Research Article |
Corresponding author: Faezeh Yazdani Moghaddam ( faezeh.um@gmail.com ) Academic editor: Nalani Schnell
© 2023 Ehsan Damadi, Faezeh Yazdani Moghaddam, Mehdi Ghanbarifardi.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Damadi E, Yazdani Moghaddam F, Ghanbarifardi M (2023) Species delimitation, molecular phylogeny and historical biogeography of the sweetlips fish (Perciformes, Haemulidae). Zoosystematics and Evolution 99(1): 135-147. https://doi.org/10.3897/zse.99.96386
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The subfamily Plectorhinchinae (sweetlips) is composed of poorly-known species with high commercially and ecologically values that exhibit phenotypic plasticity and various morphologies. Few studies have assessed the validity of sweetlips, intergeneric relationships and evolutionary survey in this subfamily, which have not yet been resolved. This study investigated the DNA sequences of (1) the mitochondrial COI gene to delimit species, and (2) two mitochondrial (COI and Cyt b), and one nuclear (RAG1) markers to infer phylogenetic relationships and evolutionary and biogeographic history. The molecular results could differentiate Diagramma punctatum from the other species, but failed to distinguish D. labiosum as a distinct species with considerably lower genetic distances for the COI (0.53%) and Cyt b (0.51%) markers. However, additional taxonomic investigations are required to shed light on this issue. All previously described nominal species of sweetlips in the northwest Indian Ocean were found to be well supported. The monophyly of Plectorhinchus is not supported and Diagramma pictum and D. punctatum should be assigned to the genus Plectorhinchus. The biogeographic history of Plectorhinchinae likely originated in the Indo-Pacific ca. 34 Ma (30–39 Ma; late Eocene/ middle Oligocene) and subsequently colonised the Western Indian Ocean and the Central Indo-Pacific. Maximum diversification within the subfamily occurred from the middle Miocene to Pliocene, coinciding with dispersal and vicariance events. Diversification was probably driven by both biological and geographical factors.
biogeography, mito-nuclear, molecular systematics, Plectorhinchus
Accurate species delimitation and phylogenetic reconstruction are vital to understand biodiversity assessments, conservation management, evolutionary patterns, and processes (
A total of 254 individuals belonging to 29 species, including both our new samples and the sequences taken from GenBank and the Barcode of Life Data systems (BOLD systems) were analysed (Suppl. material
Genomic DNA was extracted from the muscle tissue following the BioGene kit protocol. The reactions volume of polymerase chain reaction (PCR) was 25 μl, including 2 μl template DNA, 9.5 μl ddH2O, 12.5 μl Master Mix and 0.5 μl of each forward and reversed primer with 10 μM concentration. Two mitochondrial and one nuclear gene were amplified as follows: 617 bp of the CO1 was amplified using universal primers CO1LBC_F and CO1HBC_R (
The quality of new sequences was probed using the CLC Genomics Workbench v.3.6.5 software (QIAGEN Bioinformatics). The sequences were aligned in MAFFT v.7.463 and edited with BIOEDIT v.7.2 software (
A calibrated time-tree of Plectorhinchinae was estimated from the combined data set (COI, Cyt b and RAG1: 3157 total bp) in BEAST v.2.6.2 (
The ancestral area in Plectorhinchinae was inferred using the BioGeoBEARS analysis in RASP v.4 (
Molecular species delimitation was used from four different methods, including; (A): the Automatic Barcode Gap Discovery (ABGD) (
We assembled a total of 217 COI sequences (34 newly developed plus 183 archived; 617 bp) from 29 nominal Plectorhinchinae species. D. punctatum and Plectorhinchus pictus were sequenced for the first time. Novel COI barcodes were provided for Plectorhinchus flavomaculatus, P. gaterinus and P. gibbosus for the first time from the Northern Indian Ocean (NIO). Of 29 nominal species studied, the coalescent-based delimitations (bPTP, GMYC) yielded 27 MOTUs, whereas the distance-based methods (ABGD and ASAP) yielded 26 MOTUs (Fig.
