Diversity of long-spined sea urchins (Diadema spp.) in the Indo-Malay archipelago

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Vimono IB, Borsa P, Hocdé R, Arbi UY, Kadarusman, Marasabessy F, Tuhumury RAN, Faiqoh E, Pouyaud L, 2025. Diversity of long-spined sea urchins (Diadema spp.) in the Indo-Malay archipelago. Museu de Ciències Naturals de Barcelona, checklist dataset:

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El publicador y propietario de los derechos de este trabajo es Museu de Ciències Naturals de Barcelona. Esta obra está bajo una licencia Creative Commons de Atribución/Reconocimiento-NoComercial (CC-BY-NC 4.0).

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Palabras clave

Occurrences; Visual survey; COI barcoding; New records; D. paucispinum; D. savignyi; D. setosum

Contactos

Cobertura geográfica

Visual surveys were made on the reef flat or reef crest in 52 coastal locations across the Indo-Malay archipelago, as detailed in appendix 1. The identification of long-spined sea-urchin species in the field was based on iridophore colour and pattern, as well as the colour of the anal ring (Chow et al 2016; appendix 2). Diadema clarki and D. savignyi are characterised by five Y-shaped blue iridophore lines running along the naked space of the interambulacral areas (Chow et al 2016). The central axis of the Y-shaped blue lines is represented by two parallel lines and twice as long as the V-component in D. savignyi, while the Y-shaped blue line consists of a single line similar in length to the V-component in D. clarki. To the exclusion of all other Indo-West Pacific Diadema species, D. setosum exhibits an orange ring along the anal sac combined with five white dots at the end interambulacral and iridescent dotted blue lines on the aboral side (appendix 2). Photographs were taken on site (fig. 1) or shortly after capture. The coordinates of the survey sites were verified in Google Earth (https:// earth.google.com/). Maps of records for each species were completed under Illustrator (Smith 2010).

Cobertura taxonómica

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Cobertura temporal

Datos del proyecto

Long-spined sea urchins (Diadema spp.) are among the most abundant echinoids of coral reefs and lagoons. They play a key ecological role as mainly omnivorous grazers and detritus feeders, helping to control algal growth and maintain the balance of the reef ecosystems (Lawrence and Sammarco 1982; Sammarco 1982; Hughes et al 1987; Alves et al 2003; Knowlton 2006; Dumont et al 2013; Lessios 2016; Do Hung Dang et al 2020; Muthiga and McClanaghan 2007, 2020). The genus Diadema includes eight extant species (Kroh 2015; WoRMS Editorial Board 2023): D. africanum Rodríguez, Hernández, Clemente & Coppard, 2013, D. antillarum (Philippi, 1845), D. clarki Ikeda, 1939, D. mexicanum A. Agassiz, 1863, D. palmeri Baker, 1967, D. paucispinum A. Agassiz, 1863, D. savignyi (Audouin, 1809), and D. setosum (Leske, 1778). Three of these species (D. antillarum, D. paucispinum and D. setosum) each harbour a pair of geographically differentiated mitochondrial lineages, and may each represent a pair of cryptic species (Lessios et al 2001). Another of the mitochondrial lineages reported by Lessios et al (2001), “Diadema sp.” from the Marshall Islands and the Japanese archipelago, has recently been identified as D. clarki (Chow et al 2016). Hybridization between D. savignyi and D. setosum has been observed in the western Pacific Ocean, although this is assumed to be a marginal phenomenon (Lessios and Pearse 1996). Occasional hybrids between D. paucispinum and each of the two latter species have also been documented (Lessios and Pearse 1996). The geographic setting of the present study is the Indo-Malay archipelago, which mostly coincides with the so-called ‘Coral Triangle’ (Allen 2007; Hoeksema 2007; Barber 2009; Veron 2009; Carpenter et al 2011). This region is reputed as the epicentre of marine biodiversity (Gray 1997; Barber 2009; Gaither and Rocha 2013; Keyse et al 2018). Coral reefs and adjacent ecosystems in this region are severely threatened by coastal development, mining, pollution, deforestation and overfishing (Burke et al 2012). Studying the ecology of species in these ecosystems should help improve our knowledge about them, which in turn could help monitor threats, and inform conservation policies (Danielsen et al 2000; Nichols and Williams 2006). The geographic complexity of the Indo-Malay archipelago favoured geographic refugia during episodes of low sea level in the Pleistocene (Gray 1997; Carpenter et al 2011; Pellissier et al 2014), promoting speciation (Coyne and Orr 1989; Servedio and Noor 2003). In this region, taxa from both the Indian and the western Pacific oceans co-occur with endemics (Woodland 1983; Allen 2007; Veron et al 2009). To date, no review of Echinoderm diversity in this region has been published, unlike in e.g. reef fishes (Allen 2007), Scleractinian corals (Hoeksema 2007; Veron et al 2009), Echinolittorina spp. gastropods (Reid et al 2006) or giant clams (DeBoer et al 2014). However, a few studies have explored within-species genetic diversity in a handful of Echinoderm species. These include the seastars Linckia laevigata and Protoreaster nodosus (Crandall et al 2008a, 2014), the pincushion seastar Culcita novaeguineae (Yasuda et al 2014) and the long-spined sea urchin Diadema setosum (Vimono et al 2023). The recent report of D. clarki in the eastern Indonesian seas (Moore et al 2019), then unknown from this region of the Indo-West Pacific, and the paucity of records for other Diadema species (Moore et al 2019, and references therein) call for a comprehensive inventory of long-spined sea-urchin species in the Indo-Malay archipelago. This is the purpose of the present paper. In the present study, records were genetically validated by sequencing the cytochrome-oxidase subunit I (COI) gene. The COI marker, which has been chosen as a potential universal barcode in animals (Hebert et al 2003), provides accurate species diagnosis in echinoderms and may help flag potential cryptic species (Ward et al 2008).

