Mammal Habitat Use Research Articles

Environmental DNA reveals fine‐scale spatial and temporal variation of marine mammals and their prey species in a Scottish marine protected area

AbstractMarine mammal foraging grounds are popular focal points for marine protected area (MPA) implementation, despite being temporally dynamic, requiring continuous monitoring to infer prey availability and abundance. Marine mammal distributions are assumed to be driven by their prey in foraging areas, but limited understanding of prey distributions often prevents us from exploring how shifting prey availability impacts both seasonal and long‐term marine mammal distributions. Environmental DNA (eDNA) metabarcoding could enhance the understanding of marine mammal habitat use in relation to their prey through simultaneous monitoring of both. However, eDNA applications focused on marine mammals or predator–prey dynamics have been limited to date. In this study, we assess spatiotemporal changes in the distribution and abundance of cetaceans, minke whales (Balaenoptera acutorostrata), bottlenose dolphins (Tursiops truncatus) and harbor porpoises (Phocoena phocoena) in relation to key prey species in a newly established MPA, employing eDNA metabarcoding. We recovered 105 molecular operational taxonomic units (OTUs) from marine vertebrates using two primer sets targeting 12S and 16S genes, along with 112 OTUs from a broader eukaryotic primer set targeting 18S rRNA. Overall, key forage fish prey species, sandeels and clupeids, were the most abundant teleost fishes detected, although their availability varied temporally and with distance from shore. We also found clear spatial partitioning between coastal bottlenose dolphins and the more pelagic minke whales and harbor porpoises, paralleling availability of their main prey species. Other species of conservation interest were also detected including the critically endangered European eel (Anguilla anguilla), Atlantic bluefin tuna (Thunnus thynnus), and the invasive pink salmon (Oncorhynchus gorbuscha). This study demonstrates the application of eDNA to detect spatiotemporal trends in the occurrence and abundance of cetacean predators and their prey, furthering our understanding of fine‐scale habitat use within MPAs. Future long‐term monitoring of predator–prey dynamics with eDNA could improve our ability to predict climate‐induced shifts in foraging grounds and enhance rapid responses with appropriate management actions.

Dusky dolphin (Lagenorhynchus obscurus) habitat use in a mussel farming region and changes over time

ABSTRACT Information on marine mammal habitat use in coastal areas can provide a better understanding of anthropogenic effects on species. Admiralty Bay, New Zealand has extensive near-shore mussel farms and is an important dusky dolphin (Lagenorhynchus obscurus) foraging habitat. Prior dusky dolphin research indicated a declining trend in regional abundance from the late 1990s to mid-2000s. We describe dusky dolphin behaviour, habitat patch use and movement patterns in Admiralty Bay in 2011–2012 and compare findings to previous research to capture long-term trends. Sampling methods included small-boat group follows and photo-identification and shore-based theodolite tracking. Dolphin encounter rate, mean group size, and individual resighting rate showed a negative trend from previous years. Coordinated prey ball herding, a foraging technique documented in previous years, was rarely observed during this study. Dolphins were more likely to forage near farms (excluding specialised prey herding), though they seldom entered farms. Near shore, swimming speed was slower, reorientation rate was higher, and linearity was lower in the presence of farms than in their absence. This research builds upon prior studies, suggesting a continued decline in dusky dolphin presence, and highlights differences in habitat patch use in a human-altered ecosystem.

Seasonal acoustic presence of marine mammals at the South Orkney Islands, Scotia Sea.

Increased knowledge about marine mammal seasonal distribution and species assemblage from the South Orkney Islands waters is needed for the development of management regulations of the commercial fishery for Antarctic krill (Euphausia superba) in this region. Passive acoustic monitoring (PAM) data were collected during the autumn and winter seasons in two consecutive years (2016, 2017), which represented highly contrasting environmental conditions due to the 2016 El Niño event. We explored differences in seasonal patterns in marine mammal acoustic presence between the two years in context of environmental cues and climate variability. Acoustic signals from five baleen whale species, two pinniped species and odontocete species were detected and separated into guilds. Although species diversity remained stable over time, the ice-avoiding and ice-affiliated species dominated before and after the onset of winter, respectively, and thus demonstrating a shift in guild composition related to season. Herein, we provide novel information about local marine mammal species diversity, community structure and residency times in a krill hotspot. Our study also demonstrates the utility of PAM data and its usefulness in providing new insights into the marine mammal habitat use and responses to environmental conditions, which are essential knowledge for the future development of a sustainable fishery management in a changing ecosystem.

