A genomic assessment of population structure and gene flow in an aquatic salamander identifies the roles of spatial scale, barriers, and river architecture

Abstract

Population structure and gene flow of species in lotic environments can be constrained by river network architecture, species life history and heterogeneous local barriers. Identifying the factors that influence population structure and gene flow, especially in species limited to movement within a river network, is vital for understanding the evolutionary and demographic history of a species. We explored population structure and gene flow for a fully aquatic salamander, the common mudpuppy (Necturus maculosus), in Kentucky (USA) using genomic data. We examined population structure using both parametric and nonparametric methods, and we tested for a history of lineage divergence among identified genetic clusters. We quantified the partitioning of genetic variation at different hierarchical levels, and we tested for signatures of isolation by distance. Additionally, we used coalescent‐based model selection to identify a best‐fit model of gene flow between our three sampled basins. We found the greatest support for population structure between the Kentucky River basin and the combined Licking and Kinniconick basins, with further subdivision within both the Kentucky and Licking River basins. However, we found no evidence for a history of lineage divergence among these structured units. The movement of N. maculosus is constrained by the lotic network architecture, which likely drives the evolution of this hierarchical population structure, with increasing differentiation between sites nested in river basins, and even greater differentiation between basins. However, we also found evidence for population structure not explained by river architecture, with an isolated population embedded within the Kentucky River basin. This study demonstrates the heterogeneity in population structure that can evolve in aquatic species occupying lotic systems and illustrates the potential for genomic data to disentangle these complex patterns.

A spatial genomic approach identifies time lags and historical barriers to gene flow in a rapidly fragmenting Appalachian landscape

“…Our study adds to a growing list highlighting the potential for genomic data sets to detect weak, recent or otherwise subtle spatial genetic patterns (González-Serna, Cordero, & Ortego, 2018;McCartney-Melstad et al, 2018;Murphy, Jones, Price, & Weisrock, 2018;Tan et al, 2018). Considering the problems time lags present for conservation planning, the use of SNP data sets and spatially informed analyses of genetic diversity will probably become increasingly important for placing patterns of population structuring in their proper genomic, temporal and geographical contexts.…”

Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes

“…This study also demonstrates the power of reduced representation genome scans for identifying sex-linked genes in organisms that lack pre-existing genetic resources. Our results further suggest that genome size may not necessarily be a limiting factor in generating informative genome-scale data to answer evolutionary questions in salamanders [see also Nunziata et al (2017); Murphy et al (2018); Weisrock et al (2018); Hu et al (2019)].…”

Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota

“…Hydrological structure can impact genetic structure of amphibians through several mechanisms. Amphibians commonly use riparian areas to disperse, making river systems important migration corridors that facilitate connectivity within amphibian metapopulations (Mullen, Arthur Woods, Schwartz, Sepulveda, & Lowe, ; Shephard & Burbrink ; Howell, Muths, Hossack, Sigafus, & Chandler, ; Murphy, Jones, Price, & Weisrock, ). Additionally, in the prairie pothole region, overwintering habitats impose the greatest constraints on the distribution of R. pipiens (Mushet ).…”