Are all data types and connectivity models created equal? Validating common connectivity approaches with dispersal data

Aim

There is enormous interest in applying connectivity modelling to resistance surfaces for identifying corridors for conservation action. However, the multiple analytical approaches used to estimate resistance surfaces and predict connectivity across resistance surfaces have not been rigorously compared, and it is unclear what methods provide the best inferences about population connectivity. Using a large empirical data set on puma (Puma concolor), we are the first to compare several of the most common approaches for estimating resistance and modelling connectivity and validate them with dispersal data.

Location

Southern California, USA.

Methods

We estimate resistance using presence‐only data, GPS telemetry data from puma home ranges and genetic data using a variety of analytical methods. We model connectivity with cost distance and circuit theory algorithms. We then measure the ability of each data type and connectivity algorithm to capture GPS telemetry points of dispersing pumas.

Results

We found that resource selection functions based on GPS telemetry points and paths outperformed species distribution models when applied using cost distance connectivity algorithms. Point and path selection functions were not statistically different in their performance, but point selection functions were more sensitive to the transformation used to convert relative probability of use to resistance. Point and path selection functions and landscape genetics outperformed other methods when applied with cost distance; no methods outperformed one another with circuit theory.

Main conclusions

We conclude that path or point selection functions, or landscape genetic models, should be used to estimate landscape resistance for wildlife. In cases where resource limitations prohibit the collection of GPS collar or genetic data, our results suggest that species distribution models, while weaker, may still be sufficient for resistance estimation. We recommend the use of cost distance‐based approaches, such as least‐cost corridors and resistant kernels, for estimating connectivity and identifying functional corridors for terrestrial wildlife.

     

Neuroanatomy: uninhibited connectivity in neocortex?

The mouse neocortex is now the focus of research using twenty-first century techniques of circuit analyses, which are revealing different wiring strategies for excitatory and inhibitory connections and providing important insights into the possible computations of cortical circuits.     

What can genetics tell us about population connectivity?

Genetic data are often used to assess ‘population connectivity’ because it is difficult to measure dispersal directly at large spatial scales. Genetic connectivity, however, depends primarily on the absolute number of dispersers among populations, whereas demographic connectivity depends on the relative contributions to population growth rates of dispersal vs. local recruitment (i.e. survival and reproduction of residents). Although many questions are best answered with data on genetic connectivity, genetic data alone provide little information on demographic connectivity. The importance of demographic connectivity is clear when the elimination of immigration results in a shift from stable or positive population growth to negative population growth. Otherwise, the amount of dispersal required for demographic connectivity depends on the context (e.g. conservation or harvest management), and even high dispersal rates may not indicate demographic interdependence. Therefore, it is risky to infer the importance of demographic connectivity without information on local demographic rates and how those rates vary over time. Genetic methods can provide insight on demographic connectivity when combined with these local demographic rates, data on movement behaviour, or estimates of reproductive success of immigrants and residents. We also consider the strengths and limitations of genetic measures of connectivity and discuss three concepts of genetic connectivity that depend upon the evolutionary criteria of interest: inbreeding connectivity, drift connectivity, and adaptive connectivity. To conclude, we describe alternative approaches for assessing population connectivity, highlighting the value of combining genetic data with capture‐mark‐recapture methods or other direct measures of movement to elucidate the complex role of dispersal in natural populations.     

Functional connectivity of the entorhinal–hippocampal space circuit

The mammalian space circuit is known to contain several functionally specialized cell types, such as place cells in the hippocampus and grid cells, head-direction cells and border cells in the medial entorhinal cortex (MEC). The interaction between the entorhinal and hippocampal spatial representations is poorly understood, however. We have developed an optogenetic strategy to identify functionally defined cell types in the MEC that project directly to the hippocampus. By expressing channelrhodopsin-2 (ChR2) selectively in the hippocampus-projecting subset of entorhinal projection neurons, we were able to use light-evoked discharge as an instrument to determine whether specific entorhinal cell groups—such as grid cells, border cells and head-direction cells—have direct hippocampal projections. Photoinduced firing was observed at fixed minimal latencies in all functional cell categories, with grid cells as the most abundant hippocampus-projecting spatial cell type. We discuss how photoexcitation experiments can be used to distinguish the subset of hippocampus-projecting entorhinal neurons from neurons that are activated indirectly through the network. The functional breadth of entorhinal input implied by this analysis opens up the potential for rich dynamic interactions between place cells in the hippocampus and different functional cell types in the entorhinal cortex (EC).     

Does habitat fragmentation reduce genetic diversity and subpopulation connectivity?

