Research Article
Research Article
Altrichthys alelia, a new brooding damselfish (Teleostei, Perciformes, Pomacentridae) from Busuanga Island, Philippines
expand article infoGiacomo Bernardi, Gary C. Longo§, T.E. Angela L. Quiros
‡ University of California Santa Cruz, Santa Cruz, United States of America
§ National Oceanic and Atmospheric Administration, Seattle, United States of America
Open Access


A new species of damselfish, Altrichthys alelia sp. n. is described from specimens collected in shallow water (1–8m depth) off Busuanga Island, Palawan Province, Philippines. It differs from the other two species in the genus, A. curatus and A. azurelineatus, in various features including having golden upper body lacking dark edges of dorsal and caudal fins, higher modal number of tubed lateral line scales, as well as differences in two mitochondrial markers, one nuclear marker, and RAD markers.


Apelagic fishes, Acanthochromis, CO1, Control region, RAD markers


The damselfish genus Altrichthys Allen, 1999 includes two species, the azure damselfish, Altrichthys azurelineatus (Fowler & Bean, 1928), and the guardian damselfish, Altrichthys curatus Allen, 1999, that occur on shallow coral reefs in the Calamian Archipelago, northern Palawan Province, Philippines (Allen 1999, Bernardi 2011, Bernardi et al. 2017). While conducting exploratory dives in the less-studied area of northern Busuanga Island, in the region of San José, we observed and collected Altrichthys individuals that after closer examination and laboratory work showed unique morphological and genetic characters that distinguish them from previously described Altrichthys species. We can therefore confirm the presence of a third Altrichthys species that we hereby describe as the new species Altrichthys alelia (Figure 1).

Figure 1. 

Holotype of Altrichthys alelia, shortly after capture. Photo by Gary C. Longo.

Methods and materials

Specimens were collected with hand nets while free or scuba diving in less than 8m depth. Counts and measurements follow Allen (1999). Measurements were made days to a few weeks after collection and were taken to the nearest 0.1 mm with digital calipers. Collection abbreviations are as follows: PNM = National Musem of the Philippines, CAS = California Academy of Sciences.

Fin clip tissue samples were stored in 95% ethanol and DNA was extracted using DNeasy Blood & Tissue kits (Qiagen) according to the manufacturer’s protocol. DNA was extracted from two Altrichthys alelia individuals (juvenile individuals 6 and 8, in CAS 241439), and from five individuals of each sister species, A. azurelineatus and A. curatus collected at Uson Island and Sangat Island (Figure 2). Extractions were PCR amplified for two mitochondrial (control region and cytochrome oxidase 1) and one nuclear marker (RAG2) following published protocols (Bernardi 2011) (Genbank accession numbers KY963970- KY963994; KY969587, KY969588). Phylogenetic reconstructions were done based on the Neighbor-Joining method generated in R (R Core Team 2013) with the ape package (Paradis et al. 2004) using Kimura-2 parameter substitution models, and a Maximum Likelihood method implemented in GARLI (Zwickl 2006). Node support was obtained using 1000 bootstrap replicates and retaining values that support nodes in more than 50% of the bootstrap replicates.

Figure 2. 

Type locality of Altrichthys alelia. Busuanga Island, Palawan Province, Philippines, near the village of Maricaban, next to the resort “El Rio y Mar”, 12.1911°N; 120.1022°E. Highlighted in red are Tara Island and Uson Island, where specimens of Altrichthys were first collected, as well as Uson Island and Sangat Island where sister species A. azurelineatus and A. curatus were collected.

In addition, we constructed RAD libraries using a variation of the original protocol with restriction enzyme SbfI (Miller et al. 2007, 2012, Baird et al. 2008, Longo and Bernardi 2015, Omar et al. 2016). Individually barcoded samples were sequenced on an Illumina HiSeq 2500 at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Analysis of the sequences followed previously published protocols (Longo and Bernardi 2015).


Alelia’s damselfish

Altrichthys alelia Bernardi, Longo, & Quiros, sp. n.

Type locality

San José, Busuanga Island, Philippines, 12.1911°N ; 120.1022°E.


PNM 15195; 54.7 mm S.L., San José, Busuanga Island, Philippines, 12.1911°N ; 120.1022°E, 3m, hand net, G. Bernardi, G. Longo and A. Quiros (Figures 1, 2).


CAS 241438, 3 adult specimens, SL 51.0-54.1 mm; CAS 241439, 8 juvenile individuals, SL 13.9 – 19.7mm. Both lots collected with Holotype, Busuanga Island, Philippines, 3m, hand net, G. Bernardi, G. Longo and A. Quiros.

Comparative material

Altrichthys azurelineatus. Holotype: USNM 89957 (one specimen, Uson Island), Paratypes USNM 96398 (one specimen Tara island), USNM 96425 (one specimen, Tara Island). Altrichthys azurelineatus 5 specimens from Uson Island, A. curatus 5 specimens from Uson Island and Sangat Island.

