Cryptic genetic divergence of the red dwarf rasbora,Microrasbora rubescens, in and around Inle Lake: implications for the origin of endemicity in the ancient lake in Myanmar

Abstract

Inle Lake, an ancient lake located in the Shan Plateau of Myanmar, is a biogeographically attractive region with high fish endemism. Some endemic species inhabit the lake as well as the surrounding areas. The genetic and ecological relationships between populations in the lake and surrounding areas provide important insights into the process underlying ichthyofaunal formation in Inle Lake. In this study, the authors focused on red dwarf rasbora Microrasbora rubescens, an endemic genus and species in this region, and estimated its population structure and evolutionary scenario based on genome-wide polymorphism, mtDNA and geometric morphometric analyses using samples from Inle Lake and three areas surrounding the lake. The results showed that M. rubescens comprises at least three genetically divergent lineages (Inle, Heho and Hopong) with distinct geographic structures consistent with nuclear and mtDNA data.In contrast, there was no clear regional differentiation in morphology. The divergence time estimation based on mtDNA suggests that the Hopong lineage diverged at 2.7 Ma and the Inle and Heho lineages diverged at 1.9 Maconsistent with the nuclear DNA results. The deep divergence observed in the endemic species supports the ancient history of ichthyofaunal development in this region. The distinct regional differentiation and morphological conservatism of this species might have been shaped by niche conservatism in stagnant water environments that limit dispersal and morphological diversification. Future comprehensive genetic and morphological analyses and comparisons for other native species should reveal the geographic and ecological processes that shaped the ichthyofauna in this region.

Origin of endemic species in a moderately isolated ancient lake: The case of a snakehead in Inle Lake, Myanmar

“…Clade 2 showed differentiation corresponding to 1.11 (0.58-1.77) Ma from Clade 1, widely distributed in the Inle region; this range includes the formation of Inle Lake (1.5 Ma; Hampton et al, 2018). Similar to that in C. harcourtbutleri, regional genetic differentiation was reported in several endemic fish species in the Inle region (Fuke et al, 2022;Kano et al, 2022). Three of the five species examined showed genetic differentiation between Inle Lake and Hopong populations (Kano et al, 2022).…”

“…Among these, the red dwarf rasbora, Microrasbora rubescens (Cyprinidae), endemic to the Inle region, showed a contrasting pattern to C. harcourtbutleri . In the latter, two genetic groups co‐occur with morphological divergence, whereas the rasbora exhibited a large genetic differentiation (roughly corresponding to 2.7 Ma) among regions, without any morphological differentiation (Fuke et al, 2022). This morphological invariability could be explained through niche conservatism.…”

“…The mtDNA cyt b region was amplified using PCR with the following primers: L‐Glu (5′‐ CTA ACC AGG ACT AAT GGC TTG AA‐3′) and H‐Thr (5′‐CGG CTT ACA AGA CCG GCG CTC TGA‐3′) (Takahashi et al, 2016). The PCR conditions were as follows: initial denaturation at 94°C for 120 s; 30 cycles of denaturation at 94°C for 15 s, annealing at 52°C for 15 s, extension at 72°C for 30 s and final extension at 72°C for 420 s. Sequencing was performed on an ABI 3130xl Genetic Analyzer (Applied Biosystems) following the method of Fuke et al (2022) or outsourced to Macrogen Japan and sequenced on ABI 3730xl DNA analyser. The sequences were checked for quality and edited using the mapping function of Unipro UGENE 41.0 (Okonechnikov et al, 2012); multiple alignments were performed using MAFFT (Katoh & Standley, 2013).…”

“…Annandale (1918) suggested that the unique fish fauna of Inle Lake includes widely distributed species that colonized the lake from surrounding areas and some endemic species derived through geographical isolation. In addition, several species treated as endemic species of Inle Lake also occur in the surrounding areas, and some of them are known to show genetic differentiation among regions (Fuke et al, 2022; Kano et al, 2022). The fishes of the Inle region, defined here as the area including Inle Lake and surrounding regions in Shan Plateau, will provide good materials for exploring the processes by which the interactions of in situ diversification and colonization shape local biodiversity.…”

“…Fifteen endemic fish species have been reported from the lake, and there might still be several undescribed species (Kano et al, 2016(Kano et al, , 2022. The native fish fauna of Inle Lake is composed of a wide range of taxa (28 genera from 13 families; Kano et al, 2016Kano et al, , 2022, which are believed to be formed through non-radiative processes (Fuke et al, 2022). Annandale (1918) suggested that the unique fish fauna of Inle Lake includes widely distributed species that colonized the lake from surrounding areas and some endemic species derived through geographical isolation.…”