A molecular phylogeny of the freshwater‐fish genusRasbora(Teleostei: Cyprinidae) in Sri Lanka reveals a remarkable diversification—And a cryptic species

Cryptic species, biogeography, and patterns of introgression in the fish genus Mogurnda (Eleotridae) from the Australian wet tropics: A purple patch for purple-spots

Accurately delimiting species is an essential first step towards understanding the true biodiversity of an ecosystem and any subsequent efforts to identify and protect taxa at risk of extinction. Current molecular evidence suggests that purple-spotted gudgeons (genus Mogurnda) harbour high levels of cryptic biodiversity across their broad distributional range. The present study uses a large single nucleotide polymorphism (SNP) dataset plus a companion allozyme dataset to clarify taxonomic uncertainty, patterns of introgression, and biogeographic relationships among Mogurnda populations within the Queensland Wet Tropics (QWT), a known biodiversity hotspot. Both datasets were strongly concordant in identifying a total of seven taxa split among distinct southern, northern, and lowlands groups. No two taxa were found in strict sympatry, but many appear to be parapatric and occur within the same drainage basin. Although clear evidence of introgression was only evident at six sites (∼4%), the genomic signature of modest historic admixture between proximally-distributed taxa was detected at multiple other sites. Nevertheless, all primary genetic and phylogenetic analyses strongly supported the integrity and diagnosability of these seven taxa. We therefore nominate these as novel candidate species for what appears to be yet another hyper-cryptic complex within the Australian freshwater ichthyological fauna. These results offer up intriguing ecological scenarios and conservation implications for multiple candidate species with narrow ranges in specialised habitat. We conclude by exploring the major biogeographic patterns displayed by QWT Mogurnda.

Phylogenetic and phylogeographic insights into Sri Lankan killifishes (Teleostei: Aplocheilidae)

Three nominal species of the killifish genus Aplocheilus are reported from the lowlands of Sri Lanka. Two of these, Aplocheilus dayi and Aplocheilus werneri, are considered endemic to the island, whereas Aplocheilus parvus is reported from both Sri Lanka and Peninsular India. Here, based on a collection from 28 locations in Sri Lanka, also including a dataset of Asian Aplocheilus downloaded from GenBank, we present a phylogeny constructed from the mitochondrial cytochrome b (cytb), mitochondrial cytochrome c oxidase subunit 1 (cox1), and nuclear recombination activating protein 1 (rag1), and investigate the interrelationships of the species of Aplocheilus in Sri Lanka. The endemic Sri Lankan aplocheilid clade comprising A. dayi and A. werneri is recovered as the sister group to the clade comprising A. parvus from Sri Lanka and Aplocheilus blockii from Peninsular India. The reciprocal monophyly of A. dayi and A. werneri is not supported in our molecular phylogeny. A. dayi and A. werneri display strong sexual dimorphism, but species-level differences are subtle, explained mostly by pigmentation patterns. Their phenotypes exhibit a parapatric distribution and may represent locally adapted forms of a single species. Alternatively, the present study does not rule out the possibility that A. dayi and A. werneri may represent an incipient species pair or that they have undergone introgression or hybridization in their contact zones. We provide evidence that the Nilwala-Gin region of southwestern Sri Lanka may have acted as a drought refugium for these fishes.

Biogeography and evolutionary history of Puntius sensu lato (Teleostei: Cyprinidae) in Sri Lanka

Sri Lanka's biota is derived largely from Southeast Asian lineages which immigrated via India following its early-Eocene contact with Laurasia. The island is now separated from southeastern India by the 30 km wide Palk Strait which, during sea-level low-stands, was bridged by the 140 km-wide Palk Isthmus. Consequently, biotic ingress and egress were mediated largely by the climate of the isthmus. Because of their dependence on perennial aquatic habitats, freshwater fish are useful models for biogeographic studies. Here we investigate the timing and dynamics of the colonization of-and diversification on-Sri Lanka by a group of four closely-related genera of cyprinid fishes (Puntius sensu lato). We construct a molecular phylogeny based on two mitochondrial and two nuclear gene markers, conduct divergence timing analyses and ancestral-range estimations to infer historical biogeography, and use haplotype networks to discern phylogeographic patterns. The origin of Puntius s.l. is dated to ~ 20 Ma. The source of diversification of Puntius s.l. is Sri Lanka-Peninsular India. Species confined to perhumid rainforests show strong phylogeographic structure, while habitat generalists show little or no such structure. Ancestral range estimations for Plesiopuntius bimaculatus and Puntius dorsalis support an 'Out of Sri Lanka' scenario. Sri Lankan Puntius s.l. derive from multiple migrations across the Palk Isthmus between the early Miocene and the late Pleistocene. Species dependent on an aseasonal climate survived aridification in rainforest refugia in the island's perhumid southwest and went on to recolonize the island and even southern India when pluvial conditions resumed. Our results support an historical extinction of Sri Lanka's montane aquatic fauna, followed by a recent partial recolonization of the highlands, showing also that headwater stream capture facilitated dispersal across basin boundaries.