Landscape drivers of mammal habitat use and richness in a protected area and its surrounding agricultural lands

Protected areas (PAs) are key to conserving biodiversity and ecosystem services globally, but their effectiveness increasingly depends on the ability of the surrounding agricultural areas to support biodiversity and secure connectivity at the landscape level. This requires monitoring the broader multi-use landscapes in which PAs exist and identifying the landscape characteristics that support rich, functional wildlife communities. Here, we investigated the species richness and habitat use patterns of a mammal community in relation to different landscape variables and land use and land cover (LULC) types in a PA and its surrounding agricultural lands in the Cerrado. We first used a hierarchical multi-species occupancy model with input camera trap data and eight landscape variables (vegetation productivity, phenology, and heterogeneity, distance to water, roads and settlements, and the PA, slope, and elevation) to estimate the species richness and habitat use of 29 mammal species across the landscape. We then analyzed the relationships between the species richness and habitat use and the landscape variables at the site level, as well as the distribution of species at the landscape level in relation to the different natural and agricultural LULC types. We found that most species are present in the native forest areas across the landscape and that many species are also present in the croplands surrounding the PA. The results also showed that species’ habitat use was especially determined by the productivity and heterogeneity of the vegetation cover, with a particularly strong positive relation in grasslands and pastures. These results suggest that the private properties surrounding the PA might be playing an essential role in supporting biodiversity in this region and provide insights on management practices that could largely contribute to maintaining or promoting a multifunctional landscape, such as maintaining the remaining forests or increasing the productivity and the heterogeneity (e.g., by increasing tree cover) in pastures.

Forest cover mediates large and medium-sized mammal occurrence in a critical link of the Mesoamerican Biological Corridor.

Connectivity of natural areas through biological corridors is essential for ecosystem resilience and biodiversity conservation. However, robust assessments of biodiversity in corridor areas are often hindered by logistical constraints and the statistical challenges of modeling data from multiple species. Herein, we used a hierarchical community occupancy model in a Bayesian framework to evaluate the status of medium and large-sized mammals in a critical link of the Mesoamerican Biological Corridor (MBC) in Costa Rica. We used camera traps deployed from 2013-2017 to detect 18 medium (1-15 kg) and 6 large (>15 kg) mammal species in a portion of two Jaguar Conservation Units (JCUs) and the Corridor linking them. Camera traps operated for 16,904 trap nights across 209 stations, covering an area of 880 km2. Forest cover was the most important driver of medium and large-sized mammal habitat use, with forest specialists such as jaguars (Panthera onca) and pumas (Puma concolor) strongly associated with high forest cover, while habitat generalists such as coyotes (Canis latrans) and raccoons (Procyon lotor) were associated with low forest cover. Medium and large-sized mammal species richness was lower in the Corridor area ([Formula: see text] = 9.78±1.84) than in the portions evaluated of the two JCUs ([Formula: see text] = 11.50±1.52). Puma and jaguar habitat use probabilities were strongly correlated with large prey species richness (jaguar, r = 0.59, p<0.001; puma, r = 0.72, p<0.001), and correlated to a lesser extent with medium prey species richness (jaguar, r = 0.36, p = 0.003; puma, r = 0.23, p = 0.064). Low estimated jaguar habitat use probability in one JCU (Central Volcanic Cordillera: [Formula: see text] = 0.15±0.11) suggests that this is not the jaguar stronghold previously assumed. In addition, the western half of the Corridor has low richness of large mammals, making it necessary to take urgent actions to secure habitat connectivity for mammal populations.

Environmental drivers of habitat use by common bottlenose dolphins (Tursiops truncatus) in the Indian River Lagoon, Florida, USA

AbstractAnthropogenic impacts in estuarine systems can influence marine mammal habitat use, population dynamics, fitness, and mortality events. The objective was to examine habitat use among the resident common bottlenose dolphin (Tursiops truncatus) population inhabiting the Indian River Lagoon, Florida, and the influences of variation in environmental factors and prey availability in 2003–2015. We utilized photo‐identification surveys, stratified random samples of prey, and environmental variables collected monthly. Kernel density estimation was used to determine the magnitude‐per‐unit area of dolphins across the IRL by wet and dry seasons each year, the values were used as a response variable in classification and regression tree analyses with fish community and environmental variables as predictors. Spatial patterns in dolphin density in the IRL were associated with salinity and dissolved oxygen levels, which are in part associated with freshwater discharges of nutrient and algae laden waters from the region's storm water management system. These findings isolate locations of concern for management of dolphin habitat, and anthropogenic drivers of dolphin distributions requiring further research.

