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A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America

Journal of Nematology
Volume 51 (2019): Issue 1 (January 2019)
By:
Open Access
|Dec 2019

Figures & Tables

Figure 1:

Distribution of sampling sites by county for the Pratylenchus survey.
Distribution of sampling sites by county for the Pratylenchus survey.

Figure 2:

Bayesian tree of unique COI haplotypes derived from 915 Pratylenchus specimen data set. Nodes are labeled according to tree building approach, with bootstrap values indicated in green for neighbor-joining, blue for maximum-likelihood, and red for posterior probability in Bayesian analysis. The absence of a value reflects the absence of that node, or bootstrap values below 50 in a particular tree building approach. Terminal nodes are labeled by Nematode Identification Numbers (NIDs) and taxon name.
Bayesian tree of unique COI haplotypes derived from 915 Pratylenchus specimen data set. Nodes are labeled according to tree building approach, with bootstrap values indicated in green for neighbor-joining, blue for maximum-likelihood, and red for posterior probability in Bayesian analysis. The absence of a value reflects the absence of that node, or bootstrap values below 50 in a particular tree building approach. Terminal nodes are labeled by Nematode Identification Numbers (NIDs) and taxon name.

Figure 3:

Maximum likelihood tree of haplotype groups reflecting group membership support based on consensus tree topology, and species delimitation methods. These methods are indicated by colored bars: Automatic Barcoding Gap Discovery (ABGD) green bar, Generalized Mixed Yule Coalescent (GMYC) red bar, and statistical parsimony analysis (TCS) blue bar. TCS groups marked with an asterisk indicate a merging of two groups at a 90% connection limit.
Maximum likelihood tree of haplotype groups reflecting group membership support based on consensus tree topology, and species delimitation methods. These methods are indicated by colored bars: Automatic Barcoding Gap Discovery (ABGD) green bar, Generalized Mixed Yule Coalescent (GMYC) red bar, and statistical parsimony analysis (TCS) blue bar. TCS groups marked with an asterisk indicate a merging of two groups at a 90% connection limit.

Figure 4:

Bayesian evolutionary analysis by sampling trees (BEAST) analysis of estimated divergence times using the mitochondrial substitution genome rate of 7.2 ×10−8 per site per generation, a calibration originally calculated for the nematode Caenorhabditis briggsae (Howe et al., 2010). The rate assumes two Pratylenchus generations per year. Divergence age confidence intervals of 95% are provided at nodes.
Bayesian evolutionary analysis by sampling trees (BEAST) analysis of estimated divergence times using the mitochondrial substitution genome rate of 7.2 ×10−8 per site per generation, a calibration originally calculated for the nematode Caenorhabditis briggsae (Howe et al., 2010). The rate assumes two Pratylenchus generations per year. Divergence age confidence intervals of 95% are provided at nodes.

Figure 5:

Matrix exhibiting Pratylenchus species of the Great Plains and their host associations. The number of fields with a specific plant host-Pratylenchus species combination is indicated by the number within the green circles.
Matrix exhibiting Pratylenchus species of the Great Plains and their host associations. The number of fields with a specific plant host-Pratylenchus species combination is indicated by the number within the green circles.

Figure 6:

TCS networks depicting Pratylenchus neglectus haplotype abundance and relationships among haplotypes. Dashed lines encircling haplotypes indicate 95% connection limits. Hash marks between haplotypes indicate number of mutational steps between haplotypes. Relative size of the circles reflects abundance of specimens exhibiting that specific haplotype. (A) Colors indicate geographic origin of the haplotypes in the Pratylenchus survey; (B) colors indicate the host in the field at time of the survey.
TCS networks depicting Pratylenchus neglectus haplotype abundance and relationships among haplotypes. Dashed lines encircling haplotypes indicate 95% connection limits. Hash marks between haplotypes indicate number of mutational steps between haplotypes. Relative size of the circles reflects abundance of specimens exhibiting that specific haplotype. (A) Colors indicate geographic origin of the haplotypes in the Pratylenchus survey; (B) colors indicate the host in the field at time of the survey.

Figure 7:

TCS network at 95% connection limit depicting Pratylenchus scribneri haplotype abundance and relationships among haplotypes. Hash marks between haplotypes indicate number of mutational steps between haplotypes. Relative size of the circles reflects abundance of specimens exhibiting that specific haplotype. (A) Colors indicate geographic origin of the haplotypes in the Pratylenchus survey; (B) colors indicate the host in the field at time of the survey.
TCS network at 95% connection limit depicting Pratylenchus scribneri haplotype abundance and relationships among haplotypes. Hash marks between haplotypes indicate number of mutational steps between haplotypes. Relative size of the circles reflects abundance of specimens exhibiting that specific haplotype. (A) Colors indicate geographic origin of the haplotypes in the Pratylenchus survey; (B) colors indicate the host in the field at time of the survey.

Figure 8:

TCS networks depicting (A) the single haplotype of Pratylenchus thornei and (B) the two networks exhibited by Pratylenchus hexincisus. Dashed lines encircling haplotypes indicate 95% connection limits. Hash marks between haplotypes indicate number of mutational steps between haplotypes. Relative size of the circles reflects abundance of specimens exhibiting that specific haplotype. Colors indicate geographic origin of the haplotypes in the Pratylenchus survey.
TCS networks depicting (A) the single haplotype of Pratylenchus thornei and (B) the two networks exhibited by Pratylenchus hexincisus. Dashed lines encircling haplotypes indicate 95% connection limits. Hash marks between haplotypes indicate number of mutational steps between haplotypes. Relative size of the circles reflects abundance of specimens exhibiting that specific haplotype. Colors indicate geographic origin of the haplotypes in the Pratylenchus survey.

Figure 9:

County location of surveyed fields with Pratylenchus neglectus (red), P. scribneri (blue), and fields with a mixture of both species (gray).
County location of surveyed fields with Pratylenchus neglectus (red), P. scribneri (blue), and fields with a mixture of both species (gray).
DOI: https://doi.org/10.21307/jofnem-2019-081 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X
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Language: English
Page range: 1 - 21
Submitted on: May 24, 2019
Published on: Dec 10, 2019
Published by: Society of Nematologists, Inc.
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year
Keywords:
COI,
DNA barcoding,
Species delimitation,
ABGD,
GMYC,
TCS,
Root lesion nematode,
Taxonomy
Related subjects:
Life sciences,
Life sciences, other

© 2019 Mehmet Ozbayrak, Tim Todd, Timothy Harris, Rebecca Higgins, Kirsten Powers, Peter Mullin, Lisa Sutton, Thomas Powers, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

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