Effects of landscape features on population genetic variation of a tropical stream fish, Stone lapping minnow, Garra cambodgiensis, in the upper Nan River drainage basin, northern Thailand

Abstract

Spatial genetic variation of river-dwelling freshwater fishes is typically affected by the historical and contemporary river landscape as well as life-history traits. Tropical river and stream landscapes have endured extended geological change, shaping the existing pattern of genetic diversity, but were not directly affected by glaciation. Thus, spatial genetic variation of tropical fish populations should look very different from the pattern observed in temperate fish populations. These data are becoming important for designing appropriate management and conservation plans, as these aquatic systems are undergoing intense development and exploitation. This study evaluated the effects of landscape features on population genetic diversity of Garra cambodgiensis, a stream cyprinid, in eight tributary streams in the upper Nan River drainage basin (n = 30-100 individuals/location), Nan Province, Thailand. These populations are under intense fishing pressure from local communities. Based on 11 microsatellite loci, we detected moderate genetic diversity within eight population samples (average number of alleles per locus = 10.99 ± 3.00; allelic richness = 10.12 ± 2.44). Allelic richness within samples and stream order of the sampling location were negatively correlated (P < 0.05). We did not detect recent bottleneck events in these populations, but we did detect genetic divergence among populations (Global F_ST = 0.022, P < 0.01). The Bayesian clustering algorithms (TESS and STRUCTURE) suggested that four to five genetic clusters roughly coincide with sub-basins: (1) headwater streams/main stem of the Nan River, (2) a middle tributary, (3) a southeastern tributary and (4) a southwestern tributary. We observed positive correlation between geographic distance and linearized F_ST (P < 0.05), and the genetic differentiation pattern can be moderately explained by the contemporary stream network (STREAMTREE analysis, R² = 0.75). The MEMGENE analysis suggested genetic division between northern (genetic clusters 1 and 2) and southern (clusters 3 and 4) sub-basins. We observed a high degree of genetic admixture in each location, highlighting the importance of natural flooding patterns and possible genetic impacts of supplementary stocking. Insights obtained from this research advance our knowledge of the complexity of a tropical stream system, and guide current conservation and restoration efforts for this species in Thailand.

Keywords: Garra cambodgiensis; Landscape genetics; Microsatellite variation; Spatial genetic variation; Tropical stream fish; Upper Nan River.

Figure 1. Locations of population samples of Garra cambodgiensis in the upper Nan River drainage basin, Thailand taken from November–December 2016.

The map also illustrates (A) stream orders, flooded areas and elevation and (B) land use types in the drainage basin. GIS data provided by the Nan Provincial Administrative Organization.

Figure 2. UPGMA dendrogram of eight population samples of Garra cambodgiensis based on Nei’s genetic distance (Nei, 1978) (indicated by a scale bar) with 1,000 bootstrap replicates at 11 microsatellite loci (bootstrap values are shown at nodes).

Figure 3. Bar plot of membership coefficients of individuals assigned to genetic clusters (K = 4 and 5) generated by a Bayesian clustering algorithm, implemented in the TESS software.

The individual coefficients (vertical bars) were grouped by population samples. Membership to each cluster is represented by a different color. The bar plot illustrates (A) four and (B) five genetic clusters.

Figure 4. MEMGENE analysis for eight population samples of Garra cambodgiensis in the upper Nan River basin.

Circles of a similar size and color suggest individuals with similar MEMGENE scores imposed on a map of the upper Nan River basin (large black and large white circle describe opposite extremes on the MEMGENE axes). (A) MEMGENE axis 1 explains 57.8% of the variability and (B) MEMGENE axis 2 explains 42.2%. Both axes indicate spatial genetic differentiation between the northern (upstream) and southern (downstream) sites.