Can the Sri Lankan endemic-endangered fish Labeo fisheri (Teleostei: Cyprinidae) adapt to a new habitat?

Labeo fisheri is an endemic and endangered freshwater fish of Sri Lanka. Mainly restricted to the upper reaches of the Mahaweli River basin, it has been previously reported living in deep rapids and among large rocks and boulders. An accidental record of a Labeo fisheri specimen from Victoria Reservoir led us to further study this habitat during the period from January to August 2017. This study was carried out to confirm the presence of a population of Labeo fisheri within the Victoria Reservoir and report its new habitat type in deep stagnant waters. We further investigated the food habits by analyzing the gut contents of L. fisheri in the Victoria Reservoir. Seven individuals were recorded from fishermen’s gill net catch in three fish landing sites along Victoria Reservoir, with an average total length of 24.80 ± 4.30 cm, average standard length of 19.70 ± 3.86 cm and average body weight of 197.69 ± 107.12 g. Based on gut content analysis, only phytoplankton, especially diatoms and cyanobacteria, were found in the gut of L. fisheri. This new population is facing the direct threat of fishing. Effective conservation measures are doubtful, since a fishery is well established in the Victoria Reservoir and the fishing gear used is not species-specific. More research is necessary to understand the population dynamics of L. fisheri in the Victoria Reservoir. In order to conserve it at this locality, community-based conservation measures are recommended. 

Molecular phylogeny and phylogeography of ricefishes (Teleostei: Adrianichthyidae: Oryzias) in Sri Lanka

Ricefishes of the genus Oryzias occur commonly in the fresh and brackish waters in coastal lowlands ranging from India across Southeast Asia and on to Japan. Among the three species of Oryzias recorded from peninsular India, two widespread species, O. carnaticus and O. dancena, have previously been reported from Sri Lanka based on museum specimens derived from a few scattered localities. However, members of the genus are widespread in the coastal lowlands of Sri Lanka, a continental island separated from India by the shallow Palk Strait. Although recent molecular phylogenies of Adrianichthyidae represent near-complete taxon representation, they lack samples from Sri Lanka. Here, based on sampling at 13 locations representative of the entire geographic and climatic regions of the island's coastal lowlands, we investigate for the first time the molecular phylogenetic relationships and phylogeography of Sri Lankan Oryzias based on one nuclear and two mitochondrial markers. Sri Lankan Oryzias comprise two distinct non-sister lineages within the javanicus species group. One of these is represented by samples exclusively from the northern parts of the island; it is recognized as O. dancena. This lineage is recovered as the sister group to the remaining species in the javanicus group. The second lineage represents a species that is widespread across the island's coastal lowlands. It is recovered as the sister group of O. javanicus and is identified as O. cf. carnaticus. Ancestral-range estimates suggest two independent colonizations of Indian subcontinent and Sri Lanka by widespread ancestral species of Oryzias during two discrete temporal windows: late Miocene and Plio-Pleistocene. No phylogeographic structure is apparent in Sri Lankan Oryzias, suggesting that there are no strong barriers to gene flow and dispersal along the coastal floodplains, as is the case also for other generalist freshwater fishes in the island.

Molecular phylogeny and phylogeography of the freshwater-fish genus Pethia (Teleostei: Cyprinidae) in Sri Lanka

BACKGROUND

Sri Lanka is a continental island separated from India by the Palk Strait, a shallow-shelf sea, which was emergent during periods of lowered sea level. Its biodiversity is concentrated in its perhumid south-western 'wet zone'. The island's freshwater fishes are dominated by the Cyprinidae, characterized by small diversifications of species derived from dispersals from India. These include five diminutive, endemic species of Pethia (P. bandula, P. cumingii, P. melanomaculata, P. nigrofasciata, P. reval), whose evolutionary history remains poorly understood. Here, based on comprehensive geographic sampling, we explore the phylogeny, phylogeography and morphological diversity of the genus in Sri Lanka.

