Three-dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity

Using ecological niche modelling to prioritise areas for conservation of the critically endangered Buffy-Headed marmoset (Callithrix flaviceps)

Endemic to the Atlantic Forest in Southeastern Brazil, the critically endangered Buffy-Headed marmoset (Callithrix flaviceps) is lacking the required attention for effective conservation. We modelled its ecological niche with the main objectives of (1) defining suitable habitat and (2) prioritising areas for conservation and/or restoration. The current geographical range of Callithrix flaviceps in the Atlantic Forest of Southeast Brazil. We used Ensemble Species Distribution Modelling to define current habitat suitability considering four climate and two landscape variables. To identify areas to prioritise for conservation and/or restoration, we predicted future habitat suitability considering the intermediate (RCP4.5) and extreme (RCP8.5) climate change scenarios for the years 2050 and 2070. Among the variables included to predict current species distribution, tree canopy cover, precipitation seasonality and temperature seasonality were the most important whereas digital elevation model and precipitation during the wettest month were the least important. Callithrix flaviceps was most likely to occur in areas with tree canopy cover >80%, high precipitation seasonality and temperature seasonality between 21 and 23°C. From the future suitability prediction maps, the Caparaó National Park stands out as a likely key area for the preservation of the species. Furthermore, high climatic suitability but low landscape suitability suggests that habitat restoration in 'Serra das Torres' (South of the current distribution area) might be a useful strategy. However, creating ecological corridors on the west side of Caparaó would be necessary to improve connectivity. More surveys within and beyond the current geographical range are required to define more precisely the distribution of the species. Our results support the notion that seasonality is important for Callithrix flaviceps and that as a montane species, it prefers colder environments and higher altitudes. Within both climate change scenarios, Caparaó National Park was predicted to be highly suitable, with a high probability of presence.

Landscape resistance index aiming at functional forest connectivity

Resistance models may quantify the ability of the landscape to impede species' movement and represent suitable habitats. Moreover, the performance of resistance models parameterized by land-use/land cover attributes evidence that the integrity of the environments subject to urban sprawl is poorly understood. In this sense, the study assumed we could identify the forest functional connectivity in a landscape considering the disparity in the landscape mosaic. In this context, we sought to develop a landscape resistance index through structural equation modeling (SEM), supported by the criteria of heat emission, biomass, and anthropogenic barriers, obtained by remote sensing, called observed variables. The landscape studied in the Green Belt Biosphere Reserve of São Paulo has significant remnants of the Atlantic Forest, a biodiversity hotspot. However, our results indicated criteria variability in the landscape modeled through the SEM, obtaining a significant adjustment of the landscape resistance index, with comparative fit index (CFI) of 1.00 and root mean square error of approximation (RMSEA) of 0.00. The index reflects the resistance levels of the land use/land cover, expressed by the class interval, ranging from 0% (1.73) to 100% (493.88), with the highest values associated with the anthropized uses and forest isolation. Thus, our index based on environmental attributes reflects the structure of functional forest connectivity and offers a framework to design forest corridors across landscapes.

Spatial and temporal patterns in the population genomics of the European cockchafer Melolontha melolontha in the Alpine region

The European cockchafer Melolontha melolontha is an agricultural pest in many European countries. Populations have a synchronized 3 or 4 years life cycle, leading to temporally isolated populations. Despite the economic importance and availability of comprehensive historical as well as current records on cockchafer occurrence, population genomic analyses of M. melolontha are missing. For example, the effects of geographic separation caused by the mountainous terrain of the Alps and of temporal isolation on the genomic structure of M. melolontha still remain unknown. To address this gap, we genotyped 475 M. melolontha adults collected during 3 years from 35 sites in a central Alpine region. Subsequent population structure analyses discriminated two main genetic clusters, i.e., the South Tyrol cluster including collections located southeast of the Alpine mountain range, and a northwestern alpine cluster with all the other collections, reflecting distinct evolutionary history and geographic barriers. The "passo di Resia" linking South and North Tyrol represented a regional contact zone of the two genetic clusters, highlighting genomic differentiation between the collections from the northern and southern regions. Although the collections from northwestern Italy were assigned to the northwestern alpine genetic cluster, they displayed evidence of admixture with the South Tyrolean genetic cluster, suggesting shared ancestry. A linear mixed model confirmed that both geographic distance and, to a lower extent, also temporal isolation had a significant effect on the genetic distance among M. melolontha populations. These effects may be attributed to limited dispersal capacity and reproductive isolation resulting from synchronized and non-synchronized swarming flights, respectively. This study contributes to the understanding of the phylogeography of an organism that is recognized as an agricultural problem and provides significant information on the population genomics of insect species with prolonged temporally shifted and locally synchronized life cycles.

