Determination of genetic diversity between natural and cultured populations of Common Dentex () fish in the East Aegean Sea

Ali Kayaci; Mehmet Fatih Can; Yusuf Güner; Fatih Güleç

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Determination of genetic diversity between natural and cultured populations of Common Dentex (Dentex dentex) fish in the East Aegean Sea

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| 18. März 2023

Oceanological and Hydrobiological Studies

Band 52 (2023): Heft 1 (March 2023)

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Article Category: Original research paper

Online veröffentlicht: 18. März 2023

Seitenbereich: 52 - 67

Eingereicht: 02. Dez. 2022

Akzeptiert: 21. Dez. 2022

DOI: https://doi.org/10.26881/oahs-2023.1.04

© 2023 Ali Kayaci et al. published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Six different locations where fish samples were obtained

Some pictures of the common dentex samples obtained from the locations

Sample coding system used in the present study

On the left axis is the Cycle number (Ct, orange line) and on the right axis is the melting temperature (Tm, blue line) data of the QPCR experiments for the COI target gene of the D. dentex samples collected from different locations.

Median Joining network to sample haplotypes and representation of haplogroups of Common Dentex

Phylogenetic reconstruction of 53 Common Dentex COI sequences grouped with respect to locations using Nei’s Dxy distance matrix. W: wild, C: culture.

The cladogram NJ tree created with the Treeview obtained according to Wright’s F statistic for the common dentex samples at the stations in the study. W: wild, C: culture.

Haplotype structure of D. dentex samples with respect to nucleotide variation in the COI region

Nucleotide positions in COI region
Haplotype Number	Frequency	19	20	37	47	54	65	80	98	111	126	129	131	150	165	171	192	238	247	284	342	398	399	406	407	441	447	455
H 1	25	T	A	G	A	A	T	A	C	T	T	A	A	C	T	T	G	T	A	A	A	C	T	T	C	T	T	G
H 2	1	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 3	1	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	C	.	.	.	.	.
H 4	1	.	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	C	.
H 5	1	.	.	.	.	.	.	.	A	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 6	1	G	.	.	C	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 7	1	G	C	A	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 8	1	G	C	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.
H 9	2	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 10	1	G	C	A	.	.	G	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.
H 11	1	G	C	A	C	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 12	1	G	C	A	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 13	1	G	C	A	.	G	G	.	.	.	.	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.
H 14	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	.	.	.	.
H 15	2	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 16	2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.
H 17	1	G	.	A	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.
H 18	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.
H 19	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.
H 20	1	.	.	.	.	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 21	1	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	C	.	.	.	.	G	.	.	.	.
H 22	1	G	C	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 23	1	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.
H 24	1	.	.	.	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H 25	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	A	.	C
H 26	1	.	.	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

Sampling locations of common dentex and number of the samples per location

No.	Sampling Location	Sample Code	Number of samples
1	Karaburun- Natural	I-W	9
2	Karaburun- Culture	I-C	9
3	Çeşme-Natural	II-W	5
4	Kuşadası-Natural	III-W	10
5	Güllük-Natural	IV-W	5
6	Bodrum-Natural	V-W	4
7	Çanakkale-Natural	VI-W	6
8	Antalya-Natural	VII-W	5
TOTAL			53

Haplotype groups and sample codes in the same haplotype group

Haplotypes	Sample Code
H 1	I-W-D.dentex-1, I-W-D.dentex-2, I-W-D.dentex-3, I-W-D.dentex-7, I-W-D.dentex-8, I-W-D.dentex-9, I-W-D.dentex-10, I-C-D.dentex-9, II-W-D.dentex-4, II-W-D.dentex-5, III-W-D. dentex-2, III-W-D.dentex-4, III-W-D.dentex-8, III-W-D.dentex-9, III-W-D.dentex-10, IV-W-D.dentex-2, IV-W-D.dentex-4, IV-W-D.dentex-5, IV-W-D.dentex-6, V-W-D.dentex-2, V-W-D. dentex-4, VI-W-D.dentex-2, VI-W-D.dentex-4, VI-W-D.dentex-5, VII-W-D.dentex-5
H 2	I-W-D.dentex-4	H 15	III-W-D.dentex-1, III-W-D.dentex-5
H 3	I-W-D.dentex-5	H 16	III-W-D.dentex-3, VI-W-D.dentex-3
H 4	I-C-D.dentex-1	H 17	III-W-D.dentex-6
H 5	I-C-D.dentex-2	H 18	III-W-D.dentex-7
H 6	I-C-D.dentex-3	H 19	V-W-D.dentex-1
H 7	I-C-D.dentex-4	H 20	V-W-D.dentex-3
H 8	I-C-D.dentex-5	H 21	VI-W-D.dentex-1
H 9	I-C-D.dentex-7, IV-W-D.dentex-1	H 22	VI-W-D.dentex-6
H 10	I-C-D.dentex-8	H 23	VII-W-D.dentex-1
H 11	I-C-D.dentex-10	H 24	VII-W-D.dentex-2
H 12	II-W-D.dentex-1	H 25	VII-W-D.dentex-3
H 13	II-W-D.dentex-2	H 26	VII-W-D.dentex-4
H 14	II-W-D.dentex-3	H 26	VII-W-D.dentex-4

