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Data from: A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation
Salisbury, Sarah J.; McCracken, Gregory R.; Keefe, Donald; Perry, Robert; Ruzzante, Daniel E. — 2016-07-08 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. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years
Johnstone, Devon L.; O'Connell, Michael F.; Palstra, Friso P.; Ruzzante, Daniel E. — 2012-12-13 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.
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Data from: Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia
Vera-Escalona, Iván; Ruzzante, Daniel E.; Habit, Evelyn — 2015-07-07 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.
Université de Montréal Dataverse Translation missing: fr.blacklight.search.logo
Rocky Mountain alpine lake brook trout census and effective sizes [2017-2019]
Borealis
Clarke, Shannon H.; McCracken, Gregory R.; Humphries, Shelley; Ruzzante, Daniel E.; Grant, James W.A.; Fraser, Dylan J. — 2022-04-20 Data were collected each year during the summer from 2017 to 2019. Census size (Nc) estimates were generated using mark-recapture methods involving multiple recapture events, and estimated using the Schnabel method. Effective number of breeder (Nb) estimates were generated using the Linkage Disequilibrium Method in the NeEstimator V2 software, from genotypes of year 0+ individuals. Three of these lakes were subjected to size-selective harvesting beginning in the fall of 2017, and were harvested each proceeding fall.
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Data from: Invasive species and postglacial colonization: their effects on the genetic diversity of a Patagonian fish
Dryad
Vera-Escalona, Iván; Habit, Evelyn; Ruzzante, Daniel E. — 2019-02-05 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 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.
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Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (Salvelinus alpinus)
Dryad
Salisbury, Sarah J.; McCracken, Gregory R.; Perry, Robert; Keefe, Donald; K. S. Layton, Kara; Kess, Tony; Nugent, Cameron M.; Leong, Jong S.; Bradbury, Ian R.; Koop, Ben F.; Ferguson, Moira M.; Ruzzante, Daniel E. — 2020-09-30 <p>The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (<i>Salvelinus alpinus</i>) within the Quaternary period offer an ideal model to study the repeatability of evolution at the genomic level. Sympatric morphs of Arctic Charr are found across this species' circumpolar distribution. However, the specific genetic mechanisms driving this morph differentiation are largely unknown despite the cultural and economic importance of the anadromous morph. We used a newly designed 87k SNP chip to investigate the character and consistency of the genomic differences among sympatric morphs within three recently deglaciated and geographically proximate lakes in Labrador, Canada. We found genetically distinct small and large morph Arctic Charr in all three lakes consistent with resident and anadromous morphs, respectively. A degree of reproductive isolation among sympatric morphs is likely given genome-wide distributions of outlier SNPs and high genome-wide <i>F</i><sub>ST</sub>s. Across all lakes, outlier SNPs were largely non-overlapping suggesting a lack of genetic parallelism driving morph differentiation. Alternatively, several genes and paralogous copies of the same gene consistently differentiated morphs across multiple lakes suggesting their importance to the manifestation of morphs. Our results confirm the utility of Arctic Charr as a model for investigating the predictability of evolution and support the importance of both genetic parallelism and non-parallelism to the incipient speciation of Arctic Charr morphs.</p>
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Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish
Dryad
K. S. Layton, Kara; Dempson, J. Brian; Snelgrove, Paul V.R.; Duffy, Steven J.; Messmer, Amber M.; Paterson, Ian; Jeffery, Nicholas W.; Kess, Tony; Horne, John B.; Salisbury, Sarah J.; Ruzzante, Daniel E.; Bentzen, Paul; Côté, David; Nugent, Cameron M.; Ferguson, Moira M.; Leong, Jong S.; Koop, Ben F.; Bradbury, Ian R. — 2020-01-17 <p>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 combatting ongoing wide spread 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 northeastern Canada, Arctic charr (<i>Salvelinus alpinus</i>). 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 northeastern 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 SNP panel and with the microsatellite loci (&gt;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.</p>
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Data from: Whole-genome sequencing approaches for conservation biology: advantages, limitations, and practical recommendations
Fuentes-Pardo, Angela P.; Ruzzante, Daniel E. — 2017-08-07 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 (huWGR) or resolved haplotypes (hrWGR), 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 non-model 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 fulfills 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 non-model species and fields including conservation biology.

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(auteur : Ruzzante, Daniel E.)

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