Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus)

Benthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490–0.900, nucleotide diversity, π = 0.0010–0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118–0.216; π = 0.0004–0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.


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Pelvic fin length (VL) The length is measured from anteriormost pelvic base to the tip of the longest pelvic-fin ray.

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Pectoral fin length (PL) The length is taken from by the uppermost of pectoral base to the tip of the longest rays.

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Anal base length (ABL) Distance from origin of anal base to the base of the posteriormost ray.

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Predorsal length (PDL) The distance from the median anterior margin of the upper lip to the origin of the dorsal base of first dorsal base fin.

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Preanal length (PAL) The distance from the median anterior margin of the upper lip to the origin of the anal base.

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Prepectoral length (PPL) The distance from the median anterior margin of the upper lip to the base of the uppermost pectoralfin ray.

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Prepelvic length (PVL) The distance from the median anterior margin of the upper lip to the base of the anteriormost pelvicfin ray. 26 Length of longest anal branched ray (LABR) The length from base to the tip of longest anal branched ray.

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Length of longest dorsal branched ray (LDBR) The length from base to the tip of longest dorsal branched ray.

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Length of first dorsal spine (LDS1) The distance from base to the tip of first dorsal spine ray.

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Caudal peduncle depth (CPD) The least depth of the peduncle. Supracleithral spine Number of prominent spine exposed from bone. 5 Preopercular spine 6 Subopercular spine 7 Basipterygial processes 8 Dorsal-fin ray Counted separately part of each spine and soft rays (Spinesunpaired and unsegmented elements, labeling design by roman numerals; soft rayspaired and segmented elements, labeling design by Arabic numerals). *For the last pterygiophore, supporting one or two ray elements): counted as 1 ½ if some aspects have 2 rays. 9 Anal-fin ray Counted in a procedure similar to the dorsal-fin ray count. 10 Pectoral-fin ray Due to pectoral and pelvic fin is double fin, counting all soft rays only the left fin of fish body. 11 Pelvic-fin ray 12 Branched (upper + lower) at caudal fin ray Counted the branched caudal rays by separate upper and lower portions (upper caudal rays -rays connected to upper hypural plate, epurals and neural spine; lower caudal rays -rays connected to lower hypural plate parhypural and hemal spine).
Supplementary Figure S1: Mismatch distribution (pairwise number of differences) of Uranoscopus cognatus based on the CO1 gene in (a) WCT and (b) ECPM; and RAG1 gene in (c) WCT and (d) ECPM, showing the expected observed pairwise differences between the sequences with the respective frequency. The graphs were created in DnaSP 5.10 (http://www.ub.edu/dnasp/).