Terrain Ruggedness and Canopy Height Predict Short-Range Dispersal in the Critically Endangered Black-and-White Ruffed Lemur

Dispersal is a fundamental aspect of primates' lives and influences both population and community structuring, as well as species evolution. Primates disperse within an environmental context, where both local and intervening environmental factors affect all phases of dispersal. To date, research has primarily focused on how the intervening landscape influences primate dispersal, with few assessing the effects of local habitat characteristics. Here, we use a landscape genetics approach to examine between- and within-site environmental drivers of short-range black-and-white ruffed lemur (Varecia variegata) dispersal in the Ranomafana region of southeastern Madagascar. We identified the most influential drivers of short-range ruffed lemur dispersal as being between-site terrain ruggedness and canopy height, more so than any within-site habitat characteristic evaluated. Our results suggest that ruffed lemurs disperse through the least rugged terrain that enables them to remain within their preferred tall-canopied forest habitat. Furthermore, we noted a scale-dependent environmental effect when comparing our results to earlier landscape characteristics identified as driving long-range ruffed lemur dispersal. We found that forest structure drives short-range dispersal events, whereas forest presence facilitates long-range dispersal and multigenerational gene flow. Together, our findings highlight the importance of retaining high-quality forests and forest continuity to facilitate dispersal and maintain functional connectivity in ruffed lemurs.

Assessment of drivers of spatial genetic variation of a ground-dwelling bird species and its implications for conservation

In modern wildlife ecology, spatial population genetic methods are becoming increasingly applied. Especially for animal species in fragmented landscapes, preservation of gene flow becomes a high priority target in order to restore genetic diversity and prevent local extinction. Within Central Europe, the Alps represent the core distribution area of the black grouse, Lyrurus tetrix. At its easternmost Alpine range, events of subpopulation extinction have already been documented in the past decades. Molecular data combined with spatial analyses can help to assess landscape effects on genetic variation and therefore can be informative for conservation management. Here, we addressed whether the genetic pattern of the easternmost Alpine black grouse metapopulation system is driven by isolation by distance or isolation by resistance. Correlative ecological niche modeling was used to assess geographic distances and landscape resistances. We then applied regression-based approaches combined with population genetic analyses based on microsatellite data to disentangle effects of isolation by distance and isolation by resistance among individuals and subpopulations. Although population genetic analyses revealed overall low levels of genetic differentiation, the ecological niche modeling showed subpopulations to be clearly delimited by habitat structures. Spatial genetic variation could be attributed to effects of isolation by distance among individuals and isolation by resistance among subpopulations, yet unknown effects might factor in. The easternmost subpopulation was the most differentiated, and at the same time, immigration was not detected; hence, its long-term survival might be threatened. Our study provides valuable insights into the spatial genetic variation of this small-scale metapopulation system of Alpine black grouse.

Demographic modeling informs functional connectivity and management interventions in Graham’s beardtongue

Functional connectivity (i.e., the movement of individuals across a landscape) is essential for the maintenance of genetic variation and persistence of rare species. However, illuminating the processes influencing functional connectivity and ultimately translating this knowledge into management practice remains a fundamental challenge. Here, we combine various population structure analyses with pairwise, population-specific demographic modeling to investigate historical functional connectivity in Graham’s beardtongue (Penstemon grahamii), a rare plant narrowly distributed across a dryland region of the western US. While principal component and population structure analyses indicated an isolation-by-distance pattern of differentiation across the species’ range, spatial inferences of effective migration exposed an abrupt shift in population ancestry near the range center. To understand these seemingly conflicting patterns, we tested various models of historical gene flow and found evidence for recent admixture (~ 3400 generations ago) between populations near the range center. This historical perspective reconciles population structure patterns and suggests management efforts should focus on maintaining connectivity between these previously isolated lineages to promote the ongoing transfer of genetic variation. Beyond providing species-specific knowledge to inform management options, our study highlights how understanding demographic history may be critical to guide conservation efforts when interpreting population genetic patterns and inferring functional connectivity.

Coupling urban 3-D information and circuit theory to advance the development of urban ecological networks

Ongoing, rapid urban growth accompanied by habitat fragmentation and loss challenges biodiversity conservation and leads to decreases in ecosystem services. Application of the concept of ecological networks in the preservation and restoration of connections among isolated patches of natural areas is a powerful conservation strategy. However, previous approaches often failed to objectively consider the impacts of complex 3-D city environments on ecological niches. We used airborne lidar-derived information on the 3-D structure of the built environment and vegetation and detailed land use and cover data to characterize habitat quality, niche diversity, and human disturbance and to predict habitat connectivity among 38 identified habitat core areas (HCAs) in Nanjing, China. We used circuit theory and Linkage Mapper to create a landscape resistance layer, simulate habitat connectivity, and identify and prioritize important corridors. We mapped 64 links by using current flow centrality to evaluate each HCA's contribution and the links that facilitate intact connectivity. Values were highest for HCA links located in the west, south, and northeast of the study area, where natural forests with complex 3-D structures predominate. Two smaller HCA areas had high centrality scores relative to their extents, which means they could act as important stepping stones in connectivity planning. The mapped pinch-point regions had narrow and fragile links among the HCAs, suggesting they require special protection. The barriers with the highest impact scores were mainly located at the HCA connections to Purple Mountain and, based on these high scores, are more likely to indicate important locations that can be restored to improve potential connections. Our novel framework allowed us to sufficiently convey spatially explicit information to identify targets for habitat restoration and potential pathways for species movement and dispersal. Such information is critical for assessing existing or potential habitats and corridors and developing strategic plans to balance habitat conservation and other land uses based on scientifically informed connectivity planning and implementation.