The estimation of levels of genetic variation has received considerable attention because it is generally thought to be indicative of overall species vitality and the potential for evolutionary responses to environmental changes. Here, we use allozymes markers and two distinct collections of Cakile maritima, an annual species from sandy coastal habitats (2000 generation and 2005 generation collected from 9 populations in their natural habitats), to assess the magnitude of expected genetic change. We compared genetic diversity between generations (all populations combined), and then between populations at each generation. Based on 13 loci scored from the eight enzymes examined, a high genetic diversity was detected at both the population and generation level as compared to other herbaceous species. However, allelic richness reduction in the 2005 generation suggested restricted gene flow and a high risk of future genetic bottlenecks, if larger tracts of coastal areas disappear. Most loci showed deviation from Hardy‐Weinberg equilibrium due to excess of heterozygotes in all populations suggesting that this species has an allogamic mode of reproduction. It appears most likely that this species has experienced a recent decrease in population size, and that genetic drift in small populations has resulted in a loss of alleles occurring at low frequency. Despite the deterioration process, maintenance of high genetic diversity suggests that there are some ecological factors determining population structure.     

Intrinsic curvature: a marker of millimeter-scale tangential cortico-cortical connectivity?

In this paper, we draw a link between cortical intrinsic curvature and the distributions of tangential connection lengths. We suggest that differential rates of surface expansion not only lead to intrinsic curvature of the cortical sheet, but also to differential inter-neuronal spacing. We propose that there follows a consequential change in the profile of neuronal connections: specifically an enhancement of the tendency towards proportionately more short connections. Thus, the degree of cortical intrinsic curvature may have implications for short-range connectivity.     

How does temporal variation in habitat connectivity influence metapopulation dynamics?

Metapopulation persistence depends on connectivity between habitat patches. While emphasis has been placed on the spatial dynamics of connectivity, much less has been placed on its short‐term temporal dynamics. In many terrestrial and aquatic ecosystems, however, transient (short‐term) changes in connectivity occur as habitat patches are connected and disconnected due, for example, to climatic or hydrological variability. We evaluated the implications of transient connectivity using a network‐based metapopulation model and a series of scenarios representing temporal changes in connectivity. The transient loss of connectivity can influence metapopulation persistence, and more strongly autocorrelated temporal dynamics affect metapopulation persistence more severely. Given that many ecosystems experience short‐term and temporary loss of habitat connectivity, it is important that these dynamics are adequately represented in metapopulation models; failing to do so may yield overly optimistic‐estimates of metapopulation persistence in fragmented landscapes.     

How do neural connectivity and time delays influence bimanual coordination?

Multilevel crosstalk as a neural basis for motor control has been widely discussed in the literature. Since no natural process is instantaneous, any crosstalk model should incorporate time delays, which are known to induce temporal coupling between functional elements and stabilize or destabilize a particular mode of coordination. In this article, we systematically study the dynamics of rhythmic bimanual coordination under the influence of varying connection topology as realized by callosal fibers, cortico-thalamic projections, and crossing peripheral fibers. Such connectivity contributes to various degrees of neural crosstalk between the effectors which we continuously parameterize in a mathematical model. We identify the stability regimes of bimanual coordination as a function of the degree of neural crosstalk, movement amplitude and the time delays involved due to signal processing. Prominent examples include explanations of the decreased stability of the antiphase mode of coordination in split brain patients and the role of coupling in mediating bimanual coordination.     

Biotic wetland connectivity—supporting a new approach for wetland policy

Wetlands are key habitats connected physically and socially with processes occurring over a much wider territory. The biotic connection through dispersal mechanisms among wetlands is of primary importance to wetland management and policies. However, traditional wetland conservation approaches are based on the preservation of isolated sites considered to be of special importance (typically owing to their importance for concentrations of migratory waterbirds). Research linking local species richness and bird migration suggests that the effect of wetland loss on regional diversity might be much larger than what would be expected from direct habitat loss. Since the biotic connection among wetlands serviced by waterbirds appears to be more efficient within a limited range, the distribution of wetlands in space is a key aspect determining wetland connectedness even in the absence of direct hydrologic links. Protected areas should thus be defined with regard to waterfowl movements and waterbird migration as functional processes contributing to aquatic species migration and local species richness. This calls for a regional approach to wetland management within a continental context. This paper aims at defining an operational view of the dispersion function of wetlands and its implication for conservation policies. For this purpose, we examined the conservation policies of the Ramsar Convention (the international treaty that protects wetlands) and the European Union (as an example of relevant continental level policy-making) from the viewpoint of bird-mediated dispersal of aquatic organisms. We propose nine specific avenues for the inclusion of bird-mediated dispersal in the policy documents examined. Non-governmental organisations and other organisations working in waterbird conservation should also recognise the importance of their policies for aquatic biodiversity at broader levels and avoid compartmentalising their conservation activities.     

Will reduced host connectivity curb the spread of a devastating epidemic?

