Cody M. Aylward

Implementing ecological connectivity conservation in large landscapes requires cutting-edge science combined with consideration of ecological, socioeconomic, and cultural factors that collectively shape the outcomes of conservation efforts. We outline a theory of change (ToC) for connectivity conservation to improve the ecological condition of landscapes and biodiversity and the ecosystem services upon which humans depend. We review connectivity conservation efforts on four continents in large landscapes that span gradients of latitude, fragmentation, biodiversity value, socioeconomic characteristics, and the richness of data used to assess connectivity and target action. We share the substantial but variable progress made in each landscape and outline specific challenges to achieving conservation goals. Opportunities and challenges in public and private sectors can further leverage the potential of large-scale connectivity conservation to reduce isolation and improve gene flow in functional landscapes worldwide.

Populations on the periphery of a species range generally occupy marginal or less continuous habitat and can have greater extinction risk than populations in the range‐center. For climate‐sensitive populations on the trailing edge of a species' distribution (i.e. low latitude or low elevation), the effects of climate change are expected to compound these threats, increasing the vulnerability of these populations. The spruce grouse Canachites canadensis is a boreal forest specialist that is expected to experience range contraction at the trailing edge of its range due to climate change. In this study, we investigated the genetic structure, genetic diversity, and connectivity of spruce grouse in Minnesota, along the southeastern range limit in the United States. Clustering algorithms and genetic diversity indices suggested a single continuous population occurred throughout northern Minnesota. We detected no signatures of recent inbreeding or population bottlenecks. We used maximum likelihood population effects modeling and identified coniferous forest land cover and lower average spring temperatures as predictors of gene flow. We used two approaches based on circuit theory to map the potential for gene flow and identified regions of consistently high gene flow in the northwest and northeast of the study area. Omniscape, which incorporated additional parameters representing the likely origins of dispersers and the maximum dispersal distance, suggested a more continuous gene flow landscape than did Circuitscape. Our work highlights the current genetic integrity of one of the largest populations of the eastern subspecies of spruce grouse C. c. canadensis in the United States, identifies key landscape attributes for functional connectivity, and demonstrates complementary approaches of Circuitscape and Omniscape for gene flow mapping.

During animal migration, ephemeral communities of taxa at all trophic levels co‐occur over space and time. The interactions between predators and prey along migration corridors are ecologically and evolutionarily significant. However, these interactions remain understudied in terrestrial systems and warrant further investigations using novel approaches. We investigated the predator–prey interactions between a migrating avivorous predator and ephemeral avian prey community in the fall migration season. We tested for associations between avian traits and prey selection and hypothesized that prey traits (i.e. relative size, flocking behaviour, habitat, migration tendency and availability) would influence prey selection by a sexually dimorphic raptor on migration. To document prey consumption, we sampled trace prey DNA from beaks and talons of migrating sharp‐shinned hawks Accipiter striatus (n = 588). We determined prey availability in the ephemeral avian community by extracting weekly abundance indices from eBird Status and Trends data. We used discrete choice models to assess prey selection and visualized the frequency of prey in diet and availability on the landscape over the fall migration season. Using eDNA metabarcoding, we detected prey species on 94.1% of the hawks sampled (n = 525/588) comprising 1396 prey species detections from 65 prey species. Prey frequency in diet and eBird relative abundance of prey species were correlated over the migration season for top‐selected prey species, suggesting prey availability is an important component of raptor‐songbird interactions during fall. Prey size, flocking behaviour and non‐breeding habitat association were prey traits that significantly influenced predator choice. We found differences between female and male hawk prey selection, suggesting that sexual size dimorphism has led to distinct foraging strategies on migration. This research integrated field data collected by a volunteer‐powered raptor migration monitoring station and public‐generated data from eBird to reveal elusive predator–prey dynamics occurring in an ephemeral raptor‐songbird community during fall migration. Understanding dynamic raptor‐songbird interactions along migration routes remains a relatively unexplored frontier in animal ecology and is necessary for the conservation and management efforts of migratory and resident communities.

Coastal wetland ecosystems support unique biodiversity and are imminently threatened by climate change-driven sea level rise. However, the impact of climate change on their demographic and evolutionary histories is poorly understood. To improve our understanding, we examined how past climatic events have shaped the evolutionary history of the salt marsh harvest mouse (Reithrodontomys raviventris), an endangered species and a salt marsh habitat specialist, completely restricted to coastal wetlands in the San Francisco Estuary (SFE). We used whole mitochondrial genome sequences of 102 salt marsh harvest mice to characterize phylogeography and demographic history. Then, we predicted the ancient distribution of salt marsh habitat and examined correspondence between divergence, demographic history, and changes in ancient marsh habitat caused by sea level rise. A Bayesian Skyline Plot revealed demographic expansions during periods of sea level rise, particularly during the formation of the modern SFE (~ 10 kya), and rapid decline consistent with recent anthropogenic landscape change. Bayesian estimates of divergence time were consistent with subspecies divergence ~ 10 kya, and subpopulation divergence ~ 5 kya, consistent with multiple episodes of vicariance caused by Holocene sea level rise. Spatial Analysis of Molecular Variance and Φ_ST revealed a mismatch between the morphological and molecular subspecies assignment of two populations. Our study implicates sea level rise as a force of demographic change and evolutionary divergence in coastal marsh ecosystems. Our study also aids conservation of an endangered species by clarifying genetic subspecies boundaries and highlighting the unique nature of isolated populations that are increasingly threatened by modern sea level rise.

