Multi-species genetic connectivity in a terrestrial habitat network

Reduced gene flow and bottleneck in the threatened giant armadillo (Priodontes maximus): implications for its conservation

The progressive fragmentation and loss of habitats represent the main threats for endangered species, causing genetic consequences that may have potential implications for a population's long-term persistence. Large mammals are the most affected species among vertebrates. The giant armadillo Priodontes maximus is a large South American mammal threatened species, showing nocturnal, solitary and fossorial behavior, occurring at low population densities, and its population dynamics are still poorly known. In this study, we carried out the first assessment of genetic variability and population genetic structure of the species, using a panel of 15 polymorphic microsatellites developed by high-throughput genome sequencing. The spatial Bayesian clustering, Fst and Dest results indicated the presence of two genetic clusters (K = 2) in the study area. These results suggest a reduction in gene flow between individuals inhabiting the Brazilian savanna (Cerrado) and the Pantanal wetlands, with the increased human-driven habitat modifications possibly contributing for this scenario. A bottleneck signal was detected in both populations, and a subpopulation structuring in the Cerrado may also be reflecting consequences of the extensive habitat modifications. Findings from this study provide important and useful information for the future maintenance of genetic diversity and long-term conservation of this flagship species.

Using sentinel nodes to evaluate changing connectivity in a protected area network

It has been recognized that well-connected networks of protected areas are needed to halt the continued loss of global biodiversity. The recently signed Kunming-Montreal biodiversity agreement commits countries to protecting 30% of terrestrial lands in well-connected networks of protected areas by 2030. To meet these ambitious targets, land-use planners and conservation practitioners will require tools to identify areas important for connectivity and track future changes. In this study we present methods using circuit theoretic models with a subset of sentinel park nodes to evaluate connectivity for a protected areas network. We assigned a lower cost to natural areas within protected areas, under the assumption that animal movement within parks should be less costly given the regulation of activities. We found that by using mean pairwise effective resistance (MPER) as an indicator of overall network connectivity, we were able to detect changes in a parks network in response to simulated land-use changes. As expected, MPER increased with the addition of high-cost developments and decreased with the addition of new, low-cost protected areas. We tested our sentinel node method by evaluating connectivity for the protected area network in the province of Ontario, Canada. We also calculated a node isolation index, which highlighted differences in protected area connectivity between the north and the south of the province. Our method can help provide protected areas ecologists and planners with baseline estimates of connectivity for a given protected area network and an indicator that can be used to track changes in connectivity in the future.

Does scale or method matter for conservation? Application of directional and omnidirectional connectivity models in spatial prioritizations

Introduction

The maintenance of habitat connections between fragmented habitat patches is vital for the conservation of wildlife populations and ecosystem functioning. The awareness of connectivity issues for species conservation has resulted in a growth of connectivity modeling and the application of these results in conservation planning. Such connectivity modeling efforts can include several decisions or data limitations, which could influence the connectivity results and ultimately a systematic conservation plan (SCP). However, there has been little investigation of how these different decisions on species, scale, and extent influence the ultimate conservation planning outcomes.

Methods

We modeled the connectivity of northern bobwhite (Colinus virginianus), North American river otter (Lontra canadensis), and black bear (Ursus americanus), three species with varying ecological requirements, through the Congaree Biosphere Region, South Carolina, USA. We modeled habitat suitability for each species using boosted regression trees and converted these results into resistance layers for the connectivity analyses. We compared models for each species at multistate regional and local extents using directional and omnidirectional circuit theory approaches. We then used the results from each modeling combination as conservation goals for three different SCPs to determine how connectivity modeling decisions may influence geographic conservation decisions.

Results

There was substantial positive spatial correlation between the three connectivity models of each species, and there appeared to be general agreement among mammals as to most important primary corridors. Across all species, the greatest agreement was between the omnidirectional and local directional models as compared with the regional directional plan, which highlighted a unique corridor. The omnidirectional conservation plan required the least amount of planning units to achieve its conservation goals, followed by the local and then regional directional plans that required over 200 km2 more land area to be conserved.

Discussion

Our results indicate that overall variations in connectivity modeling decisions may have only a moderate impact on the identification of important movement corridors for conservation at the local scale. Practitioners should base modeling decisions on the ecology of the study region, conservation question, and available computing resource.

