Gene flow and genetic structure of two of Arkansas’s rarest darter species (Teleostei: Percidae), the Arkansas Darter, Etheostoma cragini, and the Least Darter, E. microperca

Distinguishing the effects of naturally caused historical fragmentation from those of contemporary landscape modification is critically important to understanding the consequences of human influences on patterns of gene flow and population dynamics. Nonetheless, relatively few recent studies focusing on this issue have dealt with species that showed evidence of historical fragmentation. In the current study, we disentangled the effects of fragmentation operating over separate timescales on two darter species, Etheostoma cragini and E. microperca, from the Ozark Highlands. Formerly more wide-spread within this region in Arkansas, these species now occur only in highly isolated habitats (i.e., spring-runs). We separated fragmentation effects at distinct spatial and temporal scales by using several molecular loci (i.e., mtDNA/nuclear DNA/nuclear microsatellite DNA), as well as a variety of analytical approaches. Sequence divergence among Ozark and northern populations of E. microperca indicate long-standing isolation resulting from vicariant events. Both species were further isolated in unique ‘island’ habitats, sometimes at fine spatial scales, as shown by sequence divergence among Ozark Highland populations of E. cragini. Microsatellite data also revealed additional subdivision among Arkansas populations with E. cragini divided into three distinct populations and E. microperca into two. Overall, migration rates were similar among contemporary and historical time periods although patterns of asymmetric migration were inverted for E. cragini. Estimates of contemporary effective population size (Ne) were substantially lower for both species than past population sizes. Overall, historical processes involving natural fragmentation have had long-lasting effects on these species, potentially making them more susceptible to current anthropogenic impacts. Introduction Habitat fragmentation operating both over historical time scales and over more recent timescales results in species with highly fragmented distributions, significantly compromising the maintenance of genetic diversity and population viability (Keyghobadi et al. 2005; Zellmer and Knowles 2009). Distinguishing between these time scales is important to conservation efforts because knowledge of historical population structure is essential to assessing the impact of current anthropogenic effects. Several recent studies comparing past and current patterns of gene flow among populations have revealed that recent human activities have substantially altered connectivity among populations, resulting in increased bottlenecks and high levels of inbreeding (Reed et al. 2011; Apodaca et al. 2012; Blakney et al. 2014); others suggest the high levels of structure observed among populations reflect long-standing limited dispersal of the species rather than recent habitat fragmentation (Chiucchi and Gibbs, 2010). These two causes of fragmentation may also act synergistically, such that the historically fragmented populations of a species become reduced in number or each experience declines in membership due to anthropogenic effects. Populations that are both highly fragmented and exhibit reduced population sizes have high rates of local extinction and therefore higher probability of global extinction (Templeton et al. 1990). Recent fragmentation may also substantially influence metapopulation dynamics, which may play a critical role in contributing to adaptive differences observed among populations even at small spatial scales (Zellmer