Diagnosis and description

A species of Altrichthys distinguished by the following combination of characters: dorsal rays XIV, 13–14; anal rays II, 15, tubed lateral line scales 14–15 (Table 1); preorbital and sensory pores small and numerous, usually more than 30, adult coloration in life pale green on upper half grading to white on lower part; iris silvery; pale yellow to gold outer margin of dorsal and upper and lower edges of caudal fin. Fins mainly white to translucent. Juveniles up to 16mm in length are mostly white with a prominent yellow stripe along the lateral line (Figure 3). Adults are generally of the same size as other Altrichthys adults, approximately 70–80mm TL. Altrichthys alelia differs from A. curatus by having long filaments at the trailing edges of the dorsal and caudal fins, and from A. azurelineatus by lacking any black lining of the outer edges of dorsal and caudal fins. These black margins are represented by yellow/gold margins in A. alelia (Figure 4). Pored lateral line scales easily distinguish A. curatus (17–18) and A. azurelineatus (10-14). Counts for A. alelia are most similar to and overlap A. azurelineatus counts, but exhibit a higher mode (15).

Figure 3. 

Altrichthys alelia in its natural environment, near a common nesting substrate, the coral Porites cylindrica.

Figure 4. 

Altrichthys species. Juvenile and adult Altrichthys are shown from left to right: A. alelia, A. azurelineatus, and A. curatus. Note the prominent yellow line in the juvenile A. alelia, and the lack of black margins in the dorsal and caudal fins in the adult.

Morphometric and Meristic measurements of Altrichthys. Lines present, from top to bottom, numbers for Total Length (TL), Standard Length (SL), Depth, With, Eye Diameter (Eye), spine and ray counts for Dorsal and Anal fins, and Tubed Lateral Line Scales (Tubed LL scales). Number in parenthesis represent percentage of the Standard length). The first column is the species holotype.

Voucher number PNM 15195/ CAS 241438/ CAS 241438/ CAS 241438/
9 10 11 12
TL (mm) 73.6 66.8 66.2 70.2
SL (mm) 54.9 51.6 51.0 54.1
Depth (mm) 31.6 (57.6%) 30.2 (58.5%) 30.0 (58.8%) 31.2 (57.7%)
Width (mm) 9.6 (17.5%) 11.0 (21.3%) 11.6 (22.7%) 11.1 (20.5%)
Eye (mm) 5.2 (9.5%) 5.4 (10.5%) 5.6 (11.0%) 5.7 (10.5%)
Dorsal fin XIII, 14 XIV, 13 XIV, 13 XIII, 14
Anal fin II,15 II,15 II,15 II,15
Tubed LL scales 15 14 14 15

In addition, Sanger sequencing results show that Altrichthys alelia individuals form a group most closely related to, but distinct from, A. azurelineatus (Figure 5). Altrichthys alelia sequences differed from their closest relative A. azurelineatus by one fixed difference at the nuclear locus RAG2. For mitochondrial markers, Altrichthys alelia sequences differed from A. azurelineatus by 13 and 15 fixed mutations for cytochrome oxidase I and control region markers, respectively, thus corresponding to a Kimura-2 sequence divergence of 2.3% and 5.9% respectively. These divergences are consistent with values obtained in other sister species of fish (Ward et al. 2005). RAD DNA sequencing results were also consistent with A. alelia and A. azurelineatus being distinct species and more closely related to each other than either are to A. curatus (Table 2). Indeed, RAD sequencing generated 8383 variable SNPs for the 5 sequenced individuals (2 A. alelia, 1 A. azurelineatus, 2 A. curatus). Of those 8383 SNPs, 1584.5 (18.9%) showed differences between A. alelia and A. azurelineatus; while 7224.5 (86.2%) and 6495 (76.4%) showed differences between A. curatus and A. alelia and between A. curatus and A. azurelineatus, respectively (Table 2).

Figure 5. 

Phylogenetic reconstructions of Altrichthys species based on mitochondrial control region (313 aligned base pairs) and cytochrome oxydase 1 (CO1, 611 aligned base pairs). The closely related Acanthochromis polyacanthus was used as an outgroup. Sample labels refer to collection sites: BUS, El Rio y Mar Resort, Busuanga Island, COR, Balinsasayaw Resort, Uson Island; SAN, Sangat Island; DLR, Dive Link Resort, Uson Island. Numbers above nodes refer to percent of 1000 bootstrap replicates used in Neighbor-Joining (left) and Maximum Likelihood (right) reconstruction methods.

Results of RAD sequencing in three species. Results are based on 8383 variable SNPs for 5 sequenced individuals (2 A. alelia, 1 A. azurelineatus, 2 A. curatus). Figures refer to the number of SNPs and their percentage (over 8383 total SNPs).

A. alelia A. azurelineatus A. curatus
A. alelia 123 / 1.47%
A. azurelineatus 1584.5 / 18.9% – / –
A. curatus 7224.5 / 86.2% 6495 / 76.4% 8 / 0.0%


Known from northern Busuanga Island at San José, Palawan Province, Philippines (Figure 2).