First insights in terrestrial mammals monitoring in the Candelaria and Machay Reserves in the Ecuadorian Tropical Andes

Habitat disturbance leads to biodiversity decline and modifications in the landscape structure and composition, affecting both dispersal movements and ecological processes at different temporal and spatial scales. The Ecuadorian Tropical Andes harbour suitable habitats for the distribution of a wide variety of species; however, there is a lack of studies focused on mammal diversity and its association with the habitat attributes in the central-eastern slopes. Here, we reported the diversity of terrestrial mammals recorded between 2019 and 2021 in a camera-trap monitoring study in the Candelaria and Machay reserves in the upper basin of the Pastaza River, Ecuador. We performed site-occupancy probability analysis to assess the influence of spatial variables in the species' occurrence and also, based on natural marks, we reported preliminary findings in Andean bear individual identification. We detected 22 species of terrestrial mammals. Alpha diversity was similar between reserves with slightly higher species richness in Machay. Evenness indices showed unequal species distribution, with the Andean bear and domestic dogs exhibiting greater dominance. In addition, species composition was dissimilar between reserves, where the species turnover mostly explained the beta diversity. We observed that Andean bear and puma detections increased according to the natural vegetation cover. Conversely, domestic dogs were frequently detected in cells with an increasing proportion of pastures and crops. Additionally, we identified 26 Andean bears and six individuals recaptured during our study. Our results caution about the disturbance derived from human activities since we recorded unprecedented detections of domestic dogs in wild habitats. Nonetheless, it highlights the importance of private conservation areas (e.g. Candelaria, Machay and others) for supporting the occurrence and dispersal of terrestrial mammal species between larger areas in the upper basin of the Pastaza River.

Missing Interactions: The Current State of Multispecies Connectivity Analysis

Designing effective habitat and protected area networks, which sustain species-rich communities is a critical conservation challenge. Recent decades have witnessed the emergence of new computational methods for analyzing and prioritizing the connectivity needs of multiple species. We argue that the goal of prioritizing habitat for multispecies connectivity should be focused on long-term persistence of a set of species in a landscape or seascape. Here we present a review of the literature based on 77 papers published between 2010 and 2020, in which we assess the current state and recent advances in multispecies connectivity analysis in terrestrial ecosystems. We summarize the four most employed analytical methods, compare their data requirements, and provide an overview of studies comparing results from multiple methods. We explicitly look at approaches for integrating multiple species considerations into reserve design and identify novel approaches being developed to overcome computational and theoretical challenges posed by multispecies connectivity analyses. There is a lack of common metrics for multispecies connectivity. We suggest the index of metapopulation capacity as one metric by which to assess and compare the effectiveness of proposed network designs. We conclude that, while advances have been made over the past decade, the field remains nascent by its ability to integrate multiple species interactions into analytical approaches to connectivity. Furthermore, the field is hampered its ability to provide robust connectivity assessments for lack of a clear definition and goal for multispecies connectivity conservation.

Predicting wildlife corridors for multiple species in an East African ungulate community

Wildlife corridors are typically designed for single species, yet holistic conservation approaches require corridors suitable for multiple species. Modelling habitat linkages for wildlife is based on several modelling steps (each involving multiple choices), and in the case of multi-species corridors, an approach to optimize single species corridors to few or a single functional corridor for multiple species. To model robust corridors for multiple species and simultaneously evaluate the impact of methodological choices, we develop a multi-method approach to delineate corridors that effectively capture movement of multiple wildlife species, while limiting the area required. Using wildlife presence data collected along ground-based line transects between Lake Manyara and Tarangire National Parks, Tanzania, we assessed species-habitat association in both ensemble and stacked species distribution frameworks and used these to estimate linearly and non-linearly scaled landscape resistances for seven ungulate species. We evaluated habitat suitability and least-cost and circuit theory-based connectivity models for each species individually and generated a multi-species corridor. Our results revealed that species-habitat relationships and subsequent corridors differed across species, but the pattern of predicted landscape connectivity across the study area was similar for all seven species regardless of method (circuit theory or least-cost) and scaling of the habitat suitability-based cost surface (linear or non-linear). Stacked species distribution models were highly correlated with the seven species for all model outputs (r = 0.79 to 0.97), while having the greatest overlap with the individual species least-cost corridors (linear model: 61.6%; non-linear model: 60.2%). Zebra was the best single-species proxy for landscape connectivity. Overall, we show that multi-species corridors based on stacked species distribution models achieve relatively low cumulative costs for savanna ungulates as compared to their respective single-species corridors. Given the challenges and costs involved in acquiring data and parameterizing corridor models for multiple species, zebra may act as a suitable proxy species for ungulate corridor conservation in this system.

