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

States	Corn	Wheat	Dry beans	Potatoes	Barley	Alfalfa	Sugar beets	Total field	Field %
Nebraska	97	8	0	5	0	0	0	110	44.72
Kansas	43	19	0	0	0	1	0	63	25.61
Wyoming	0	0	18	8	3	0	0	29	11.79
North Dakota	0	19	0	0	0	0	0	19	7.72
Montana	6	0	0	1	4	4	0	15	6.10
Colorado	5	0	0	2	0	1	2	10	4.07
Total field	151	46	18	16	7	6	2	246
Field %	61.38	18.70	7.32	6.50	2.85	2.44	0.81

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.

Table 2.

Haplotype group representatives and their highest identity matches from GenBank as of August 29, 2019.

Haplotype group (this study)	Blasted NID No. (this study)	COI Match Accession No.	Corresponding GenBank Name	Identity%	D2–D3 Match Accession No.	Corresponding GenBank Name	Identity%
P. neglectus	N10756	KY424103	P. neglectus	99.8	MG906766	P. neglectus	99.7
P. penetrans	N6260	KY816936	P. penetrans	99.8	JX046986	P. penetrans	98.9
P. thornei	N7566	KY828316	P. thornei	99.5	KYT213559	P. thornei	100
P. alleni	N3717	MK045330	P. alleni	99.3	MN251270	P. alleni	100
P. zeae	N8934	KY424056	P. zeae	99.5
P. crenatus	N8539	KY816943	P. crenatus	100	KY468865	P. crenatus	98.1
P. vulnus	N7113	GQ332425	P. vulnus	99.3
P. scribneri	N7839	MH016378	P. scribneri	99.5	MK292133 KY828290 EU130841	P. scribneri P. hexincisus P. agilis	99.7 99.7 99.7
P. hexincisus	N7726	MH016378	P. scribneri	81.0	KX842632 EU130841 KY828291	P. scribneri P. agilis P. hexincisus	100 98.8 98.9
Pratylenchus sp. 1	N6350	KU198944	Pratylenchus sp.	83.0	MN251269	Pratylenchus sp.	99.6
Pratylenchus sp. 2	N8139	MK045330	P. alleni	79.3	MN251273	Pratylenchus sp.	100
Pratylenchus sp. 3	N3908	MK045330	P. alleni	83.4
Pratylenchus sp. 4	N6402	KY424092	P. scribneri	88.6
Pratylenchus sp. 5	N10767	KY424092	P. scribneri	87.3	MH730449	P. scribneri	99.2
Pratylenchus sp. 6	N6245	KY424092	P. scribneri	88.5
Pratylenchus sp. 7	N10770	KY424093	P. scribneri	85.2
Pratylenchus sp. 8	N10685	KY424092	P. scribneri	89.1	KT175531	P. pseudocoffeae	96.2
Pratylenchus sp. 9 (1)	N10841	KY424092	P. scribneri	80.1	KT175531	P. pseudocoffeae	95.8
Pratylenchus sp. 9 (2)	N8930	KY424092	P. scribneri	79.7	KT175531	P. pseudocoffeae	95.7
Pratylenchus sp. 10 (1)	N10856	MK045330	P. alleni	78.7
Pratylenchus sp. 10 (2)	N10853	MK045330	P. alleni	79.5

Table 3.

Estimates of evolutionary divergence (p-distances) over sequence pairs within (bold) and between groups.

	P. alleni	P. crenatus	P. hexincisus	P. neglectus	P. penetrans	P. scribneri	P. thornei	P. vulnus	P. zeae
P. alleni	0
P. crenatus	0.308	0.001
P. hexincisus	0.216	0.355	0.022
P. neglectus	0.28	0.33	0.362	0.009
P. penetrans	0.322	0.348	0.399	0.298	0.038
P. scribneri	0.172	0.327	0.199	0.317	0.351	0.003
P. thornei	0.332	0.357	0.391	0.3	0.319	0.359	0
P. vulnus	0.235	0.328	0.321	0.317	0.325	0.29	0.33	0.007
P. zeae	0.33	0.377	0.399	0.334	0.354	0.367	0.329	0.348	0.002
sp. 1	0.209	0.3	0.283	0.304	0.332	0.231	0.326	0.263	0.327
sp. 2	0.228	0.357	0.222	0.373	0.396	0.232	0.389	0.342	0.409
sp. 3	0.182	0.352	0.231	0.324	0.357	0.189	0.359	0.291	0.344
sp. 4	0.174	0.316	0.207	0.316	0.331	0.118	0.348	0.274	0.356
sp. 5	0.195	0.33	0.181	0.334	0.352	0.125	0.359	0.302	0.361
sp. 6	0.187	0.334	0.197	0.315	0.358	0.108	0.354	0.296	0.364
sp. 7	0.171	0.299	0.212	0.3	0.333	0.153	0.327	0.256	0.341
sp. 8	0.165	0.308	0.221	0.299	0.345	0.12	0.327	0.278	0.359
sp. 9	0.202	0.33	0.244	0.338	0.353	0.206	0.347	0.265	0.361
sp. 10	0.195	0.342	0.214	0.35	0.35	0.211	0.351	0.262	0.372
	sp. 1	sp. 2	sp. 3	sp. 4	sp. 5	sp. 6	sp. 7	sp. 8	sp. 9	sp. 10
sp. 1	0.005
sp. 2	0.294	0.077
sp. 3	0.223	0.205	0.004
sp. 4	0.219	0.233	0.186	n/c^a
sp. 5	0.253	0.209	0.199	0.132	0
sp. 6	0.236	0.223	0.191	0.112	0.079	0
sp. 7	0.199	0.235	0.185	0.16	0.163	0.159	0
sp. 8	0.204	0.254	0.196	0.127	0.158	0.132	0.136	0
sp. 9	0.237	0.246	0.221	0.2	0.201	0.202	0.207	0.206	0.048
sp. 10	0.25	0.212	0.226	0.207	0.208	0.21	0.216	0.213	0.156	0.034

1 The number of base differences per site from averaging over all sequence pairs between groups are shown. The analysis involved 915 nucleotide sequences. ^aNot possible to estimate evolutionary distances.

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.

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.

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.

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 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 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.

County location of surveyed fields with *Pratylenchus neglectus* (red), *P. scribneri* (blue), and fields with a mixture of both species (gray).

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Articles in this issue

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 online: Dec 10, 2019

Published in print: Jan 1, 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,

Pratylenchus,

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.

Volume 51 (2019): Issue 1 (January 2019)

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

Figures & Tables

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Table 1.

Figure 2:

Table 2.

Table 3.

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