Standardizing Ecosystem Morphological Traits from 3D Information Sources

3D-imaging technologies provide measurements of terrestrial and aquatic ecosystems' structure, key for biodiversity studies. However, the practical use of these observations globally faces practical challenges. First, available 3D data are geographically biased, with significant gaps in the tropics. Second, no data source provides, by itself, global coverage at a suitable temporal recurrence. Thus, global monitoring initiatives, such as assessment of essential biodiversity variables (EBVs), will necessarily have to involve the combination of disparate data sets. We propose a standardized framework of ecosystem morphological traits - height, cover, and structural complexity - that could enable monitoring of globally consistent EBVs at regional scales, by flexibly integrating different information sources - satellites, aircrafts, drones, or ground data - allowing global biodiversity targets relating to ecosystem structure to be monitored and regularly reported.

Population genetic structure and habitat connectivity for jaguar (Panthera onca) conservation in Central Belize

BACKGROUND

Connectivity among jaguar (Panthera onca) populations will ensure natural gene flow and the long-term survival of the species throughout its range. Jaguar conservation efforts have focused primarily on connecting suitable habitat in a broad-scale. Accelerated habitat reduction, human-wildlife conflict, limited funding, and the complexity of jaguar behaviour have proven challenging to maintain connectivity between populations effectively. Here, we used non-invasive genetic sampling and individual-based conservation genetic analyses to assess genetic diversity and levels of genetic connectivity between individuals in the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We used expert knowledge and scientific literature to develop models of landscape permeability based on circuit theory with fine-scale landscape features as ecosystem types, distance to human settlements and roads to predict the most probable jaguar movement across central Belize.

RESULTS

We used 12 highly polymorphic microsatellite loci to identify 50 individual jaguars. We detected high levels of genetic diversity across loci (HE = 0.61, HO = 0.55, and NA = 9.33). Using Bayesian clustering and multivariate models to assess gene flow and genetic structure, we identified one single group of jaguars (K = 1). We identified critical areas for jaguar movement that fall outside the boundaries of current protected areas in central Belize. We detected two main areas of high landscape permeability in a stretch of approximately 18 km between Sittee River Forest Reserve and Manatee Forest Reserve that may increase functional connectivity and facilitate jaguar dispersal from and to Cockscomb Basin Wildlife Sanctuary. Our analysis provides important insights on fine-scale genetic and landscape connectivity of jaguars in central Belize, an area of conservation concern.

CONCLUSIONS

The results of our study demonstrate high levels of relatively recent gene flow for jaguars between two study sites in central Belize. Our landscape analysis detected corridors of expected jaguar movement between the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We highlight the importance of maintaining already established corridors and consolidating new areas that further promote jaguar movement across suitable habitat beyond the boundaries of currently protected areas. Continued conservation efforts within identified corridors will further maintain and increase genetic connectivity in central Belize.

Assessing changes in functional connectivity in a desert bighorn sheep metapopulation after two generations

Determining how species move across complex and fragmented landscapes and interact with human-made barriers is a major research focus in conservation. Studies estimating functional connectivity from movement, dispersal or gene flow usually rely on a single study period and rarely consider variation over time. We contrasted genetic structure and gene flow across barriers for a metapopulation of desert bighorn sheep (Ovis canadensis nelsoni) using genotypes collected 2000-2003 and 2013-2015. Based on the recently observed but unexpected spread of a respiratory pathogen across an interstate highway previously identified as a barrier to gene flow, we hypothesized that bighorn sheep changed how they interacted with that barrier, and that shifts in metapopulation structure influenced gene flow, genetic diversity and connectivity. Population assignment tests, genetic structure and genetic recapture demonstrated that bighorn sheep crossed the interstate highway in at least one location in 2013-2015, sharply reducing genetic structure between two populations, but supported conclusions of an earlier study that such crossings were very infrequent or unknown in 2000-2003. A recently expanded population established new links and caused decreases in genetic structure among multiple populations. Genetic diversity showed only slight increases in populations linked by new connections. Genetic structure and assignments revealed other previously undetected changes in movements and distribution, but much was consistent. Thus, we observed changes in both structural and functional connectivity over just two generations, but only in specific locations. Movement patterns of species should be revisited periodically to enable informed management, particularly in dynamic and fragmented systems.