Effects of cost surface uncertainty on current density estimates from circuit theory

Background

Conservation practitioners are often interested in developing land use plans that increase landscape connectivity, which is defined as the degree to which the landscape facilitates or impedes movement among resource patches. Landscape connectivity is often estimated with a cost surface that indicates the varying costs experienced by an organism in moving across a landscape. True, or absolute costs are rarely known however, and therefore assigning costs to different landscape elements is often a challenge in creating cost surface maps. As such, we consider it important to understand the sensitivity of connectivity estimates to uncertainty in cost estimates.

Methods

We used simulated landscapes to test the sensitivity of current density estimates from circuit theory to varying relative cost values, fragmentation, and number of cost classes (i.e., thematic resolution). Current density is proportional to the probability of use during a random walk. Using Circuitscape software, we simulated electrical current between pairs of nodes to create current density maps. We then measured the correlation of the current density values across scenarios.

Results

In general, we found that cost values were highly correlated across scenarios with different cost weights (mean correlation ranged from 0.87 to 0.92). Changing the spatial configuration of landscape elements by varying the degree of fragmentation reduced correlation in current density across maps. We also found that correlations were more variable when the range of cost values in a map was high.

Discussion

The low sensitivity of current density estimates to relative cost weights suggests that the measure may be reliable for land use applications even when there is uncertainty about absolute cost values, provided that the user has the costs correctly ranked. This finding should facilitate the use of cost surfaces by conservation practitioners interested in estimating connectivity and planning linkages and corridors.

A Multispecies Assessment to Identify the Functional Connectivity of Amphibians in a Human-Dominated Landscape

Preserving functional connectivity is a key goal of conservation management. However, the spatially confined conservation areas may not allow for dispersal and gene flow for the intended long-term persistence of populations in fragmented landscapes. We provide a regional multi-species assessment to quantify functional connectivity for five amphibian species in a human dominated landscape in the Swiss lowlands. A set of resistance maps were derived based on expert opinion and a sensitivity analysis was conducted to compare the effect of each resistance scenario on modelled connectivity. Deriving multi-species corridors is a robust way to identify movement hotspots that provide valuable baseline information to reinforce protective measures and green infrastructure.

Contribution of Connectivity Assessments to Green Infrastructure (GI)

A major goal of green infrastructure (GI) is to provide functional networks of habitats and ecosystems to maintain biodiversity long-term, while at the same time optimizing landscape and ecosystem functions and services to meet human needs. Traditionally, connectivity studies are informed by movement ecology with species-specific attributes of the type and timing of movement (e.g., dispersal, foraging, mating) and movement distances, while spatial environmental data help delineate movement pathways across landscapes. To date, a range of methods and approaches are available that (a) are relevant across any organism and movement type independent of time and space scales, (b) are ready-to-use as standalone freeware or custom GIS implementation, and (c) produce appealing visual outputs that facilitate communication with land managers. However, to enhance the robustness of connectivity assessments and ensure that current trends in connectivity modeling contribute to GI with their full potential, common denominators on which to ground planning and design strategies are required. Likewise, comparable, repeatable connectivity assessments will be needed to put results of these scientific tools into practice for multi-functional GI plans and implementation. In this paper, we discuss use and limitations of state-of-the-art connectivity methods in contributing to GI implementation.

Circuit-theory applications to connectivity science and conservation

Conservation practitioners have long recognized ecological connectivity as a global priority for preserving biodiversity and ecosystem function. In the early years of conservation science, ecologists extended principles of island biogeography to assess connectivity based on source patch proximity and other metrics derived from binary maps of habitat. From 2006 to 2008, the late Brad McRae introduced circuit theory as an alternative approach to model gene flow and the dispersal or movement routes of organisms. He posited concepts and metrics from electrical circuit theory as a robust way to quantify movement across multiple possible paths in a landscape, not just a single least-cost path or corridor. Circuit theory offers many theoretical, conceptual, and practical linkages to conservation science. We reviewed 459 recent studies citing circuit theory or the open-source software Circuitscape. We focused on applications of circuit theory to the science and practice of connectivity conservation, including topics in landscape and population genetics, movement and dispersal paths of organisms, anthropogenic barriers to connectivity, fire behavior, water flow, and ecosystem services. Circuit theory is likely to have an effect on conservation science and practitioners through improved insights into landscape dynamics, animal movement, and habitat-use studies and through the development of new software tools for data analysis and visualization. The influence of circuit theory on conservation comes from the theoretical basis and elegance of the approach and the powerful collaborations and active user community that have emerged. Circuit theory provides a springboard for ecological understanding and will remain an important conservation tool for researchers and practitioners around the globe.

