Genetic structure and recent population expansion in the commercially harvested deep-sea decapod, Metanephrops challengeri (Crustacea: Decapoda)

Figures & data

Figure 1. Map of New Zealand indicating sampling locations and areas of interest. AI: Auckland Islands; CR: Chatham Rise; CP: Castlepoint; CK: Cape Kidnappers; WI: White Island; MI: Mercury Islands. Latitude, longitude, 200 m isobath, and 1000 m isobath shown.

Table 1. Sampling information, summary statistics, estimates of genetic diversity, and neutrality test statistics for 321 partial NZ scampi CO1 sequences. For neutrality test values (Tajima's D and Fu's F-statistic), bold values indicate statistical significance. Key: n: Sample Size, S: Segregating Sites, T_S: Transitions, T_V: Transversions, H_N: Number of Haplotypes, H_P: Number of Private Haplotypes, H_D: Haplotype Diversity, π: Nucleotide Diversity (standard deviation), k: Average Number of Nucleotide Substitutions.

Sample site	Lat, long	n	S	Ts	Tv	HN	HP	HD	π	k	Tajima's D (p-value)	Fu's F-statistic (p-value)
Mercury Islands	36°20′S, 176°12′E	63	41	29	12	25	16	0.882	0.00724 (0.0008)	4.479	−1.604 ( 0.027)	−9.819 ( 0.004)
White Island	37°36′S, 177°10′E	48	30	24	7	24	15	0.922	0.00629 (0.0005)	3.889	−1.421 (0.058)	−13.123 ( <0.000)
Cape Kidnappers	39°52′S, 177°20′E	63	23	17	7	19	9	0.839	0.00541 (0.0006)	3.348	−0.984 (0.168)	−6.145 ( 0.017)
Castlepoint	40°53′S, 176°39′E	55	30	19	11	32	21	0.919	0.00680 (0.0006)	4.215	−1.212 (0.102)	−19.343 ( <0.000)
Chatham Rise	43°24′S, 176°03′E	46	24	18	6	21	10	0.850	0.00581 (0.0005)	3.603	−1.05 (0.148)	−8.775 ( 0.001)
Auckland Islands	51° 12′S, 166°41′E	46	20	14	7	22	21	0.885	0.00345 (0.0004)	2.136	−1.715 ( 0.022)	−18.649 ( <0.000)
All Sites		321	79	55	27	107	92	0.914	0.00810 (0.0003)	5.004	−1.766 ( 0.007)	−24.952 ( <0.000)

Figure 2. Bayesian analysis of population structure with k = 5. A total of 321 samples are represented. Colours represent different genetic clusters defined by BAPS. MI = Mercury Islands; WI: White Island; CK: Cape Kidnappers; CP: Castlepoint; CR: Chatham Rise; AI: Auckland Islands.

Figure 3. Median-joining haplotype network of 321 partial NZ scampi CO1 sequences. Each hatch mark represents one mutational step, while small black circles represent hypothetical unsampled haplotypes.

Table 2. Analysis of Molecular Variance (AMOVA) analyses of M. challengeri using 321 CO1 sequences with 3 a priori geographic groupings. (1) AI, MI-CR: Group 1: Auckland Islands, Group 2: Chatham Rise, Castlepoint, Cape Kidnappers, White Island, Mercury Islands. (2) AI, CR, MI-CP: Group 1: Auckland Islands, Group 2: Chatham Rise, Group 3: Castlepoint, Cape Kidnappers, White Island, Mercury Islands. (3) AI+CR, MI-CP: Group 1: Auckland Islands, Chatham Rise, Group 2: Castlepoint, Cape Kidnappers, White Island, Mercury Islands. d.f. = degrees of freedom, Var = variance component, %Var = variance component in percentage of total variation.

Groups	Among groups					Among populations within groups					Within populations
	d.f	Var	%Var	ɸCT	P-value	d.f	Var	%Var	ɸSC	P-value	d.f	Var	%Var	ɸST	P-value
AI, MI-CR	1	0.0502	10.12	0.1012	0.16901	4	0.00847	1.71	0.01899	0.00069	315	0.43751	88.18	0.11824	<0.00000
AI, CR, MI-CP	2	0.02622	5.55	0.05545	0.13129	3	0.00910	1.93	0.02038	0.00069	315	0.43751	92.53	0.07470	<0.00000
AI+CR, MI-CP	1	0.00260	0.56	0.00563	0.32337	4	0.02203	4.77	0.04795	<0.00000	315	0.43751	94.67	0.05331	<0.00000

Table 3. Pairwise ɸ_ST values determined by CO1 haplotype frequencies. Pairwise ɸ_ST values were determined using 321 CO1 sequences and the haplotype frequencies between sampling localities. These are situated below the diagonal while the p-value associated with each comparison is located above the diagonal. Bold values indicate statistical significance after Bonferroni correction.

	Auckland Islands	Chatham Rise	Castlepoint	Cape Kidnappers	White Island	Mercury Islands
Auckland Islands	–	<0 . 0000	<0 . 0000	<0 . 0000	<0 . 0000	<0 . 0000
Chatham Rise	0 . 14058	–	0.70003	0.55994	0.01940	0 . 00158
Castlepoint	0 . 11063	0.0000	–	0.51866	0.02861	0.00554
Cape Kidnappers	0 . 13850	0.0000	0.00208	–	0.06009	0 . 00149
White Island	0 . 10273	0.04614	0.01786	0.01514	–	0.21127
Mercury Islands	0 . 09644	0 . 03791	0.03946	0 . 03878	0.00480	–

Figure 4. Bayesian skyline plots with differing mutation rates reconstructing changes in NZ scampi effective population size through time. A: 7 × 10⁻⁹ substitutions/site/year. B: 1 × 10⁻⁸ substitutions/site/year. C: 1.3 × 10⁻⁸ substitutions/site/year. The blue-shaded areas represent 95% confidence intervals.

Data availability statement

The DNA sequences generated for this study are available on Figshare. DOI:10.6084/m9.figshare.11465565