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Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides)

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Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides) https://t.co/vZFFue8PML
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446 days ago
New preprint: Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides) https://t.co/HOLZUsjic4 HT @PeerJPreprints
Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides) https://t.co/DAI3izLTmN
RT @justincbagley: Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek…
RT @justincbagley: Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek…
RT @justincbagley: Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek…
RT @justincbagley: Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek…
RT @justincbagley: Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek…
446 days ago
RT @justincbagley: Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek…
RT @justincbagley: Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek…
RT @justincbagley: Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek…
RT @justincbagley: Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek…
Very happy our preprint on quaking aspen GBS phylogeography just published in @PeerJPreprints! - https://t.co/gVJ7HtsSek. Please RT! Coauthored w/@balfouriana @ee_gutierrez @NeanderHeming @upendra_35 Karen Mock, & Steve Strauss! #Biodiversity #Biogeography #Genetics #Genomics https://t.co/OL83BSjhaH
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RT @upendra_35: Happy to see our crowd funded project (https://t.co/09ygXHThfa) finally shaped into a preprint in @PeerJPreprints https://t…
PeerJ: Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides) https://t.co/iVy0g7HtMD
Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides) https://t.co/XmduK63bFb
Happy to see our crowd funded project (https://t.co/09ygXHThfa) finally shaped into a preprint in @PeerJPreprints https://t.co/DHjiLnfu6M #Biodiversity #Biogeography #Genetics #Genomics #PlantScience.
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Supplemental Information

Appendix S1: Supplementary methods and results

DOI: 10.7287/peerj.preprints.27162v1/supp-1

Data S1: Sample list, collection site details, and summary of individual assignments to genetic clusters in ADMIXTURE and DAPC analyses

DOI: 10.7287/peerj.preprints.27162v1/supp-2

Data S2: ENM modeling results summary, including model selection results and diagnostic statistics from ENMeval (Muscarella et al.2014) and MaxEnt model metrics from ENMwizard (Heming et al.2018)

DOI: 10.7287/peerj.preprints.27162v1/supp-3

Table S1: Per-locus genetic summary statistics for P. tremuloides and P. trichocarpa individuals in this study

DOI: 10.7287/peerj.preprints.27162v1/supp-4

Table S2: Pairwise FST estimates between P. tremuloides genetic clusters, and their 95% confidence intervals (CIs)

DOI: 10.7287/peerj.preprints.27162v1/supp-5

Table S3: Hierarchical analysis of genetic variance among P. tremuloides SNPs

Results are given for variance partitioning within genetic clusters (Fclust/total), within subpopulations by cluster (Fpop/clust), and within individual trees relative to populations. Ranges given in parentheses are 95% confidence intervals.

DOI: 10.7287/peerj.preprints.27162v1/supp-6

Figure S1: Plot of ADMIXTURE cross-validation error versus K, showing that K= 3 is the best fit for the full P. tremuloidesand P. trichocarpa dataset of 34,796 SNPs (sensuAlexander & Lange 2011)

DOI: 10.7287/peerj.preprints.27162v1/supp-7

Figure S2: Plot of Bayesian information criterion (BIC) scores for k-means clustering solutions over a range of K, from the first step of DAPC, with K = 3 being the best solution

DOI: 10.7287/peerj.preprints.27162v1/supp-8

Figure S3: Results of DAPC cross-validation in Restablishing that the appropriate number of principal components to retain ranges from 20–100 with similarly high (>90%) prediction success

DOI: 10.7287/peerj.preprints.27162v1/supp-9

Figure S4: DAPC loading values plotted for all 34,796 SNPs, with SNP name labels beside the SNPs with the highest loadings

DOI: 10.7287/peerj.preprints.27162v1/supp-10

Figure S5: Genetic patterns of heterozygote and singleton alleles within and among P. tremuloides genetic clusters, calculated while excluding putatively admixed edge populations (Qmax < 0.75)

Results are analogous to corresponding panels of Fig. 3 (see Fig. 3 caption for details), but based on different sampling.

DOI: 10.7287/peerj.preprints.27162v1/supp-11

Figure S6: Heatmap of interindividual Nei’s D estimates

Results were reordered by row and column means, and flanked by dendrograms of the values. Color key and histogram at top left show the distribution of mean D-values.

DOI: 10.7287/peerj.preprints.27162v1/supp-12

Figure S7: Heatmap of unordered interpopulation FST estimates flanked by clustering dendrograms from the distances

Color key and histogram at top left show the distribution of mean FSTvalues.

DOI: 10.7287/peerj.preprints.27162v1/supp-13

Figure S8: Results of isolation by distance tests

Results are based on generalized linear modeling analyses of linearized FST versus log[geographic distance (km)] of P. tremuloides (top left) and its genetic clusters 1 (top right), 2 (bottom left), and 3 (bottom right).

DOI: 10.7287/peerj.preprints.27162v1/supp-14

Figure S9: Unrooted maximum-likelihood tree topology from the ingroup-only TreeMix analysis

Results are show the tree graph estimated when a single migration event was allowed (A), and residual plot of the graph (B). Scale bars and legends same as in Fig. 2.

DOI: 10.7287/peerj.preprints.27162v1/supp-15

Figure S10:

Results of TreeMix analyses on the full dataset conducted over varying levels of k block sizes (10 to 5000 bp) accounting for linkage disequilibrium. Scale bars and legends same as in Figs. 2 and S9.

DOI: 10.7287/peerj.preprints.27162v1/supp-16

Figure S11: Projection of the final present-day ecological niche model of P. tremuloides onto three late Pleistocene climatic scenarios

The ENM was built with MaxEnt and bioclimatic variables obtained from WorldClim v1, and the three Pleistocene time-slices (B–D) correspond to scenarios described in the Fig. 4 caption and Table 1. Model projections show continuous suitability values obtained using the cloglog format of MaxEnt after the application of a 10th-percentile threshold. Extent of LGM ice sheets is indicated in white.

DOI: 10.7287/peerj.preprints.27162v1/supp-17

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Justin C Bagley analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, curated the data, produced and submitted online Mendeley Data accession of supporting files (for reproducibility).

Neander M Heming analyzed the data, prepared figures and/or tables, approved the final draft, assisted with Mendeley Data accession submission.

Eliécer E Gutiérrez analyzed the data, prepared figures and/or tables, approved the final draft.

Upendra K Devisetty performed the experiments, approved the final draft.

Karen E Mock conceived and designed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Andrew J Eckert contributed reagents/materials/analysis tools, approved the final draft.

Steven H Strauss conceived and designed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Our final sequence dataset is available in raw and genotype file formats within the following Mendeley Data accession (citation given below):

Bagley, J., Heming, N. H., & Gutiérrez, E. E. (2018). Data for: Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides). Mendeley Data, v1. Available at:

<http://dx.doi.org/10.17632/jhkhvdgyfy.1>.

Data Deposition

The following information was supplied regarding data availability:

- Mendeley Data

- Accession jhkhvdgyfy.1

- URL: http://dx.doi.org/10.17632/jhkhvdgyfy.1

Funding

This research was funded through crowdfunding support via an Experiment.com project (https://experiment.com/projects/the-lost-aspens-of-the-willamette-valley-did-catastrophic-floods-carry-them-from-the-rockies). Additionally, JCB received stipend support from U.S. NSF grant EF-1442486 to AJE, and NMH was supported by a postdoctoral fellowship from the Brazilian federal agency CAPES. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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