diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors

Keenan, Kevin G.; McGinnity, P.; Cross, Tom F.; Crozier, W. W.; Prodöhl, Paulo A.

doi:10.1111/2041-210x.12067

Cited by 1,166 publications

(1,036 citation statements)

References 25 publications

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“…To allow for comparison with previous microsatellite results (Cunningham et al., 2009),

G_{italicST}^{″}

(Meirmans & Hedrick, 2011) was estimated using diveRsity (Keenan, McGinnity, Cross, Crozier, & Prodöhl, 2013) within R for both microsatellite and RAD data, and pairwise linearized genetic distance (

G_{italicST}^{″}

/(1‐

G_{italicST}^{″}

)) was plotted against shortest geographic distance along the continental shelf estimated from Google Earth.…”

Section: Methodsmentioning

confidence: 99%

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Drinan

Gruenthal

Canino

et al. 2018

Evolutionary Applications

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The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation by distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction‐site‐associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation‐by‐distance signal along coastlines that mirrored previous microsatellite results and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea, with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coastal samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs. offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation by distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low F ST marine species.

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“…To allow for comparison with previous microsatellite results (Cunningham et al., 2009),

G_{italicST}^{″}

G_{italicST}^{″}

/(1‐

G_{italicST}^{″}

)) was plotted against shortest geographic distance along the continental shelf estimated from Google Earth.…”

Section: Methodsmentioning

confidence: 99%

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Drinan

Gruenthal

Canino

et al. 2018

Evolutionary Applications

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“…The population genomic diversity of populations was estimated according to the expected ( H E ) and observed heterozygosity ( H O ), using the PopGeneKit package (Paquete, 2012), and the estimated number of alleles ( A ), allelic richness ( A R ), and inbreeding coefficients ( F is ), using the R package diversity (Keenan, McGinnity, Cross, Crozier, & Prodohl, 2013). Both packages were written in R (R Development Core Team, 2016).…”

Section: Methodsmentioning

confidence: 99%

“…Both packages were written in R (R Development Core Team, 2016). Genetic differentiation was estimated through the overall and pairwise F ST values (Weir & Cockerham, 1984), using the R package diversity (Keenan et al., 2013). Population structure was inferred using the discriminant analysis of principal components (DAPC) (Jombart, Devillard, & Balloux, 2010), a multivariate analysis to evaluate the genetic population structure, using the R package adegenet (Jombart, 2008).…”

Section: Methodsmentioning

confidence: 99%

Phenotypic plasticity and local adaptation favor range expansion of a Neotropical palm

Brancalion

Oliveira

Zucchi

et al. 2018

Ecology and Evolution

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One of the most intriguing questions in plant ecology is which evolutionary strategy allows widely distributed species to increase their ecological range and grow in changing environmental conditions. Phenotypic plasticity and local adaptations are major processes governing species range margins, but little is known about their relative contribution for tree species distribution in tropical forest regions. We investigated the relative role of phenotypic plasticity and local adaptation in the ecological distribution of the widespread palm Euterpe edulis in the Brazilian Atlantic Forest. Genetic sampling and experiments were performed in old‐growth remnants of two forest types with higher (Seasonal Semideciduous Forests vs. Submontane Rainforest) and lower biogeographic association and environmental similarities (Submontane Rainforest vs. Restinga Forest). We first assessed the molecular genetic differentiation among populations, focusing on the group of loci potentially under selection in each forest, using single‐nucleotide polymorphism (SNPs) outliers. Further, we looked for potential adaptive divergence among populations in a common garden experiment and in reciprocal transplants for two plant development phases: seedling establishment and sapling growth. Analysis with outlier loci indicated that all individuals from the Semideciduous Forest formed a single group, while another group was formed by overlapping individuals from Submontane Rainforest and Restinga Forest. Molecular differentiation was corroborated by reciprocal transplants, which yielded strong evidence of local adaptations for seedling establishment in the biogeographically divergent Rainforest and Semideciduous Forest, but not for Restinga Forest and Submontane Rainforest. Phenotypic plasticity for palm seedling establishment favors range expansion to biogeographically related or recently colonized forest types, while persistence in the newly colonized ecosystem may be favored by local adaptations if climatic conditions diverge over time, reducing gene flow between populations. SNPs obtained by next‐generation sequencing can help exploring adaptive genetic variation in tropical trees, which impose several challenges to the use of reciprocal transplants.

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“…This analysis included SNPs sequenced in at least 80% of individuals in all cohorts within a colony and was carried out using diveRsity (Keenan, McGinnity, Cross, Crozier, & Prodohl, 2013) in R. A R was calculated with rarefaction to standardize to the sample size of the smallest cohort. We also compared these metrics of genomewide diversity among colonies (with cohorts combined) to assess changes in diversity along the axis of spatial expansion during this period of recovery.…”

Section: Methodsmentioning

confidence: 99%

Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds

Cammen

Schultz

Bowen

et al. 2018

Ecology and Evolution

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Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site‐associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half‐century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well‐described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations.

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diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors

Cited by 1,166 publications

References 25 publications

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Phenotypic plasticity and local adaptation favor range expansion of a Neotropical palm

Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds

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