The white‐nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans, is threatening the cave‐dwelling bat fauna of North America by killing individuals by the thousands in hibernacula each winter since its appearance in New York State less than ten years ago. Epidemiological models predict that WNS will reach the western coast of the USA by 2035, potentially eliminating most populations of susceptible bat species in its path (Frick et al. 2015; O'Regan et al. 2015). These models were built and validated using distributional data from the early years of the epidemic, which spread throughout eastern North America following a route driven by cave density and winter severity (Maher et al. 2012). In this issue of Molecular Ecology, Wilder et al. (2015) refine these findings by showing that connectivity among host populations, as assessed by population genetic markers, is crucial in determining the spread of the pathogen. Because host connectivity is much reduced in the hitherto disease free western half of North America, Wilder et al. make the reassuring prediction that the disease will spread more slowly west of the Great Plains.     

Importance of spatio–temporal connectivity to maintain species experiencing range shifts

Climate change can affect the habitat resources available to species by changing habitat quantity, suitability and spatial configuration, which largely determine population persistence in the landscape. In this context, dispersal is a central process for species to track their niche. Assessments of the amount of reachable habitat (ARH) using static snap-shots do not account, however, for the temporal overlap of habitat patches that may enhance stepping-stone effects. Here, we quantified the impacts of climate change on the ARH using a spatio–temporal connectivity model. We first explored the importance of spatio–temporal connectivity relative to purely spatial connectivity in a changing climate by generating virtual species distributions and analyzed the relative effects of changes in habitat quantity, suitability and configuration. Then, we studied the importance of spatio–temporal connectivity in three vertebrate species with divergent responses to climate change in North America (grey wolf, Canadian lynx and white-tailed deer). We found that the spatio–temporal connectivity could enhance the stepping-stone effect for species predicted to experience range contractions, and the relative importance of the spatio–temporal connectivity increased with the reduction in habitat quantity and suitability. Conversely, for species that are likely to expand their ranges, spatio–temporal connectivity had no additional contribution to improve the ARH. We also found that changes in habitat amount (quantity and suitability) were more influential than changes in habitat configuration in determining the relative importance of spatio–temporal connectivity. We conclude that spatio–temporal connectivity may provide less biased and more realistic estimates of habitat connectivity than purely spatial connectivity.     

Do wooded streets provide connectivity for bats in an urban landscape?

The effects of urbanization on bats are poorly understood, but published data suggests it might be detrimental to them. Even though urban parks provide refuge to native biota, the nature of the urban landscape exacerbates the insularization process. In order to evaluate if wooded streets in an urban landscape provide connectivity for bats, we compared bat community structure in three different types of habitats: urban parks, wooded streets and non-wooded streets. Sampling occurred monthly from August 2006 to July 2007 in the city of Vitória, southeastern Brazil. Richness, relative abundance and diversity were higher in urban parks and lower in non-wooded streets. Jaccard’s similarity index showed that the wooded streets are more similar to non-wooded streets than to urban parks. Urbanization may benefit generalist species by providing new resources, but for specialist species critical resources may be lost and persistence endangered. There is evidence that wooded streets may provide some degree of connectivity for birds in urban landscapes, but our results suggest that this is not the case, with wooded streets being used by few individuals of a few species. Vegetation cover is important to maintain bat diversity in urban centers. Activities like landscape planning and gardening should include biodiversity data in their outputs in order to better design a landscape that improves the likelihood of persistence of bats.     

Structure of α-conotoxin BuIA: influences of disulfide connectivity on structural dynamics

Background  

α-Conotoxins have exciting therapeutic potential based on their high selectivity and affinity for nicotinic acetylcholine receptors. The spacing between the cysteine residues in α-conotoxins is variable, leading to the classification of sub-families. BuIA is the only α-conotoxin containing a 4/4 cysteine spacing and thus it is of significant interest to examine the structure of this conotoxin.     

Do landscape barriers affect functional connectivity of populations of an endangered damselfly?

1. Landscape genetic approaches were used to assess functional connectivity of populations of the endangered damselfly Coenagrion mercuriale in a fragmented agricultural landscape in Switzerland. Spatial genetic clustering methods combined with interpolation by kriging and landscape genetic corridor analysis were applied to identify landscape elements that enhance or hinder dispersal and gene flow. 2. Spatial genetic clustering analysis divided the sampled populations into a northern and a southern genetic group. The boundary between the two groups coincided with a hill ridge intersecting the study area. Landscape corridor analysis identified five landscape elements that significantly affected gene flow. Elevation change, Euclidian distance, patches of forest and flowing waterbodies acted as barriers, whereas open agricultural land enhanced gene flow between populations of C. mercuriale. 3. This study showed that movement of C. mercuriale was not restricted to its preferred habitat (i.e. streams). Populations linked via continuous open agricultural land were functionally well connected if they were not more than about 1.5–2 km apart. In contrast, substantial elevation change and larger forest patches separated populations. These findings may serve as a basis to define conservation units and should be considered when planning connectivity measures, such as determining the locations of stepping stones, or the restoration of streams.     

