Functional connectivity, quantified using landscape genetics, can inform conservation through the identification of factors linking genetic structure to landscape mechanisms. We used breeding habitat metrics, landscape attributes, and indices of grouse abundance, to compare fit between structural connectivity and genetic differentiation within five long‐established Sage‐Grouse Management Zones (MZ) I‐V using microsatellite genotypes from 6,844 greater sage‐grouse (Centrocercus urophasianus) collected across their 10.7 million‐km2 range. We estimated structural connectivity using a circuit theory‐based approach where we built resistance surfaces using thresholds dividing the landscape into “habitat” and “nonhabitat” and nodes were clusters of sage‐grouse leks (where feather samples were collected using noninvasive techniques). As hypothesized, MZ‐specific habitat metrics were the best predictors of differentiation. To our surprise, inclusion of grouse abundance‐corrected indices did not greatly improve model fit in most MZs. Functional connectivity of breeding habitat was reduced when probability of lek occurrence dropped below 0.25 (MZs I, IV) and 0.5 (II), thresholds lower than those previously identified as required for the formation of breeding leks, which suggests that individuals are willing to travel through undesirable habitat. The individual MZ landscape results suggested terrain roughness and steepness shaped functional connectivity across all MZs. Across respective MZs, sagebrush availability (<10%–30%; II, IV, V), tree canopy cover (>10%; I, II, IV), and cultivation (>25%; I, II, IV, V) each reduced movement beyond their respective thresholds. Model validations confirmed variation in predictive ability across MZs with top resistance surfaces better predicting gene flow than geographic distance alone, especially in cases of low and high differentiation among lek groups. The resultant resistance maps we produced spatially depict the strength and redundancy of range‐wide gene flow and can help direct conservation actions to maintain and restore functional connectivity for sage‐grouse.

Genetic networks can characterize complex genetic relationships among groups of individuals, which can be used to rank nodes most important to the overall connectivity of the system. Ranking allows scarce resources to be guided toward nodes integral to connectivity. The greater sage‐grouse (Centrocercus urophasianus) is a species of conservation concern that breeds on spatially discrete leks that must remain connected by genetic exchange for population persistence. We genotyped 5,950 individuals from 1,200 greater sage‐grouse leks distributed across the entire species’ geographic range. We found a small‐world network composed of 458 nodes connected by 14,481 edges. This network was composed of hubs—that is, nodes facilitating gene flow across the network—and spokes—that is, nodes where connectivity is served by hubs. It is within these hubs that the greatest genetic diversity was housed. Using indices of network centrality, we identified hub nodes of greatest conservation importance. We also identified keystone nodes with elevated centrality despite low local population size. Hub and keystone nodes were found across the entire species’ contiguous range, although nodes with elevated importance to network‐wide connectivity were found more central: especially in northeastern, central, and southwestern Wyoming and eastern Idaho. Nodes among which genes are most readily exchanged were mostly located in Montana and northern Wyoming, as well as Utah and eastern Nevada. The loss of hub or keystone nodes could lead to the disintegration of the network into smaller, isolated subnetworks. Protecting both hub nodes and keystone nodes will conserve genetic diversity and should maintain network connections to ensure a resilient and viable population over time. Our analysis shows that network models can be used to model gene flow, offering insights into its pattern and process, with application to prioritizing landscapes for conservation.

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Connectivity of populations influences the degree to which species maintain genetic diversity and persist despite local extinctions. Natural landscape features are known to influence connectivity, but global anthropogenic landscape change underscores the importance of quantifying how human-modified landscapes disrupt connectivity of natural populations. Grasslands of western North America have experienced extensive habitat alteration, fragmenting populations of species such as blacktailed prairie dogs (Cynomys ludovicianus). Population sizes and the geographic range of prairie dogs have been declining for over a century due to habitat loss, disease, and eradication efforts. In many places, prairie dogs have persisted in the face of emerging urban landscapes that carve habitat into smaller and smaller fragments separated by uninhabitable areas. In extreme cases, prairie dog colonies are completely bounded by urbanization. Connectivity is particularly important for prairie dogs because colonies suffer high probabilities of extirpation by plague, and dispersal permits recolonization. Here we explore connectivity of prairie dog populations using analyses of 11 microsatellite loci for 9 prairie dog colonies spanning the fragmented landscape of Boulder County, Colorado. Isolation-by-resistance modeling suggests that wetlands and high intensity urbanization limit movement of prairie dogs. However, prairie dogs appear to move moderately well through low intensity development (including roads) and freely through cropland and grassland. Additionally, there is a marked decline in gene flow between colonies with increasing geographic distance, indicating isolation by distance even in an altered landscape. Our results suggest that prairie dog colonies retain some connectivity despite fragmentation by urbanization and agricultural development.

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Characterizing genetic structure across a species’ range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity. Wide-ranging species residing in continuously distributed habitat pose substantial challenges for the characterization of genetic structure as many analytical methods used are less effective when isolation by distance is an underlying biological pattern. Here, we illustrate strategies for overcoming these challenges using a species of significant conservation concern, the Greater Sage-grouse (Centrocercus urophasianus), providing a new method to identify centers of genetic differentiation and combining multiple methods to help inform management and conservation strategies for this and other such species. Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation and, following our novel method, 12 subpopulation centers of differentiation. Gene flow was greater, and differentiation reduced in areas of contiguous habitat (eastern Montana, most of Wyoming, much of Oregon, Nevada, and parts of Idaho). As expected, areas of fragmented habitat such as in Utah (with 6 subpopulation centers) exhibited the greatest genetic differentiation and lowest effective migration. The subpopulation centers defined here could be monitored to maintain genetic diversity and connectivity with other subpopulation centers. Many areas outside subpopulation centers are contact zones where different genetic groups converge and could be priorities for maintaining overall connectivity. Our novel method and process of leveraging multiple different analyses to find common genetic patterns provides a path forward to characterizing genetic structure in wide-ranging, continuously distributed species.

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