Personas asociadas al proyecto:

Métodos de muestreo

Long-spined sea urchin Diadema spp. individuals were collected by hand picking on reef flats and crests, from 0.5 m to 4 m deep, between 2019 and 2021 (table 1). Additional sampling details are provided in appendix 1. The tissue collected consisted of a piece of 10-20 mm3 of gonad, or of muscle excised from the interior of the mouth. Tissue samples were either immediately placed into 2-mL tubes filled with 96% ethanol or temporarily (up to one week) preserved in salt when ethanol was not available (Caputo et al 2011). Salt-preserved samples were transferred to 96% ethanol upon return to the laboratory. Entire specimens were preserved in 70% ethanol. The protocols for DNA extraction, DNA amplification of a 1157-bp long fragment of the COI gene by polymerase-chain reaction, and Sanger nucleotide sequencing have been detailed previously (Vimono et al 2022, 2023). Briefly, genomic DNA was extracted using the Nucleospin® 96 Tissue kit (Macherey-Nagel, Düren, Germany) following the manufacturer’s instructions. Two separate polymerase-chain reactions (PCRs) were run according to previous protocols (Ivanova and Grainger 2007). Vimono et al’s (2023) primer pairs DF1/DR1 and DF2/DR2 were used, respectively. Primers DR1 and DF2 were also used as sequencing primers. At least one blank per plate was used as negative control at each step, from extraction to sequencing. All tissue samples were successfully extracted and all DNA extracts were successfully amplified and sequenced (table 1).

Descripción de la metodología paso a paso:

1. Both forward and reverse sequence chromatograms were cross-inspected visually under CHROMAS v.2.6.5 (Technelysium Pty. Ltd., Brisbane), to ensure accuracy. The ends of sequences that eventually showed ambiguous nucleotides (i.e. weak peaks, or overlapping successive peaks) were in all cases eliminated by trimming. All nucleotide sequences generated in the present study were aligned with homologous sequences from GENBANK (Benson et al 2017) nos. AY012728-AY012747 (Diadema spp.: Lessios et al 2001) chosen as references, and GenBank nos. OP310072-OP310789 (D. setosum: Vimono et al 2022), using the CLUSTALW algorithm implemented in MEGA X v.10.0.4 (Kumar et al 2018). The total sequence dataset (N = 893) was then trimmed to a core length of 586 bp between nucleotide sites homologous to sites nos. 6532 and 7117 of sequence GENBANK no. KX385835, which is the reference sequence for the complete mitochondrial genome of D. setosum (Li et al 2016). Based on this sequence dataset, the best nucleotide substitution model was selected as the one with the lowest Bayesian information criterion score under MEGA X. A maximum-likelihood (ML) tree was constructed under MEGA X. Node robustness was tested by bootstrapping nucleotide sites (1000 random pseudo-replicates) across the aligned sequence dataset, using MEGA X.

Referencias bibliográficas

1. Vimono IB, Borsa P, Hocdé R, Arbi UY, Kadarusman, Marasabessy F, Tuhumury RAN, Faiqoh E, Pouyaud L, 2025. Diversity of long-spined sea urchins (Diadema spp.) in the Indo-Malay archipelago. Arxius de Miscel·lània Zoològica 23,

Metadatos adicionales