtDNA COI), we aimed to elucidate the phylogeographic and phylogenetic relationships among the scorched mussels present in the warm-temperate region of the southwest Atlantic. We evaluated a divergence process mediated by the tropical zone over alternative phylogeographic hypotheses. Brachidontes solisianus was closely related to B. exustus I, a species with which it exhibits an antitropical distribution. Their divergence time was approximately 2.6 Ma, consistent with the intensification of Amazon River flow. Brachidontes darwinianus, an estuarine species is shown here not to be related to this B. exustus complex. We suspect ancestral forms may have dispersed from the Caribbean to the Atlantic coast via the Trans-Amazonian seaway (Miocene). The third species, B rodriguezii is presumed to have a long history in the region with related fossil forms going back to the Miocene. Although scorched mussels are very similar in appearance, their evolutionary histories are very different, involving major historical contingencies as the formation of the Amazon River, the Panama Isthmus, and the last marine transgression.
Collapse
Affiliation(s)
- Berenice Trovant
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Néstor G. Basso
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - José María Orensanz
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Enrique P. Lessa
- Departamento de Ecología y EvoluciónFacultad de CienciasUniversidad de la RepúblicaIguá 4225C.P. 11400MontevideoUruguay
| | - Fernando Dincao
- Universidade Federal do Rio Grande – FURGAv. Itália km 8 Bairro Carreiros96203‐900Rio GrandeBrazil
| | - Daniel E. Ruzzante
- Department of BiologyDalhousie University1355 Oxford St.HalifaxNova ScotiaB3H 4R2Canada
| |
Collapse
|
35
|
Ruzzante DE, McCracken GR, Parmelee S, Hill K, Corrigan A, MacMillan J, Walde SJ. Effective number of breeders, effective population size and their relationship with census size in an iteroparous species, Salvelinus fontinalis. Proc Biol Sci 2016; 283:20152601. [PMID: 26817773 PMCID: PMC4795031 DOI: 10.1098/rspb.2015.2601] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/07/2016] [Indexed: 11/12/2022] Open
Abstract
The relationship between the effective number of breeders (Nb) and the generational effective size (Ne) has rarely been examined empirically in species with overlapping generations and iteroparity. Based on a suite of 11 microsatellite markers, we examine the relationship between Nb, Ne and census population size (Nc) in 14 brook trout (Salvelinus fontinalis) populations inhabiting 12 small streams in Nova Scotia and sampled at least twice between 2009 and 2015. Unbiased estimates of Nb obtained with individuals of a single cohort, adjusted on the basis of age at first maturation (α) and adult lifespan (AL), were from 1.66 to 0.24 times the average estimates of Ne obtained with random samples of individuals of mixed ages (i.e. [Formula: see text]). In turn, these differences led to adjusted Ne estimates that were from nearly five to 0.7 times the estimates derived from mixed-aged individuals. These differences translate into the same range of variation in the ratio of effective to census population size [Formula: see text] within populations. Adopting [Formula: see text] as the more precise and unbiased estimates, we found that these brook trout populations differ markedly in their effective to census population sizes (range approx. 0.3 to approx. 0.01). Using AgeNe, we then showed that the variance in reproductive success or reproductive skew varied among populations by a factor of 40, from Vk/k ≈ 5 to 200. These results suggest wide differences in population dynamics, probably resulting from differences in productivity affecting the intensity of competition for access to mates or redds, and thus reproductive skew. Understanding the relationship between Ne, Nb and Nc, and how these relate to population dynamics and fluctuations in population size, are important for the design of robust conservation strategies in small populations with overlapping generations and iteroparity.
Collapse
Affiliation(s)
- Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Gregory R McCracken
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Samantha Parmelee
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Kristen Hill
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Amelia Corrigan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Halifax, Nova Scotia, Canada B3J 2R5
| | - John MacMillan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Halifax, Nova Scotia, Canada B3J 2R5
| | - Sandra J Walde
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| |
Collapse
|
36
|
Vera-Escalona I, Habit E, Ruzzante DE. The complete mitochondrial genome of the freshwater fish Galaxias platei and a comparison with other species of the genus Galaxias (faraway, so close?). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:176-177. [PMID: 26691291 DOI: 10.3109/19401736.2015.1115497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We present the whole mitochondrial genome for Galaxias platei, a freshwater fish widely distributed throughout the Patagonian Andes, and compare it with the mitochondrial genome of three congeneric species. The position of G. platei in the phylogenetic reconstruction differs from that shown by earlier studies using multiple markers. We discuss the results in terms of the phylogenetic position of G. platei and the use of whole mitochondrial genomes versus specific regions of multiple organelles.
