Population genetic structure of ornatus spiny lobster (Panulirus ornatus) in Indo – West Pacific region

Abstract

Overexploitation and changing ecosystem activities of human have put selective pressure on aquatic species, which may led to the decline of genetic diversity and population dis-connectivity [1-2]. Ornate spiny lobster (Panulirus ornatus) is an ecologically and economically important crustacean, widely distributed in Indo – Pacific region. Panulirus ornatus is the main species of farming in Asia - Pacific countries such as Australia and Vietnam [3-4]. Like most crustaceans, Panulirus ornatus have a complex metamorphic life cycle, and a long planktonic larval stages up to six months [5]. That could lead to high connectivity in local populations, even on inter-oceans scales.

The wild P. ornatus were collected in Vietnam, Australia and Sri Lanka, with 30 individuals per location. In Vietnam (VN), the samples collected in the Da Nang, Quang Ngai, Khanh Hoa and Binh Thuan, which represent the distribution area in the Central region. In Australia (AU), we collected in the eastern coast (Townsville and Brisbane). Due to geographical distance, lobster samples were collected only at one location (Negombo) in Sri Lanka (SR). The sampling location is shown in Fig. 1A. We applied 5 microsatellites loci [6] to investigate population connectivity and genetic structure.

Genetic diversity was highest in Australia (Ho/He =0.787/0.819) and lowest in Sri Lanka (Ho/He =0.620/0.782) populations. The Sri Lanka population also shows highest rates of inbreeding (G_IS = 0.207) (Tab. 1). Pairwise genetic differentiation showed statistically significant between three study populations. F_ST values ranging from 0.06 for the Vietnam - Sri Lanka comparison to 0.012 for Vietnam and Australia (P < 0.001) (Tab. 2). AMOVA results (data not showed) displayed the majority of the variation (69 %) in P. ornatus was found within individuals, and highly significant (F_IT = 0.311, P < 0.001). The proportion of variance explained by differences among populations was relative small (1 %), but significant (F_ST=0.01, P < 0.001). The Discriminant Analysis of Principal Component (DAPC) showed a clear distinction between the three populations with BIC value =3 (Fig. 1B). STRUCTURE analysis, plotted with a K of 3 as chosen by the Evanno method, do not showed a clear distinction between three populations. The Vietnam population was assigned to a first lineage with moderate certainty (45.6 % composition of the “red” lineage and 26.1 % of “green” and 28.3 % of “blue”). Sri Lanka and Australia populations were assigned to the second and third lineages with assigned for ‘red” (24.7 % and 29.8 %), “green” (37.9 % and 33.3 %), and “blue” (37.5 % and 36.8 %), respectively (Fig. 1C). Directional migration relative rates among recent P. ornatus populations range from 0.1 to 1 (Fig. 2 left). Among these, asymmetric directional migration seems to have occurred freely between populations, however, bootstrap analysis (nbs<0) showed that directional migration from Vietnam to Australia and Sri Lanka populations (Fig. 2 right). Observed gene flow for ornatus spiny lobster suggest that Vietnam population may act as a source for surrounding populations in the Indo -West Pacific. The current results are useful for understanding the spatial genetic of P. ornatus, with implications for locally fisheries and conservation management.

Table 1.  Panulirus ornatus sample site information and genetic diversity. Number of samples collected (N), number of alleles (N_a), effective number of alleles (N_e), observed (Ho) and expected (He) heterozygosity, inbreeding coefficient (G_IS), percentage of polymorphic loci (%P)

Sampling sites

(population code)

Geographic coordinates

N

N_a

N_e

Ho

He

G_IS

%P

Vietnam (VN)

12^o44'N

109^o30’E

30

10.8

5.774

0.653

0.815

0.199

100

Sri Lanka (SR)

9^o31’N

80^o11’E

30

11.6

6.568

0.620

0.782

0.207

100

Australia (AU)

25^o29’N

152^o6’E

30

11.6

7.091

0.787

0.819

0.039

100

Table 2. Pairwise values of F_ST (below the diagonal) and respective p-values (above the diagonal) of Panulirus ornatus. Significant F_ST values are in bold. *: P<0.01

Population

VN

SR

AU

VN

  -

*

*

SR

0.006

  -

*

AU

0.012

0.011

-

Fig.1. Sampling map and population genetics of Panulirus ornatus . (A) Sampling sites in Indo – West Pacific region (blue circles); (B) Scatter plots from DAPC analysis. Axes represent the first two Linear Discriminants (LD), the percentage of variability explained by each coordinate is shown in brackets. The circle represents clusters with 95% confidence limits and dots represent individuals; (C) STRUCTURE results from different K values (K=3) across the defined populations in Vietnam, Sri Lanka and Australia. Bar plots showing membership probabilities of lineage membership of individuals to assigned genetic clusters.

Fig. 2. The directional relative migration calculated by the divMigrate function (left), and the illustration of the significant directional asymmetric migration (right). Number of bootstraps (nbs) were presented along the links.