Do colour-morphs of an amphidromous goby represent different species? Taxonomy of Lentipes (Gobiiformes) from Japan and Palawan, Philippines, with phylogenomic approaches

Abstract

We document four male colour morphs of the Indo-Pacific goby genus Lentipes in Japan and the Philippines. Despite distinctive colour patterns, males of the different morphs could not be distinguished by meristic or morphometric charactres. In contrast, co-occurring females had very similar colouration and could not be sorted into different types. We observed that the four types are not distinguished by mitochondrial genome sequences. On the other hand, genome-wide SNPs analysis clearly separated the four types, suggesting that they indeed represent four independent lineages. We considered that the four lineages could have diverged recently, and therefore, the sorting of mitochondrial haplotypes may not have been completed yet. One of the four lineages is identified as L. armatus Sakai & Nakamura, 1979, and the other three are described in this study as new species: L. kijimuna, L. bunagaya, and L. palawanirufus. We observed that males display their species-specific body colourations during courtship. Pre-zygotic isolation due to female preferences for different male body colours is probably the primary mechanism of reproductive isolation between the four species.

Sequencing and Analysis of the Complete Mitochondrial Genome of Lentipes ikeae

“…The mitochondrial genome of L. ikeae has a total length of 16,498 bp and encodes 22 tRNA genes, 13 PCGs, two rRNAs, and one D-loop. Other Lentipes mitochondrial genomes have similar structures [ 4 ]. The A+T base content (54.9%) is greater than that of G+C bases (45.1%), revealing an AT preference, as observed in other fish, such as Oliotius Kottelat [ 26 ] and Rhinogobius [ 27 ].…”

“…L. ikeae has 22 tRNA genes, ranging in length from 67 bp to 76 bp and totaling 15,57 bp, similar to Rhinogobius [ 27 ] and Lentipes [ 4 ]. The mitochondrial genome of L. ikeae contains two rRNAs, 16S rRNA and 12S rRNA, which are not isolated or overlapping with adjacent genes.…”

“…They are mainly distributed in Cisolok, Kab Sukabumi, Java, and Indonesia [ 1 , 3 ] and occur in fast-flowing mountain streams with high gradients and small yet clear, oxygen-rich streams with rocky bottoms, typically at an altitude of 310–488 m. L. ikeae is an omnivorous species that accepts frozen red worms and mainly eats shrimp and water fleas, and even algae when there are no other food sources. In its combat mode, it has bright colors and important ornamental value, and it is a water quality indicator species [ 2 , 4 ].…”

A new species of gobiid fish Lentipes niasensis (Gobiidae: Sicydiinae) from Nias Island, Indonesia

“…Gobiid fishes of the genus Lentipes Gunther, 1861 are widely distributed in tropical and subtropical freshwater streams in the Indo-Pacific. They occur in the Andaman Islands, Australia, Indonesia, Japan, Taiwan, the Philippines, the Fiji Island, Papua New Guinea, Micronesia, the Solomon Islands, New Caledonia and the Hawaiian Islands (Maciolek 1977, Sakai & Nakamura 1979, Allen 2001Watson et al 2002, Chen 2004Chen et al 2007, Jenkins et al 2008, Moore et al 2008, Seeto & Baldwin 2010, Lynch et al 2013, Keith et al 2014, 2015, Maeda et al 2021. Members of this genus are small amphidromous gobies that occur in swift-flowing freshwater hill creeks with rocky substrates (Way et al 1998, Keith 2003, Keith et al 2015, Keith & Mennesson 2019.…”