Collapse
Affiliation(s)
- Iván Vera-Escalona
- a Department of Biology , Dalhousie University , Halifax , Nova Scotia , Canada
| | - Evelyn Habit
- b Departamento De Sistemas Acuáticos, Facultad De Ciencias Ambientales Y Centro EULA-Chile , Universidad De Concepción , Barrio Universitario S/N , Concepción , Chile
| | - Daniel E Ruzzante
- a Department of Biology , Dalhousie University , Halifax , Nova Scotia , Canada
| |
Collapse
|
37
|
Vera-Escalona I, Habit E, Ruzzante DE. Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia. Mol Ecol 2015; 24:4112-28. [PMID: 26147523 DOI: 10.1111/mec.13303] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 12/11/2022]
Abstract
Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.
Collapse
Affiliation(s)
- Iván Vera-Escalona
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, Canada
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Barrio Universitario s/n, Concepción, Chile
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, Canada
| |
Collapse
|
38
|
Vera-Escalona I, Anthes LE, Paterson IG, Ruzzante DE. Seventeen novel microsatellite markers for the southern hemisphere fish Galaxias maculatus. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0242-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
39
|
McCracken GR, Brewis HT, McBride MC, Perry R, Keefe D, Ruzzante DE. Development and characterization of 36 novel microsatellite markers for lake chub (Couesius plumbeus) using illumina paired-end sequencing. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0228-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
40
|
Vera-Escalona I, Paterson IG, Habit E, Ruzzante DE. Development and characterization of 15 novel microsatellite markers for the freshwater fish Galaxias platei. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0236-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
41
|
Gomez-Uchida D, Palstra FP, Knight TW, Ruzzante DE. Contemporary effective population and metapopulation size (N e and meta-N e): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries. Ecol Evol 2013; 3:569-80. [PMID: 23532448 PMCID: PMC3605847 DOI: 10.1002/ece3.485] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 12/14/2012] [Accepted: 12/24/2012] [Indexed: 11/15/2022] Open
Abstract
We estimated local and metapopulation effective sizes ([Formula: see text] and meta-[Formula: see text]) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that [Formula: see text] might be inversely related to within-species population divergence as reported in an earlier study (i.e., FST: S. salar> S. fontinalis> S. alpinus). Using the approximate Bayesian computation method implemented in ONeSAMP, we found significant differences in [Formula: see text] ([Formula: see text]) between species, consistent with a hierarchy of adult population sizes ([Formula: see text]). Using another method based on a measure of linkage disequilibrium (LDNE: [Formula: see text]), we found more finite [Formula: see text] values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest [Formula: see text] among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non-significant changes in [Formula: see text], suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta-[Formula: see text] might be significantly smaller than the sum of local [Formula: see text]s (null model) if gene flow is asymmetric, varies among subpopulations, and is driven by common landscape features such as waterfalls. One 'bottom-up' or numerical approach that explicitly incorporates variable and asymmetric migration rates showed this very pattern, while a number of analytical models provided meta-[Formula: see text] estimates that were not significantly different from the null model or from each other. Our study of three species inhabiting a shared environment highlights the importance and utility of differentiating species-specific and landscape effects, not only on dispersal but also in the demography of wild populations as assessed through local [Formula: see text]s and meta-[Formula: see text]s and their relevance in ecology, evolution and conservation.
Collapse
|
42
|
Elgueta A, González J, Ruzzante DE, Walde SJ, Habit E. Trophic interference by Salmo trutta on Aplochiton zebra and Aplochiton taeniatus in southern Patagonian lakes. J Fish Biol 2013; 82:430-443. [PMID: 23398060 DOI: 10.1111/j.1095-8649.2012.03489.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The length and mass ratio, diet and isotopic composition of Aplochiton zebra and Aplochiton taeniatus inhabiting a Salmo trutta-invaded and a S. trutta-free lake in southern Patagonia were compared. Results indicate that S. trutta exercises important trophic interference over A. zebra and A. taeniatus, causing changes in their dietary composition by reducing the consumption of winged Diptera through changes in feeding behaviours that involve jumping out of the water. This effect is significantly higher in A. zebra than in A. taeniatus a species that has a highly specialized diet. The dietary changes of A. zebra and A. taeniatus in sympatry with S. trutta lead to an impoverishment of their isotopic nitrogen signals (δ(15)N), suggesting a reduction of their trophic position. In the case of A. zebra, this translates into a significant decrease in its body condition factor. Such interference could lead to a population decline of this species and would explain the current distribution range decline and allopatry with S. trutta in fluvial systems.
