Dispersal and gene flow connect habitat patches, linking demographic and genetic processes within metapopulations. Demographic connectivity can prevent local extinctions and increase species persistence. It allows species to colonize new areas, making it possible for them to shift their ranges in response to changes in the environment. Genetic connectivity may impede local adaptation, but is often advantageous because it minimizes the negative effects of habitat loss and fragmentation, such as inbreeding.

This research explored different methodologies for estimating dispersal and gene flow, and estimated connectivity for two species of secretive wetland birds, the California black rail (Laterallus jamaicensis coturniculus) and the Virginia rail (Rallus limicola), from an inland metapopulation in the Sierra Nevada foothills and a coastal metapopulation in the San Francisco Bay Area, California. The research presented includes: (1) a synthesis of landscape genetics methods used to examine spatial patterns of genetic variation, (2) a validation of dispersal distances estimated from occupancy models using dispersal distances estimated from genetic parentage assignments within the inland metapopulation, (3) an estimate of the frequency and distance of long-distance dispersal events between the inland and coastal metapopulations, and (4) an assessment of the effects of habitat loss and fragmentation on gene flow within the coastal metapopulation.

Despite its importance in ecology and evolution, dispersal distances are poorly understood for many species, especially those that are secretive and rare, such as rails. For these species, indirect methods, including the use of occupancy models, genetics, and isotopic markers, may be optimal for estimating dispersal. In the Sierra Nevada foothills, Black and Virginia rails exhibited contrasting relationships between connectivity metrics and patch colonization. For black rails, model-averaged dispersal distances from occupancy models (Buffer Radius Metric = 3.46 km; Incidence Function Metric = 3.70 km) showed good agreement with the mean dispersal distance from genetic parentage assignments (5.58 ± 1.92 km). For Virginia rails, however, it was difficult to identify a spatial scale with the best fit in occupancy models, and the sample size for estimating dispersal distance from parentage assignments was limited. Combined inference from genetic and isotopic population assignments suggested that long-distance dispersal of black rails between the Sierra Nevada foothills and the San Francisco Bay Area occurred infrequently, but, somewhat surprisingly, three dispersal events greater than 100 km were recorded during the study. The first was recorded from a band return for a black rail that traveled 128 km. Two other long-distance dispersal estimates were obtained using isotopic and genetic population assignments. Within the San Francisco Bay Area, estimates of gene flow for black rails among 11 wetlands (FST range: 0.014 to 0.067) indicated rails dispersed frequently between wetlands at shorter spatial scales (tens of kilometers), but that gene flow at a larger spatial scale (greater than 50 km) between the North Bay and South Bay (FST = 0.018) was limited. Although previously thought to be dispersal-limited, black rails appear to be capable of dispersing and maintaining some level of gene flow at spatial scales less than 50 km. Therefore, wetland mitigation and restoration efforts for rails should focus on protecting and creating habitat at smaller spatial scales (tens of kilometers) to maintain demographic and genetic connectivity and metapopulation viability.