Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

Hand, Brian K.; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan P.; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P.; Ackerman, Michael W.; Garner, Brittany A.; Kimball, J. S.; Stanford, Jack A.; Luikart, Gordon

doi:10.1111/mec.13517

Cited by 40 publications

(45 citation statements)

References 87 publications

(153 reference statements)

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“…This approach is considered beneficial because ensuing models will have better predictive power, which may be tested internally with a subset of the data, or externally with independent data (Hand et al. ; Richardson et al. ).…”

Section: Discussionmentioning

confidence: 99%

Identification of landscape features influencing gene flow: How useful are habitat selection models?

Roffler

Schwartz

Pilgrim

et al. 2016

Evolutionary Applications

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Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid‐range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long‐term genetic connectivity.

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Section: Discussionmentioning

confidence: 99%

Identification of landscape features influencing gene flow: How useful are habitat selection models?

Roffler

Schwartz

Pilgrim

et al. 2016

Evolutionary Applications

Self Cite

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“…References to less recent studies can be found in several review papers (Hemmer‐Hansen et al , ; Pujolar et al , , ; Ulrik et al , ; Willette et al , ; Gaither et al , ; Guo et al , ; Elmer, ; Picq et al , , as well as references in the next section as examples of the most recent studies). In contrast, fewer fish studies have used a landscape genomic framework to detecting selection by finding statistical associations between local allele frequencies and environmental variables and those have mainly been performed on salmonids (Zueva et al , ; Hecht et al , ; Hand et al , ). For instance, Hecht et al () used RADseq to genotype nearly 2000 Chinook salmon Oncorhynchus tshawytscha (Walbaum 1792) from 46 localities at about 20 000 SNPs in order to document environmental adaptation throughout the North American range of the species, from California to Alaska.…”

Section: Modern Approaches To Study Genomics Of Local Adaptationmentioning

confidence: 99%

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

Bernatchez

2016

Journal of Fish Biology

205

216

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The first goal of this paper was to overview modern approaches to local adaptation, with a focus on the use of population genomics data to detect signals of natural selection in fishes. Several mechanisms are discussed that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. Pervasive adaptive evolution, however, seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing selection in its various forms may also play an important role in maintaining adaptive genetic variation and the evolutionary potential of species to cope with environmental change. A large body of literature on fishes also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most often via different genetic solutions, further adding to the potential options of species to cope with a changing environment. Moreover, a paradox is emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential in some circumstances. Although more empirical support is needed, several recent studies suggest that epigenetic variation could account for this apparent paradox. Therefore, epigenetic variation should be fully integrated with considerations pertaining to role of soft sweeps, polygenic and balancing selection, as well as repeated adaptation involving different genetic basis towards improving models predicting the evolutionary potential of species to cope with a changing world.

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“…Landscape features can shape both neutral genetic structure and the distribution of adaptive variation within a species (Davis, Epps, Flitcroft, & Banks, ; Grummer et al, ; Orsini, Andrew, & Eizaguirre, ). While landscape genetic studies in rivers increasingly consider adaptive variation (Brauer, Unmack, Smith, Bernatchez, & Beheregaray, ; Micheletti, Matala, Matala, & Narum, ; Vincent, Dionne, Kent, Lien, & Bernatchez, ), few studies have directly compared patterns of neutral genetic variation with patterns of variation at loci associated with adaptive phenotypic variation (but see Hand et al, ; Keller, Taverna, & Seehausen, ; O’Malley, Jacobson, Kurth, Dill, & Banks, ). This comparison could improve our understanding of the mechanisms that either facilitate or restrict gene flow in the face of selection and adaptive divergence on life history characteristics (e.g., migratory vs. resident life histories) in fragmented river networks and landscapes.…”

Section: Introductionmentioning

confidence: 99%

Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability

et al. 2020

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Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals.

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Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

Cited by 40 publications

References 87 publications

Identification of landscape features influencing gene flow: How useful are habitat selection models?

Identification of landscape features influencing gene flow: How useful are habitat selection models?

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability

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