Recycling data: An annotated marine acoustic data set that is publicly available for use in classifier development and marine mammal research

Barkley Canyon is a productive submarine canyon approximately 60 km southwest of Vancouver Island, Canada. The canyon's nutrient flow is affected by multiple regional currents, and draws aggregations of euphausiids, hake, herring, and various marine mammal species. A subset of the acoustic data collected from the 2013–2015 hydrophone deployment on the Barkley Canyon Upper Slope platform of Ocean Networks Canada's North-East Pacific Time-series Undersea Networked Experiments (NEPTUNE) observatory was manually annotated for marine mammal presence to investigate marine mammal habitat use and in support of development of a random forest classifier. This dataset, which is being made publicly available for further use, includes strong-label annotations of phonations from blue whales, fin whales, humpback whales, sperm whales, orcas, Pacific white-sided dolphins, Risso's dolphins, and other delphinids that could not be identified to species. All regional orca communities are represented within the dataset, and phonations are labelled to ecotype and pod level when possible. This dataset could be further used in a number of ways, including classifier development, investigations into habitat use and seasonality, or combining the acoustic data with data collected from co-located oceanographic instruments to investigate links between marine mammal presence and oceanographic conditions.

Small mammals respond to extreme habitat fragmentation in the Brazilian Atlantic Forest according to the landscape continuum model

There are several factors that can determine the pattern of habitat use by species in fragmented habitats. Here we investigated the applicability of the continuum model, which predicts that habitat use varies in a continuous way and not categorically like habitat and not-habitat, for small mammal habitat use. We also investigated if habitat-related guilds of species can change their habitual pattern of habitat use in an extremely altered landscape. This study was conducted in a highly fragmented area of Atlantic Forest in Brazil, where forest fragments are immersed in a pasture matrix. We captured mammals using pitfall traps placed in six sampling sites. In each of these sites, we selected four of five different habitats that were available in the local landscape: high-elevation forests without stream, low-elevation forests with stream, forest edges, pasture matrix without stream, and pasture matrix with stream. This study revealed that the theory of the continuum model can be applied for investigating patterns of use of fragmented forests by small mammals. We also observed, in general, low tolerance of forest species to the most disturbed habitat, the pasture matrix without stream. However, a small increase in the complexity of the vegetation, as observed in riparian pasture matrices, seems to mitigate this negative effect, making the abundance, richness, and diversity of small mammals comparable to forest habitats. These results indicate that the presence of streams may facilitate the use of the pasture matrix, contributing for the maintenance of the original community in the fragmented forest.

Ecological and social consequences of bison reintroduction in Colorado

Bison were instrumental in shaping North America's Great Plains. Interest in restoring this iconic species and their ecological role in grassland ecosystems is rapidly gaining momentum. To evaluate the potential for bison to enhance habitat quality for wildlife and catalyze public engagement in grassland conservation, we assessed both the ecological and social effects of a recent bison reintroduction (2015) to northern Colorado. Specifically, we explored the effect of bison reintroduction on: (a) bird density and habitat use, (b) mammal habitat use, (c) vegetation composition and structure, and (d) visitor connectedness, known as place attachment, to a shortgrass prairie. We predicted that bison reintroduction would reduce cover and height of some grasses and shrubs, which would increase density and habitat use for obligate shortgrass prairie birds, and increase habitat use for coyote and lagomorphs. In addition, we predicted that visitors would express stronger place attachment to this grassland once bison were reintroduced. To measure ecological and social responses, we surveyed birds, mammals, and plants; and conducted structured visitor surveys before and after bison reintroduction. We found few short‐term effects of bison on grassland bird density and habitat use, mammal habitat use, and vegetation composition and structure. However, we measured a significant increase in visitor place attachment to the grassland site 1 year after bison reintroduction. Our results suggest that a new bison reintroduction may have immediate positive benefits for connecting people to conservation, and that the ecological and social effects may unfold over different time scales. We recommend that future bison reintroduction efforts monitor ecological and social outcomes to advance reintroduction biology.

Acoustic versus visual monitoring of Cetaceans in coastal habitats

Monitoring the aquatic soundscape provides critical information about marine mammal habitat use. It is essential for developing mitigation strategies for areas with expanding marine shipping and industrial activity. A long baseline hydrophone array has been installed in Squally Channel, a culturally, ecologically, and economically important marine environment in northern British Columbia, Canada. The array consists of four synchronized bottom-mounted hydrophones that permanently record and radio-transmit data to a land-based laboratory in real-time. The acoustic monitoring is supplemented with a land-based visual observatory that oversees the same area of approximately 200 km2. Automated detectors have been developed for vocalizations of humpback whales, orcas, and fin whales. Acoustic data and visual surveys were analyzed for a period of more than 100 days between 2017 and 2018. We present an overview of the acoustic detection functions and their performance by call type and summarize visual survey procedures. Cetacean activity derived from automated acoustic detections and visual observations is analyzed. Finally, acoustic and visual survey methods are compared to assess a) the fraction to which different species are acoustically active while in the area, and b) the effectiveness of both acoustic and visual monitoring efforts for the purpose of cetacean monitoring.