Collapse
Affiliation(s)
- A Elgueta
- Centro de Ciencias Ambientales, EULA, Universidad de Concepción, Barrio Universitario sn, Concepción, Chile
| | | | | | | | | |
Collapse
|
43
|
Bradbury IR, Hubert S, Higgins B, Bowman S, Borza T, Paterson IG, Snelgrove PVR, Morris CJ, Gregory RS, Hardie D, Hutchings JA, Ruzzante DE, Taggart CT, Bentzen P. Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish. Evol Appl 2013; 6:450-61. [PMID: 23745137 PMCID: PMC3673473 DOI: 10.1111/eva.12026] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/28/2012] [Indexed: 12/17/2022] Open
Abstract
As populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the delineation of management units, and providing genomic tools for more precise and effective population monitoring and the successful assignment of individuals and products. We explored heterogeneity in genomic divergence and its impact on the resolution of spatial population structure in exploited populations of Atlantic cod, Gadus morhua, using genome wide expressed sequence derived single nucleotide polymorphisms in 466 individuals sampled across the range. Outlier tests identified elevated divergence at 5.2% of SNPs, consistent with directional selection in one-third of linkage groups. Genomic regions of elevated divergence ranged in size from a single position to several cM. Structuring at neutral loci was associated with geographic features, whereas outlier SNPs revealed genetic discontinuities in both the eastern and western Atlantic. This fine-scale geographic differentiation enhanced assignment to region of origin, and through the identification of adaptive diversity, fundamentally changes how these populations should be conserved. This work demonstrates the utility of genome scans for adaptive divergence in the delineation of stock structure, the traceability of individuals and products, and ultimately a role for population genomics in fisheries conservation.
Collapse
Affiliation(s)
- Ian R Bradbury
- Fisheries and Oceans Canada St. John's, NF, Canada ; Department of Biology, Marine Gene Probe Laboratory, Dalhousie University Halifax, NS, Canada ; Ocean Sciences Center and Biology Department, Memorial University of Newfoundland St. John's, NF, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Johnstone DL, O'Connell MF, Palstra FP, Ruzzante DE. Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years. Mol Ecol 2013; 22:2394-407. [PMID: 23317429 DOI: 10.1111/mec.12186] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/13/2012] [Accepted: 11/21/2012] [Indexed: 11/26/2022]
Abstract
We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb) and the generational effective population size (Ne) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed Ne estimates, suggesting that mature male parr are significantly increasing Nb and Ne over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.
Collapse
|
45
|
Halfyard EA, Gibson AJF, Ruzzante DE, Stokesbury MJW, Whoriskey FG. Estuarine survival and migratory behaviour of Atlantic salmon Salmo salar smolts. J Fish Biol 2012; 81:1626-1645. [PMID: 23020565 DOI: 10.1111/j.1095-8649.2012.03419.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
To estimate mortality rates, assess the spatio-temporal dynamics of natural mortality and examine migratory behaviour during the fresh to saltwater transition, 185 wild Atlantic salmon Salmo salar smolts were implanted with coded acoustic transmitters. Seaward migration of tagged S. salar from four river systems in an area of Nova Scotia, Canada known as the Southern Upland was monitored using fixed receivers and active telemetry over 3 years. Cumulative survival through the river, inner estuary, outer estuary and bay habitats averaged 59·6% (range = 39·4-73·5%). When standardized to distance travelled, survival rates followed two patterns: (1) constant rates of survival independent of habitat or (2) low survival most frequently associated with inner estuary habitats. In rivers where survival was independent of habitat, residency periods were also independent of habitat, post-smolts exhibited few upstream movements, took a more direct route to the ocean and reached the ocean rapidly. Alternatively, in rivers where survival was habitat specific, residency was also habitat specific with overall increased residency, more frequent upstream movements and delayed arrival to the open ocean. The sudden disappearance of most (75-100%) smolts and post-smolts assumed dead during the course of this study warrants further examination into the role of avian predators as a mortality vector.