Genetic diversity and neutrality tests of the D.dentex populations with respect to locations

Population	Sample size (n)	N Haplotype number	Haplotype Diversity (h)	PS	PIR	Nucleotide diversity (π)	Taijm’a’s D	Fu’s Fs
I-C. D.dentex	9	9	1.000	6	13	0.0097(± 0.0012)	−1.513	−0.380
I-W. D.dentex	9	3	0.417	4	7	0.0014 (± 0.0007)	−0.176	−5.174**
II-W. D.dentex	5	4	0.900	1	6	0.0076 (± 0.0022)	0.498	−0.036
III-W. D.dentex	10	5	0.756	0	1	0.0031 (± 0.0005)	−1.276	−1.320
IV-W. D.dentex	5	2	0.400	0	2	0.0008 (± 0.0007)	−0.817	0.090
V-W. D.dentex	4	3	0.833	0	7	0.0021 (± 0.0007)	−0.710	−0.887
VI-W. D.dentex	6	4	0.800	0	7	0.0049 (± 0.0014)	−1.390*	−0.219
VII-W. D.dentex	5	5	1.000	0	3	0.0059 (± 0.0014)	−1.162	−2.371*

Genetic distance calculation of D. dentex populations with respect to where the stations’ samples were collected from (Nei’s dxy and Da method)

Da
		I-C	I-W	II-W	III-W	IV-W	V-W	VI-W	VII-W
Dxy*
	Karaburun I-C	0	0.00148	−0.00045	0.00080	0.00141	0.00169	0.00060	0.00160
	Karaburun I-W	0.00701	0	0.00056	0.00009	0.00000	0.00000	−0.00008	0.00000
	Çeşme II-W	0.00815	0.00503	0	0.00014	0.00050	0.00084	0.00000	0.00084
	Kuşadası III-W	0.00717	0.00233	0.00545	0	0.00006	0.00014	−0.00028	−0.00004
	Güllük IV-W	0.00666	0.00112	0.00470	0.00201	0	0.00000	0.00000	0.00000
	Bodrum V-W	0.00757	0.00175	0.00566	0.00273	0.00147	0	0.00000	0.00000
	Çanakkale VI-W	0.00788	0.00307	0.00622	0.00370	0.00287	0.00349	0	−0.00042
	Antalya VII-W	0.00936	0.00363	0.00755	0.00444	0.00335	0.00398	0.00496	0

Distance matrix obtained according to Wright’s F statistics for the Common Dentex (Dentex dentex) sample at the stations in the study

	I-C	I-W	II-W	III-W	IV-W	V- W	VI-W	VII-W
Karaburun I-C	0.00000
Karaburun I-W	0.22466*	0.00000
Çeşme II-W	0.08522	0.00077	0.00000
Kuşadası III-W	0.03716	0.07255	−0.02564	0.00000
Güllük IV-W	−0.08257	0.16667	0.04412	0.00474	0.00000
Bodrum V-W	0.21178	−0.02273	−0.03261	0.04085	0.16667	0.00000
Çanakkale VI-W	0.03226	0.01562	−0.08541	−0.05174	−0.00737	−0.02362	0.00000
Antalya VII-W	0.02463	0.04000	−0.06047	−0.05882	−0.01205	0.00415	−0.08711	0.00000

Map coordinates of the stations where common dentex samples were obtained

Stations	Common Dentex Natural	Common Dentex Culture
(I) Karaburun	Foça offshore38°48′34.8″N26°38′09.4″E	Akvatur Fish Farm38°30′29.3″N26°23′12.4″E
(II) Çeşme*	Çeşme fish pond38°22′07.1″N26°19′39.6″E
(III) Kuşadası**	Çağlar fishery agency37°48′51.1″N27°08′58.4″E
(IV) Güllük	Güllük Gulf37°14′25.0″N27°35′32.8″E
(V) Bodrum	Bodrum Şenol Fishery37°02′08.2″N27°25′54.7″E
(VI) Çanakkale	Engin Fishery40°08′38.5″N26°24′19.6″E
(VII) Antalya	Antalya offshore36°50′4.98″N30°38′47.14″E

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Determination of genetic diversity between natural and cultured populations of Common Dentex (Dentex dentex) fish in the East Aegean Sea

Article Category: Original research paper

Online veröffentlicht: 18. März 2023

Seitenbereich: 52 - 67

Eingereicht: 02. Dez. 2022

Akzeptiert: 21. Dez. 2022

DOI: https://doi.org/10.26881/oahs-2023.1.04

© 2023 Ali Kayaci et al. published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

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Figure 7

Haplotype structure of D. dentex samples with respect to nucleotide variation in the COI region

Sampling locations of common dentex and number of the samples per location

Haplotype groups and sample codes in the same haplotype group

Genetic diversity and neutrality tests of the D.dentex populations with respect to locations

Genetic distance calculation of D. dentex populations with respect to where the stations’ samples were collected from (Nei’s dxy and Da method)

Distance matrix obtained according to Wright’s F statistics for the Common Dentex (Dentex dentex) sample at the stations in the study

Map coordinates of the stations where common dentex samples were obtained