Species | Maximum intra-group distance | Nearest-Neighbour (NN) | Distance to NN |
---|---|---|---|
Diagramma pictum | 0.17 | D. labiosum | 0.53 |
D. punctatum | 0.00 | P. centurio | 3.45 |
Plectorhinchus albovittatus | 0.00 | P. caeruleonothus | 2.31 |
P. caeruleonothus | 0.19 | P. albovittatus | 2.31 |
P. centurio | 0.35 | D. punctatum | 3.45 |
P. chaetodonoides | 0.43 | P. centurio | 8.75 |
P. chrysotaenia | 0.00 | P. playfairi | 16.30 |
P. chubbi | 0.08 | P. sordidus | 3.52 |
P. cinctus | 0.64 | P. gibbosus | 13.44 |
P. diagrammus | 0.00 | P. lessonii | 1.20 |
P. flavomaculatus | 0.31 | P. makranensis | 12.62 |
P. gaterinus | 0.28 | P. caeruleonothus | 12.18 |
P. gibbosus | 0.69 | P. cinctus | 13.44 |
P. lessonii | 0.08 | P. diagrammus | 1.20 |
P. lineatus | 0.06 | P. polytaenia | 7.17 |
P. macrolepis | 0.00 | P. plagiodesmus | 13.84 |
P. macrospilus | 0.00 | P. lessonii | 4.10 |
P. makranensis | 0.01 | P. schotaf | 5.23 |
P. orientalis | – | P. vittatus | 7.97 |
P. pictus | 0.00 | P. cinctus | 13.55 |
P. picus | 0.08 | D. punctatum | 8.38 |
P. plagiodesmus | 0.00 | P. pictus | 13.24 |
P. playfairi | 0.16 | P. chubbi | 4.61 |
P. polytaenia | 0.00 | P. lineatus | 7.17 |
P. schotaf | 0.13 | P. makranensis | 5.23 |
P. sordidus | 0.10 | P. chubbi | 3.52 |
P. unicolor | 0.23 | P. chubbi | 5.80 |
P. vittatus | – | P. orientalis | 7.97 |
Molecular diversity indices for D. pictum and D. labiosum based on mitochondrial DNA (COI) sequence data. Numbers in bold denotes significance (P < 0.05) and for Fu’s Fs (P < 0.02).
Statistics | D. pictum | D. labiosum | |||
---|---|---|---|---|---|
Japan to Indonesia (WP) | Iran to Bangladesh (NIO) | Australia (WP) |
All samples | ||
Number of individuals (N) | N = 44 | N = 26 | N = 7 | N = 76 | |
Expansion time (years) | – | – | – | 17,647-35,294 | |
Number of haplotypes (Hn) | 8 | 6 | 3 | 17 | |
Haplotype diversity (Hd ± SD) | 0.579 ± 0.075 | 0.560 ± 0.073 | 0.600 ± 0.215 | 0.624 ± 0.051 | |
Nucleotide diversity (π ± SD) | 0.0018 ± 0.0011 | 0.0021 ± 0.0016 | 0.0021 ± 0.0017 | 0.0024 ± 0.0018 | |
Tajima’s D | -1.218 | -1.636 | -1.233 | -1.783 | |
Fu’s FS | -3.739 | -1.067 | -0.189 | -8.801 | |
R2 | 0.058 | 0.060 | 0.062 | 0.038 | |
ΦST | Australia | 0.084 | 0.072 | – | |
Iran to Bangladesh | 0.049 | – | – |
Bayesian Inference tree, based on the COI showing the results of species delimitation algorithms. The vertical bars indicate species delimitation analyses. The black circles indicate nodes with supports (ML bootstrap BP ≥ 75% and BI probability PP ≥ 0.95), orange circles (BP ≤ 75% and BI PP ≥ 0.95) and blue circles (PP ≤ 0.95 and ML BP ≤ 75%).