Collapse
Affiliation(s)
- E A Halfyard
- Department of Biology, Dalhousie University, Halifax, NS, B3H4J1 Canada.
| | | | | | | | | |
Collapse
|
46
|
Fraser CI, Nikula R, Ruzzante DE, Waters JM. Poleward bound: biological impacts of Southern Hemisphere glaciation. Trends Ecol Evol 2012; 27:462-71. [DOI: 10.1016/j.tree.2012.04.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/23/2012] [Accepted: 04/24/2012] [Indexed: 10/28/2022]
|
47
|
carrea C, Barriga JP, Cussac VE, Ruzzante DE. Genetic and phenotypic differentiation among Galaxias maculatus populations in a Patagonian postglacial lake system. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01939.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Juan P. Barriga
- INIBIOMA (Universidad Nacional del Comahue-CONICET) Quintral; 1250 (8400); Bariloche; RN; Argentina
| | - Victor E. Cussac
- INIBIOMA (Universidad Nacional del Comahue-CONICET) Quintral; 1250 (8400); Bariloche; RN; Argentina
| | - Daniel E. Ruzzante
- Department of Biology; Dalhousie University; Halifax; NS; B3H 4R2; Canada
| |
Collapse
|
48
|
Arias MC, Arnoux E, Bell JJ, Bernadou A, Bino G, Blatrix R, Bourguet D, Carrea C, Clamens AL, Cunha HA, d'Alençon E, Ding Y, Djieto-Lordon C, Dubois MP, Dumas P, Eraud C, Faivre B, Francisco FO, Françoso E, Garcia M, Gardner JPA, Garnier S, Gimenez S, Gold JR, Harris DJ, He G, Hellemans B, Hollenbeck CM, Jing S, Kergoat GJ, Liu B, McDowell JR, McKey D, Miller TL, Newton E, Pagenkopp Lohan KM, Papetti C, Paterson I, Peccoud J, Peng X, Piatscheck F, Ponsard S, Reece KS, Reisser CMO, Renshaw MA, Ruzzante DE, Sauve M, Shields JD, Solé-Cava A, Souche EL, Van Houdt JKJ, Vasconcellos A, Volckaert FAM, Wang S, Xiao J, Yu H, Zane L, Zannato B, Zemlak TS, Zhang C, Zhao Y, Zhou X, Zhu L. Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2011-31 January 2012. Mol Ecol Resour 2012; 12:570-2. [PMID: 22448966 DOI: 10.1111/j.1755-0998.2012.03133.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This article documents the addition of 473 microsatellite marker loci and 71 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross-tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax.
Collapse
|
49
|
Habit E, Gonzalez J, Ruzzante DE, Walde SJ. Native and introduced fish species richness in Chilean Patagonian lakes: inferences on invasion mechanisms using salmonid-free lakes. DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00906.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Evelyn Habit
- Centro de Ciencias Ambientales; EULA; Universidad de Concepción; Barrio Universitario s/n Concepción Chile
- Centro de Investigaciones en Ecosistemas Patagónicos (CIEP); Coyhaique Chile
| | - Jorge Gonzalez
- Centro de Ciencias Ambientales; EULA; Universidad de Concepción; Barrio Universitario s/n Concepción Chile
| | | | - Sandra J. Walde
- Department of Biology; Dalhousie University; Halifax NS B3H 4R2 Canada
| |
Collapse
|
50
|
Zemlak TS, Walde SJ, Habit EM, Ruzzante DE. Climate-induced changes to the ancestral population size of two Patagonian galaxiids: the influence of glacial cycling. Mol Ecol 2011; 20:5280-94. [PMID: 22077139 DOI: 10.1111/j.1365-294x.2011.05352.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Patagonia is one of the few areas in the Southern Hemisphere to have been directly influenced by Quaternary glaciers. In this study, we evaluate the influence that Quaternary glacial ice had on the genetic diversity of two congeneric fish species, the diadromous Galaxias maculatus and the nondiadromous Galaxias platei, using multilocus estimates of effective population size through time. Mid-Quaternary glaciations had far-reaching consequences for both species. Galaxias maculatus and G. platei each experienced severe genetic bottlenecks during the period when Patagonia ice sheet advance reached its maximum positions c. 1.1-0.6 Ma. Concordant drops in effective size during this time suggest that range sizes were under similar constraints. It is therefore unlikely that coastal (brackish/marine) environments served as a significant refuge for G. maculatus during glacial periods. An earlier onset of population declines for G. platei suggests that this species was vulnerable to modest glacial advances. Declines in effective sizes were continuous for both species and lasted into the late-Pleistocene. However, G. maculatus exhibited a strong population recovery during the late-Quaternary (c. 400,000 bp). Unusually long and warm interglacials associated with the late-Quaternary may have helped to facilitate a strong population rebound in this primarily coastal species.
Collapse
Affiliation(s)
- Tyler S Zemlak
- Department of Biology, Dalhousie University, Halifax, NS, Canada.
| | | | | | | |
Collapse
|