Giant danios of Sri Lanka reveal hybridization and a new montane species

On the tropical island of Sri Lanka, a group of small, brightly striped freshwater fishes known as giant danios has quietly been rewriting the rules of island evolution. A new study, published in the journal Evolutionary Systematics, has untangled the diversification of the genus Devario on the island, revealing a story of ancient rainforest refuges, recent highland invasions, and unexpected hybridization between species. The research, led by Hiranya Sudasinghe and colleagues, combines DNA sequencing of 136 specimens from 65 locations with a detailed morphological analysis of 363 preserved museum specimens, providing the most comprehensive picture yet of how these fishes evolved on the island.

Sri Lanka’s geological history sets the stage for this evolutionary drama. The island is separated from India by the Palk Strait, a shallow sea only about 10 metres deep and 30 kilometres wide. During successive sea-level lowstands since the Oligocene, this shallow shelf was exposed as a land bridge, the Palk Isthmus, which at the Last Glacial Maximum was almost 200 kilometres wide. For most of the past 5 million years, the isthmus was emergent, providing a corridor for biotic exchange between the island and the mainland. Yet despite this connectivity, Sri Lanka exhibits remarkable biotic insularity. Previous work concluded that for most of the time the land bridge was available since the Miocene, rainfall was too strongly seasonal to support the exchange of species dependent on a perhumid climate, effectively isolating the island’s rainforest fauna.

The genus Devario, known in the popular literature as giant danios, comprises some 44 valid species ranging from Sri Lanka through the Indian Subcontinent and Myanmar to Southeast Asia and southern China. These small, brightly coloured fishes are ubiquitous in the region’s freshwaters, usually numbering among those most frequently encountered in streams and rivers. The recent literature recognized seven valid species from Sri Lanka, but the new study shows that this was an overestimate. Devario annnataliae and D. udenii are synonyms of D. micronema, while D. monticola is a synonym of D. malabaricus. The researchers also describe a new species, Devario altus, from the highlands of Sri Lanka, bringing the total to five valid species on the island.

The five Sri Lankan species of Devario form a monophyletic insular diversification that commenced during the Plio-Pleistocene. Three of them are habitat specialists confined to the rainforests of the island’s perhumid south-western wet zone, where rainfall exceeds 2.5 metres per year. Devario pathirana is restricted to the Nilwala River basin, D. memorialis to the Ma Oya basin, and D. micronema to shaded streams draining lowland rainforests from the Kelani to the Gin River basin. The new species, D. altus, is confined to a single montane site at Bopathalawa, at 1580 metres above sea level, the highest elevation at which any species of Devario has been recorded in Sri Lanka. The fifth species, D. malabaricus, is a habitat generalist associated with open lentic and lotic habitats, widely distributed from sea level to about 1500 metres, and is the only non-endemic member of the genus on the island, occurring also in peninsular India.

To reconstruct the evolutionary history of these fishes, the researchers generated DNA sequences for four molecular markers: two mitochondrial genes, cox1 and cytb, and two nuclear genes, rag1 and irbp. The dataset was derived from 136 specimens occurring at 65 locations encompassing the entire geographic range of Devario on the island. Phylogenetic inference using the Maximum Likelihood method was conducted for each individual gene alignment and for concatenated mitochondrial and nuclear datasets. The mitochondrial phylogeny recovered two major, well-supported clades. The first comprises the wet-zone endemics: D. memorialis as the sister group to a subclade containing D. micronema and D. pathirana. The second encompasses D. malabaricus and D. altus, which are sister species. The nuclear phylogeny, in contrast, did not recover the monophyly of the five species as clearly, a pattern the researchers attribute to the shallow evolutionary timescale of the diversification and to hybridization between species.

The comparison of mitochondrial and nuclear phylogenies revealed striking mitonuclear discordance, providing unambiguous evidence of hybridization in the wild. Devario malabaricus appears to have hybridized with all the other species except D. memorialis in their contact zones. Some specimens from Suriyakanda in the Walawe basin cluster with D. pathirana in the mitochondrial phylogeny but align with D. malabaricus in the nuclear phylogeny, while others show the reverse pattern. Similar discordance was found between D. malabaricus and D. micronema at several sites in the southwestern wet zone, including Andawaldola, Hiniduma, and Dellawa. The researchers suspect that habitat modification in recent decades has facilitated contact between these species, illustrating a second-order effect of environmental change on native biodiversity.