Does seasonality and pool connectivity influence fish trophic ecology in knickzone habitats?

Knickzones are large rock outcrops found in upstream and middle plateau river basins. This kind of geological formation, which is considered a macrohabitat, creates a complex of mesohabitats: pools, riffles and runs, with distinct characteristics. In the present work, the aim was to evaluate the influence of connectivity and seasonality on the trophic structure of the ichthyofauna found in knickzone pools. Fish were sampled in four connected and three isolated pools, during dry and rainy seasons, and the stomach contents of 20 species were analyzed. Seasonal differences in diet occurred, with greater contribution of algae and aquatic hexapod in the dry season and of plant fragments and organic matter in the rainy season. The high diet overlap found in the isolated pools may be related to more intensive biotic interactions among individuals confined in physically restricted habitats. Seasonality in combination with connectivity to the main channel influenced the trophic structure of fish assemblage in the knickzone. Knickzones dynamics are modulated by seasonal events, such as floods, and connectivity of habitats, being extremely important for the trophic interactions between species. Alterations to these dynamics, like the construction of hydroelectric power plants, can modify significantly the trophic ecology of knickzones.     

Ecological connectivity or Barrier Fence? Critical choices on the agricultural margins of Western Australia

Western Australia's State Barrier Fence represents a continuation of colonial era attitudes that considered kangaroos, emus and dingoes as ‘vermin’. Recent plans to upgrade and extend the Barrier Fence have shown little regard for ecological impacts or statutory environmental assessment processes.     

Using connectivity metrics in conservation planning – when does habitat quality matter?

Aim The objective of conservation planning is often to prioritize patches based on their estimated contribution to metapopulation or metacommunity viability. The contribution that an individual patch makes will depend on its intrinsic characteristics, such as habitat quality, as well as its location relative to other patches, its connectivity. Here we systematically evaluate five patch value metrics to determine the importance of including an estimate of habitat quality into the metrics. Location We tested the metrics in landscapes designed to represent different degrees of variability in patch quality and different levels of patch aggregation. Methods In each landscape, we simulated population dynamics using a spatially explicit, continuous time metapopulation model linked to within patch logistic growth models. We tested five metrics that are used to estimate the contribution that a patch makes to metapopulation viability: two versions of the probability of connectivity index, two versions of patch centrality (a graph theory metric) and the metapopulation capacity metric. Results All metrics performed best in environments where patch quality was very variable and high quality patches were aggregated. Metrics that incorporated some measure of patch quality did better in all environments, but did particularly well in environments with high variance of patch quality and spatial aggregation of good quality patches. Main conclusions Including an estimate of patch quality significantly increased the ability of a given connectivity metric to rank correctly habitat patches according to their contribution to metapopulation viability. Incorporating patch quality is particularly important in landscapes where habitat quality is highly variable and good quality patches are spatially aggregated. However, caution should be used when applying patch metrics to homogeneous landscapes, even if good estimates of patch quality are available. Our results demonstrate that landscape structure and the degree of variability in patch quality need to be assessed prior to selecting a suitable method for estimating patch value.     

Estimates of connectivity reveal non-equilibrium epiphyte occurrence patterns almost 180 years after habitat decline

Habitat loss is a major cause of species decline and extinction. Immediately after habitat loss, species occurrences are not in equilibrium with the new landscape and more closely reflect the previous landscape structure. Species with slow colonisation–extinction dynamics may display long time-lags before reaching a new equilibrium. We investigated the importance of connectivity to current and historical dispersal sources with the aim of explaining the occurrence pattern of epiphytic lichens with different traits among 104 old oaks. We used oak survey data collected from 1830 and 2009 for a Swedish landscape where oak densities declined drastically shortly after 1830. We fitted a commonly used connectivity measure and estimated the confidence interval for the spatial scale parameter. Small differences in the spatial scale parameter resulted in large differences in model fit. Connectivity to trees in 1830 better explained the occurrence of three of the four species compared to the connectivity in 2009. The explanatory power of the historical landscape structure was highest for the species with traits that may result in a low colonisation rate—both a narrow niche (here few suitable trees) and large dispersal propagules. The results suggest that oak-dependent epiphytic lichens have not reached equilibrium with the spatial landscape structure 180 years after the drastic decline in habitat. For the long-term persistence of epiphytes associated with old trees, conservation efforts should focus on (1) protecting and restoring stands where specialised species with large dispersal propagules (i.e. with low colonisation rates) occur today and (2) promoting tree regeneration in their near vicinity.