RESULTS

The phylogenetic analyses, based on mitochondrial and nuclear loci, recover Sri Lankan Pethia as polyphyletic. The reciprocal monophyly of P. bandula and P. nigrofasciata, and P. cumingii and P. reval, is not supported. Pethia nigrofasciata, P. cumingii, and P. reval show strong phylogeographic structure in the wet zone, compared with P. melanomaculata, which ranges across the dry and intermediate zones. Translocated populations of P. nigrofasciata and P. reval in the Central Hills likely originate from multiple sources. Morphological analyses reveal populations of P. nigrofasciata proximal to P. bandula, a narrow-range endemic, to have a mix of characters between the two species. Similarly, populations of P. cumingii in the Kalu basin possess orange fins, a state between the red-finned P. reval from Kelani to Deduru and yellow-finned P. cumingii from Bentara to Gin basins.

CONCLUSIONS

Polyphyly in Sri Lankan Pethia suggests two or three colonizations from mainland India. Strong phylogeographic structure in P. nigrofasciata, P. cumingii and P. reval, compared with P. melanomaculata, supports a model wherein the topographically complex wet zone harbors greater genetic diversity than the topographically uniform dry-zone. Mixed morphological characters between P. bandula and P. nigrofasciata, and P. cumingii and P. reval, and their unresolved phylogenies, may suggest recent speciation scenarios with incomplete lineage sorting, or hybridization.

Island colonization by a ‘rheophilic’ fish: the phylogeography of Garra ceylonensis (Teleostei: Cyprinidae) in Sri Lanka

Despite exhibiting multiple morphological adaptations to living in swiftly flowing water (rheophily), Garra ceylonensis is one of the most widely distributed freshwater fish in Sri Lanka. It is thus an ideal organism to reconstruct the evolutionary history of a widespread, yet morphologically specialized, freshwater fish in a tropical-island setting. We analysed the phylogenetic and phylogeographic relationships of G. ceylonensis based on two mitochondrial and one nuclear genes. G. ceylonensis is shown to be monophyletic, with a sister-group relationship to the Indian species Garra mullya. Our results suggest a single colonization of Sri Lanka by ancestral Garra, in the late Pliocene. This suggests that the Palk Isthmus, which was exposed for most of the Pleistocene, had a hydroclimate unsuited to the dispersal of fishes such as Garra. G. ceylonensis exhibits strong phylogeographic structure: six subclades are distributed as genetically distinct populations in clusters of contiguous river basins, albeit with two exceptions. Our data reveal one or more Pleistocene extirpation events, evidently driven by aridification, with relict populations subsequently re-colonizing the island. The phylogeographic structure of G. ceylonensis suggests inter-basin dispersal largely through headwater capture, likely facilitated by free-swimming post-larvae. The Peninsular-Indian species G. mullya comprises two genetically distinct parapatric clades, which may represent distinct species.

Cryptic species diversity and molecular diagnosis of Channa orientalis; an endemic freshwater fish of Sri Lanka

Fish genetic resources and diversity are very important aspects of environmental management and fisheries and are vital for making decisions on their commercial exploitation as well as conservation. The snakehead fishes in the world have significant economic importance as food and ornamental fish. A clear understanding of species' taxonomic status and genetic diversity is important for the utilization and implementation of conservation and management practices. Channa orientalis is a snakehead endemic to Sri Lanka that is heavily utilized in the ornamental fish export trade. Its genetic diversity has not yet been fully understood and it is difficult to distinguish it from closely resembling species. Therefore, we examined the genetic diversity of C. orientalis and developed a DNA-based marker that permits accurate, low cost, and reliable identification of C. orientalis. Determination of genetic diversity was mainly carried out through genetic analysis of the mitochondrial cytochrome c oxidase subunit 1 (MT-CO1) gene. The development of the DNA-based marker for the identification of C. orientalis was done through Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. Our analyses confirmed the presence of two distinct genetically divergent and geographically separated lineages of C. orientalis in Sri Lanka. The fast cost-effective gel-based PCR-RFLP marker method developed by us was successful in diagnosing C. orientalis from its closely resembling species. Thus, we believe our findings on the cryptic diversity and diagnostic methods will have important implications for the conservation and management of this endemic species.