Collected off live and extensive thickets of corals mostly Porites cylindrica.


The name Altrichthys alelia derives from the combined first names of Alessio Bernardi and Amalia Bernardi, who greatly helped during field-work on Altrichthys.

Common name

We suggest Alelia’s damselfish as a literal translation of the scientific name.


Species of the genus Altrichthys together with their close relative Acanthochromis polyacanthus are unusual as they brood their young (Allen 1999, Bernardi et al. 2017), whereas most coral reef fishes have a pelagic larval stage (Leis 1991). This behavior is clearly visible on the reef, by the presence of pairs of adult fish aggressively defending a cloud of fry that remain around the parents. An identical behavior was observed in A. alelia, where fry and adult pairs were associated, and similarly to the other Altrichthys species, Porites cylindrica is used as a nesting substrate (Bernardi et al. 2017). While Altrichthys azurelineatus and A. curatus co-occur at most locations in southern Busuanga, we did not observe any other Altrichthys species occurring in the vicinity of A. alelia.

Altrichthys alelia may have been observed previously by other scientists, but remained unnoticed. The original description of Chromis azurelineatus (Fowler & Bean, 1928), later re-described as Altrichthys azurelineatus (Allen, 1999), was based on fish collected during the Albatross expedition of 1908-1909. Three collections were made in December 1908 (Smith and Williams 1999). The collection that yielded the type specimen was made in Uson Island, using dynamite. The authors spent several days on Uson Island, and observed hundreds of A. azurelineatus there but never saw A. alelia in that locality. That specimen indeed looks like a genuine A. azurelineatus with its distinctive dark caudal fin margins (USNM, 89957, Figure 6, top right panel). The other collections of the Albatross were at Tara island, which faces the north-eastern portion Busuanga Island, a region close to the type locality of A. alelia (Figure 2). Fish collected at Tara island have “dorsal spines bright orange, color carried somewhat into membranes in another portion of the fin” (Fowler and Bean 1928). The geographic location and description are consistent with A. alelia, however the lack of diagnostic morphological and meristic characters precludes final determination if this were the case. Nevertheless, specimens from these collections lack the characteristic black margins on the caudal fin that is found in A. azurelineatus (USNM, 96398, and USNM, 96425, Figure 6, bottom left and bottm right panels). The drawing of A. azurelineatus in the original description by Fowler and Bean (1928), and later redrawn in color (Allen 1991), does not show the dark margins either (Figure 6, top left panel), as it may have been a compilation of all the various specimens collected (i.e. a combination of A. azurelineatus and A. alelia individuals). As such, that drawing is more similar to A. alelia. Finally, the picture taken on Busuanga island labeled as A. curatus in Figure 2 of Allen (1999), looks precisely like A. alelia. Due to the peculiarities of this fish, Allen (1999) suggested that “additional observations are needed”, which is what we are presenting here.

Figure 6. 

Drawing (upper left, from Fowler and Bean 1928) and photo (upper right) of the holotype of Altrichthys azurelineatus from Uson Island (USNM 89957), and paratypes (bottom photos) (USNM 96398, 96425) collected at Tara Island. Photos by Sandra J. Raredon, Division of Fishes, Smithsonian Institution.


We would like to thank Nicole Crane, Amalia Bernardi, and Alessio Bernardi for help in the field. We thank the following: Bureau of Fisheries and Aquatic Resources (Commodity Clearance 2016-20091), Palawan Council for Sustainable Development (PCSD, GP 2016-03, Wildlife Transport Permit No. 2016-05-000062-DMO – Calamianes, Fisheries inspection and quarantine clearance Permit no. 009391) and Leonora Labrador and Eva Palanca of the Coron PCSD office. Ateneo de Manila University’s Hendrik Freitag, Merab A. Chan, Jonathan Patrick H. Yan for the Memorandum of Agreement between UCSC and the Department of Biology at Ateneo de Manila. Busuanga Mayor (Samuel de Jesus) and Councilor (Ann D. Mercado), Coron Mayor (Clara Espiritu-Reyes) and Samuel Madamba, Culion Mayor (Emiliano Marasigan) and Councilor Leonilo Sarmiento for Prior Informed Consent (PIC), given in 2015. Hikari South Sea Pearl, Luna Sombrano, Agustin R. Badon II, Eric T. Dalisay, and Pinky Perpetua for assistance in obtaining the PICs. We thank El Rio y Mar Resort, Dive Link Resort, and Balinsasayaw for letting us visit their reefs, and Gerald Allen for discussing our data and invaluable information on Altrichthys. We are very grateful to Sandra J. Raredon for taking pictures of Altrichthys specimens at the Smithsonian collection, and to Don Dumale (National Museum of the Philippines) and David Catania (California Academy of Science) for providing Holotype and Paratype numbers. This work was funded by a National Geographic Grant and a UCSC Committee on Research (COR) grant to GB.


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