The phylogeographic analysis revealed contrasting patterns for the two most widespread species. Devario micronema, a habitat specialist, exhibits a strong phylogeographic structure, with distinct haplotypes not shared between adjacent river basins, indicating strong genetic differentiation across its range. Despite being geographically more widespread, D. malabaricus shows no discernible genetic structuring, suggesting extensive gene flow among its populations. Neutrality tests suggest contrasting demographic histories: for D. malabaricus, significant negative values indicate potential recent demographic expansion, whereas for D. micronema, non-significant results are consistent with relatively stable populations and limited gene flow. These patterns are critical for informing conservation management decisions, particularly in prioritizing species and habitats for protection in the southwestern wet zone.

The morphological analysis, based on 363 voucher specimens representative of all five species, characterized the species and stabilized their taxonomy. The researchers measured 33 traits, including 21 linear measurements and 12 meristic counts, and conducted principal component analyses to visualize the multivariate morphometric data. The species formed distinct clusters in morphological space, with D. altus and D. memorialis well separated from the other species. A key diagnostic character is the infraorbital process, a laterally directed dorsal extension of the posterior edge of infraorbital 1. This process is present in all specimens of D. pathirana examined, absent in all specimens of D. memorialis, present in most specimens of D. micronema and D. altus, and absent in most specimens of D. malabaricus. The differences in the presence or absence of this trait are statistically significant between the species.

Perhaps the most intriguing finding concerns the relationship between D. malabaricus and D. altus. The phenotype of D. malabaricus varies with elevation as a cline, partly converging on the phenotype of D. altus. With increasing elevation, the frequency of the infraorbital process increases, the P-stripe becomes less frequently bifurcated anteriorly, and the I+1 interstripe becomes longer. Some populations in the central hills, referred to as D. cf. malabaricus (highland phenotype), exhibit a color pattern similar to that of D. altus but contain a mix of mitochondrial haplotypes associated with both species. The researchers raise the question of whether D. altus is a relictual narrow-range endemic that survived the near-total deforestation of the Sri Lankan highlands for plantation agriculture, or whether it represents the limit of adaptation by D. malabaricus to the highland environment. Pollen-core data from a site near the type locality indicate a desiccation event lasting several thousand years straddled the Last Glacial Maximum, suggesting D. altus may have been reduced to a headwater refugium at that time.

Despite the evidence of introgression, the researchers consider Devario altus to be a valid species. It can be unambiguously distinguished phenotypically from D. malabaricus by a combination of characters, including a shallower body, a longer caudal peduncle, a continuous P-stripe, a long I+1 interstripe, and a higher frequency of the infraorbital process. It is also genetically distinct from D. malabaricus, its closest congener, by 1.2 to 1.7 percent in the cox1 DNA barcoding marker, a degree of divergence comparable to that between other recognized species pairs in the genus. The species-name altus is Latin for high, an allusion to this species being restricted to the Sri Lankan highlands. The researchers suggest the vernacular name Sri Lanka Montane Danio. Given that the montane population was previously treated under the misnomer D. monticola and is presently listed as Critically Endangered by the IUCN Red List, the formal description of D. altus provides a stable taxonomic foundation for its conservation. The study also raises the possibility of an Out of Sri Lanka scenario for the genus, in which an ancestral lineage colonized the island, diversified within the southwestern wet zone, and subsequently gave rise to D. malabaricus, which then migrated back to peninsular India. Testing this hypothesis will require comprehensive sampling of Devario populations across peninsular India, but the emerging picture is one in which this small island has served as both a cradle and a crossroads for the evolution of giant danios.

Subject of Research: Species without borders: the diversification of giant danios in Sri Lanka (Teleostei, Danionidae, Devario)

Article Title: Species without borders: the diversification of giant danios in Sri Lanka ( Teleostei , Danionidae , Devario )

Article References: Sudasinghe, H., Pethiyagoda, R., & Meegaskumbura, M. (2025). Species without borders: the diversification of giant danios in Sri Lanka (Teleostei, Danionidae, Devario). Evolutionary Systematics, 9(2), 229-258. https://doi.org/10.3897/evolsyst.9.162251

Image Credits: AI Generated

DOI: 10.3897/evolsyst.9.162251

Keywords: Species, without, borders, diversification, giant, danios, Lanka, Teleostei, Danionidae, Devario, scientific research