Median‐joining network obtained of 617 bp of mitochondrial COI for Diagramma species (A). Map depicting the geographical distribution of 17 haplotypes (B). Circle sizes are relative to haplotype frequency. Numbers between haplotypes represent mutational steps between haplotypes. Colour circles indicate species of D. pictum (red: Persian Gulf to Bangladesh, green: China and Indonesia) and D. labiosum (orange: Australia), D. punctatum (black: Red Sea).
We analysed 254 COI DNA sequences (617 bp) which show 325 variable sites; the Cyt b gene consisting of 1117 bp showed 295 variable positions; and Rag1 consisting of 1440 bp showed 184 variable sites. Neither gaps nor stop codons were observed in the final alignment. ML and BI analyses with the combined dataset (mtDNA and nuclear) revealed that the phylogenetic relationships of sweetlips species had the highest resolution (Fig.
Phylogeny recovered by the Bayesian Inference (BI) and Maximum Likelihood (ML) analyses for the Cyt b, COI and RAG1 dataset. The black circles indicate nodes with supports (ML bootstrap BP ≥ 75% and BI probability PP ≥ 0.95), orange circles (BP ≤ 75% and BI PP ≥ 0.95) and blue circles (PP ≤ 0.95 and ML BP ≤ 75%).
The Haemulidae diverged from Lutjanidae ~ 49 Ma (early to middle Eocene, 95% HPD: 43.6–55.2 Ma) and then Plectorhinchinae divided into two main clades (A–B) and two subclades (I–II) (Fig.
Time-calibrated phylogeny, based on combined mitochondrial (COI, Cyt b) and nuclear (RAG1) genes, inferred from the BEAST analysis of the Plectorhinchinae. Numbers in the horizontal purple bars represent the 95% Highest Posterior Density intervals for each estimated event. The black circles (pp ≥ 0.95) and orange circles (pp < 0.95). A: Parapristipoma, B: Plectorhinchus.
This study represents the first attempt to delimit the species boundaries and evolutionary and biogeographic history of marine fish species in Plectorhinchinae. The present study corroborates the findings of the previous molecular studies that show paraphyly of the Plectorhinchus without the inclusion of Diagramma (
According to the molecular data, Plectorhinchus is divided into two subclades (Fig.
In our analyses, specimens from 29 nominal species were delimited between 26 and 27 consensus MOTUs. In general, low interspecific genetic divergences were observed in some of the MOTUs within Plectorhinchus, which focuses on the barcoding analysis in closely-related species. This situation was formerly reported in haemulid within Anisotremus (
Our biogeographic findings exhibit a complex history highlighting the role of both biological and geographical factors in the diversification and evolution within the Haemulids. The first diversification, i.e. the split of Haemulids from Lutjanids as a sister lineage in the Eocene, could be related to the ice sheet formed in the Antarctic and reduced atmospheric CO2 level (
The findings of the present study on sweetlips (Plectorhynchinae) not only shed light on the interrelationships and evolutionary history, but also opened new avenues for research. The results of this study provide a framework to shed light on the probable origin and factors involved in the diversification of the IWP Plectorhynchinae. The contemporary species have a common ancestor that comes from the present day IWP and the current geographical distribution appears to be related to vicariance and dispersal events. It indicates that Diagramma species were divided 4.1 to 2.3 Mya ago into ancestral Diagramma punctatum in the Indian Ocean, directly followed by the WP and recently isolated species. These findings raise the possibility that recent genetic divergence have given rise to colour morphotypes as emerging species on coral reefs.
We greatly thank Dr. Joseph D. DiBattista and Dr. Brian W. Bowen for their valuable comments on population genetics. The authors are especially grateful to Mohamed Awad for providing tissue specimens from Red Sea (Egypt). We would like to thank local fishermen for their help in collecting specimens. Funding support for this research was provided by Ferdowsi University of Mashhad and University of Sistan and Baluchestan in Iran (grant number 46162).
Sampling information and GenBank accession numbers for the specimens included in the phylogenetic analyses
Data type: table (excel file)