Context: The area-isolation paradigm of metapopulation theory predicts that larger and more connected patches have a higher probability of occupancy. Although it may be too simplistic for generalist terrestrial mammals, the area-isolation paradigm may be an effective tool for assessing patch-occupancy for habitat specialists. Objectives: We tested predictions of the area-isolation paradigm for the endangered salt marsh harvest mouse (Reithrodontomys raviventris), a habitat specialist living in highly fragmented salt marsh habitat in the San Francisco Estuary (California, USA). Methods: We surveyed for salt marsh harvest mice at 47 marsh patches throughout their range using a non-invasive genetic survey technique. We used occupancy modeling to estimate the effects of patch size, patch connectivity, matrix urbanization, and several habitat characteristics on occupancy probabilities. We evaluated occupancy at both coarse (e.g., among patches) and fine (e.g., within patches) spatial scales. Results: Patch size, connectivity, and matrix urbanization had significant effects on patch-occupancy. Within patches, occupancy was positively related to the presence of high-tide escape vegetation. Our data also revealed the extirpation of several geographically distinct populations, consistent with expectations due to reduced patch sizes and connectivity over the past century. Conclusions: Patterns of salt marsh harvest mouse patch-occupancy were consistent with the area-isolation paradigm. In addition, our models provide important guidelines of patch size and connectivity that can inform habitat conservation and restoration for this endangered species. Specifically, our data suggests that selecting restoration sites that are well-connected may be more beneficial than selecting larger, isolated sites.

Noninvasive genetic surveys, often conducted by collecting fecal samples, have become a popular tool for surveying wildlife, but have primarily been applied to species with large and conspicuous scat. Although many small mammals are threatened, endangered, or data deficient, noninvasive genetic surveys have rarely been applied due to the challenges of detecting their inconspicuous fecal pellets. As part of a broader study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), we developed a noninvasive genetic survey technique for the community of small mammals in their putative range. We designed bait stations to passively collect fecal samples from rodents, and developed a multiplex primer set that amplified unique fragment sizes for salt marsh harvest mice and four other sympatric species. We tested the primer set on positive controls and on fecal pellets collected from bait stations at two regularly monitored field sites known to have very different densities of salt marsh harvest mice. The multiplex amplified DNA from all five species, even when all five species were present in a single sample. A positive species identification was made for all field-collected samples, and 43% of these field-collected samples had multispecies detections. The combination of bait stations and genetic species identification proved to be an effective means of noninvasively surveying small mammals in potential salt marsh harvest mouse habitat. The sampling technique should be applicable to a wide variety of small mammals in other systems.

The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non‐native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non‐native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non‐native rodents? RERA diet was dominated by two plants, native Salicornia and non‐native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co‐occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non‐native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant.

The critically endangered Amargosa vole (Microtus californicus scirpensis) is found only in rare marsh habitat near Tecopa, California in a plant community dominated by three-square bulrush (Schoenoplectus americanus). Since the earliest research on the Amargosa vole, the existing paradigm has been that these voles are obligatorily dependent on bulrush as their only food source and for the three-dimensional canopy and litter structure it provides for predator avoidance. However, no prior research has confirmed the diet of the Amargosa vole. In this study we characterized the Amargosa vole’ nutritional needs, analyzed the quality of bulrush by forage analysis, and performed microhistological and metabarcoding analyses of vole feces to determine what foods were consumed in the wild. All bulrush plant tissues analyzed were low in fat (from 0.9% of dry matter in roots to 3.6% in seeds), high in neutral detergent fiber (from 5.9% in rhizomes to 33.6% in seeds), and low in protein (7.3–8.4%). These findings support the conclusion that bulrush alone is unlikely to support vole survival and reproduction. Fecal microhistology and DNA metabarcoding revealed relatively diverse diets including plants in 14 families, with rushes (Juncaceae), bulrushes (Cyperaceae), and grasses (Poaceae) being the most common diet items. On microhistology, all analyzed samples contained bulrush, sedges (Carex sp.), rushes (Juncus sp.), and beaked spikerush (Eleocharis rostrellata) even from marshes where non-bulrush plants were uncommon. There was evidence of insects at Schoenoplectus targets, for which metabarcoding had poor sensitivity, saltgrass (Distichlis spicata) was the most commonly detected species, with prominent contributions from seaside arrowgrass (Triglochin concinna) and yerba mansa (Anemopsis californica) as well. Diversity of vole diets generally increased with increasing site plant diversity, but differences were not statistically significant. Confirming details about dietary behaviors is critical for informing appropriate conservation planning including habitat management and reintroduction of voles into new sites.

American marten (Martes americana) are a conservation priority in many forested regions of North America. Populations are fragmented at the southern edge of their distribution due to suboptimal habitat conditions. Facilitating gene flow may improve population resilience through genetic and demographic rescue. We used a multiscale approach to estimate the relationship between genetic connectivity and landscape characteristics among individuals at three scales in the northeastern United States: regional, subregional, and local. We integrated multiple modeling techniques and identified top models based on consensus. Top models were used to parameterize resistance surfaces at each scale, and circuit theory was used to identify potential movement corridors. Regional gene flow was affected by forest cover, elevation, developed land cover, and slope. At subregional and local scales, the effects were site specific and included subsets of temperature, elevation, developed land cover, and slope. Developed land cover significantly affected gene flow at each scale. At finer scales, lack of variance in forest cover may have limited the ability to detect a relationship with gene flow. The effect of slope on gene flow was positive or negative, depending on the site examined. Occupancy probability was a relatively poor predictor, and we caution its use as a proxy for landscape resistance. Our results underscore the importance of replication and multiscale approaches in landscape genetics. Climate warming and landscape conversion may reduce the genetic connectivity of marten populations in the northeastern United States, and represent the primary challenges to marten conservation at the southern periphery of their range.