Temporal road closures improve habitat quality for wildlife

Increasing levels of human activity threaten wildlife populations through direct mortality, habitat degradation, and habitat fragmentation. Area closures can improve habitat quality for wildlife, but may be difficult to achieve where tourism or other economic drivers are a priority. Temporal closures that limit human use during specific times of day have potential to increase habitat quality for wildlife, while continuing to provide opportunities for human use. However, the effectiveness of daily temporal closures has not been tested. We assessed how implementation of a temporal road closure affected wildlife movements in Banff National Park. Parks Canada closed a popular 17 km stretch of road between 2000 and 0800 hours to improve habitat quality for wildlife. We assessed the effectiveness of the closure on nine mammal species using three sets of data: remote cameras, road surveys, and grizzly bear (Ursus arctos) GPS data. In all three analyses, wildlife detection rates on the road doubled during the closure while remaining unchanged in reference areas. Our strong and consistent results suggest temporal closures are an important conservation tool that can increase habitat quality for wildlife while minimizing effects on people.

Persistence of remnant patches and genetic loss at the distribution periphery in island and mainland populations of the quokka

Understanding the spatial structure of populations is important in developing effective management options for threatened species, and for managing habitat connectivity for metapopulation function, and for demographic and genetic heterogeneity. We used genetic information to investigate the structure of populations of the quokka, Setonix brachyurus, in south-west Western Australia. We hypothesised that movement between known populations would be relatively rare and result in significant genetic structuring. Genetic analyses from 412 adult individuals at 14 nuclear markers (microsatellite) from 33 sampling locations identified structure, diversity and spatial separation of quokkas across their mainland distribution and on two islands. We identified nine inferred (K = 9) populations of quokka that would be otherwise difficult to define with standard ecological techniques. The highest genetic diversity was evident in a large central population of quokka in the southern forest area and genetic diversity was lower at the peripheries of the distribution. The Rottnest Island population contained 70% of the genetic diversity of the mainland populations but the genetic diversity of animals on Bald Island was markedly lower. Populations of quokka in the northern jarrah forest were the only ones to show evidence of recent or long-term population bottlenecking. Of particular interest was the recently identified population at the Muddy Lakes area (the only remaining locality on the Swan Coastal Plain), which was identified as being genetically associated with the southern forest population. Overall, spatial and population cluster analysis showed small insular populations in the northern jarrah forest area, but in the southern forests there appears to be a large panmictic population.

Identifying wildlife corridors for the restoration of regional habitat connectivity: A multispecies approach and comparison of resistance surfaces

Many large-scale connectivity initiatives have been proposed around the world with the aim of maintaining or restoring connectivity to offset the impacts on biodiversity of habitat loss and fragmentation. Frequently, these are based on the requirements of a single focal species of concern, but there is growing attention to identifying connectivity requirements for multi-species assemblages. A number of methods for modelling connectivity have been developed; likewise, different approaches have been used to construct resistance surfaces, the basic input data for connectivity analyses. In this study we modelled connectivity for a multi-species group of vertebrates representative of heavily fragmented forests in north-central Victoria, Australia. For each species, we used least-cost modelling and compared two alternate resistance surfaces, based on species distribution models and on expert opinion, respectively. We integrated the connectivity results across individual species to obtain a multi-species connectivity map for the region. A resistance surface based on expert assessment of the relative use of land-cover classes by the target species was more informative than one based on species distribution models. The former resulted in pathways more strongly aligned with existing patches and strips of native vegetation. In this region, pathways aligned with streams and their associated riparian vegetation have relatively high ecological potential and feasibility to contribute to regional connectivity for the assemblage of forest vertebrates.

HexSim: a modeling environment for ecology and conservation

CONTEXT

Simulation models are increasingly used in both theoretical and applied studies to explore system responses to natural and anthropogenic forcing functions, develop defensible predictions of future conditions, challenge simplifying assumptions that facilitated past research, and to train students in scientific concepts and technology. Researcher's increased use of simulation models has created a demand for new platforms that balance performance, utility, and flexibility.

OBJECTIVES

We describe HexSim, a powerful new spatially-explicit, individual-based modeling framework that will have applications spanning diverse landscape settings, species, stressors, and disciplines (e.g. ecology, conservation, genetics, epidemiology). We begin with a model overview and follow-up with a discussion of key formative studies that influenced HexSim's development. We then describe specific model applications of relevance to readers of Landscape Ecology. Our goal is to introduce readers to this new modeling platform, and to provide examples characterizing its novelty and utility.

CONCLUSIONS

With this publication, we conclude a >10 year development effort, and assert that our HexSim model is mature, robust, extremely well tested, and ready for adoption by the research community. The HexSim model, documentation, worked examples, and other materials can be freely obtained from the website www.hexsim.net.