Temporal and spatial distribution patterns of toothed whales in Massachusetts Bay using passive acoustics from ocean gliders

Basic information on marine mammal habitat use is necessary for informing ecosystem-based management plans and for mitigating human impacts. Massachusetts Bay is an important marine mammal foraging area in the Gulf of Maine and a region of high human activity, but little is known about toothed whale habitat use, particularly during winter months. Passive acoustic monitoring, particularly from autonomous platforms, provides advantages in studying habitat use in unfavorable conditions. The goal of this work is to use acoustic monitoring to investigate temporal and spatial occurrence patterns of toothed whale species in Massachusetts Bay during late fall/early winter using ocean gliders equipped with passive acoustic recorders. Slocum gliders were deployed in western Massachusetts Bay in 2014, 2015, and 2016. Toothed whales were detected on 92 (72%) of 128 deployment days. Detections occurred more often at night. Ongoing work includes acoustic identification of species and assessing relationships between detections and environmental conditions. These data provide the first evidence of a consistent presence of toothed whales in Massachusetts Bay during late fall and winter, and demonstrate the potential for ocean gliders as a tool to detect toothed whales in areas/times that are difficult to survey with traditional visual methods.

Large Mammal Use of Linear Remnant Forests in an Industrial Pulpwood Plantation in Sumatra, Indonesia

Riparian forests are often the last remaining areas of natural vegetation in agricultural and plantation forestry landscapes. Covering millions of hectares of land in Indonesia, industrial pulpwood plantations have rapidly replaced native forests. Our study aimed to better understand the conservation importance of linear remnants of riparian forest by examining their use by larger (&gt;1 kg) mammal species. Our study site was located within an extensive acacia ( Acacia mangium) plantation adjoining Tesso Nilo National Park in Sumatra, Indonesia. Camera traps were used to detect mammals at 57 sites to assess the effects of corridor design and land cover covariates and species behavioral traits on mammal habitat use of four linear riparian forests. We recorded 17 species (including one International Union for Conservation of Nature [IUCN] Critically Endangered, two Endangered, and four Vulnerable) in riparian forests inside the plantation, including the Sumatran tiger ( Panthera tigris sumatrae), Malay tapir ( Tapirus indicus), and sun bear ( Helarctos malayanus). Some threatened species were only detected in the park buffer zone. Species varied in their responses to riparian forests, but distance to the national park, remnant width, and percent forest cover around the camera site were common predictors of remnant use. Many mammal species used riparian forests regardless of whether they were surrounded by intact acacia forests or recently cleared land. Our results indicate that linear remnant riparian forests ≤ 200 m in width can facilitate local (&lt; 4 km) movements of many large mammal species in Sumatra, but wider riparian remnants would likely be more effective at promoting mammal movements over longer distances.

Pinyon-juniper removal has long-term effects on mammals

Removing tree cover is a common forest management practice, and pinyon-juniper woodlands in the western United States have been the focus of tree reduction efforts for decades. The scale and intensity of tree removal practices are expected to increase as technology advances and as land managers are tasked with meeting multiple objectives, including fire prevention and habitat enhancement for livestock and wildlife of conservation concern. However, the long-term consequences of pinyon-juniper removal on animal communities are virtually unknown. The objectives of this study were to assess whether mammal habitat use differs between reference pinyon-juniper woodlands and stands that were mechanically disturbed by chaining more than 40years ago, and to determine if these differences are associated with particular habitat characteristics. We used remotely triggered wildlife cameras to evaluate differences in mammal habitat use of historically chained sites (n=22) and reference sites (n=22) in northwestern Colorado. Our results demonstrate marked differences in habitat use between chained sites and reference woodlands for most detected mammal species. Bobcat, mountain lion, American black bear, golden-mantled ground squirrel, and rock squirrel all showed a negative response to historically chained sites, indicating long-term effects of tree removal on these species. In contrast, habitat use of chipmunk, mountain cottontail, and coyote did not differ between chained and reference sites. For most species, habitat use was influenced by specific vegetation characteristics, such as proportion of tree cover, which could be factored into management decisions. By understanding the long-term consequences of tree removal for diverse mammal species, we are better equipped to adapt forest management practices to benefit species of both economic and conservation concern.

Changes in Small Mammal Microhabitat Use Following Silvicultural Disturbance

Abstract Silvicultural disturbance can lead to major shifts in biotic and abiotic characteristics of forests, with significant implications for wildlife. Many studies have demonstrated site occupancy and abundance of small mammals changes following silviculture, but few have identified the habitat characteristics associated with small mammal responses. We conducted a study in the central hardwood forest region of the U.S. to examine the relationship between small mammal habitat use and habitat variables at the microsite scale, before and after silvicultural disturbance, while explicitly accounting for imperfect detection. Following the creation of harvest openings, vegetation cover and coarse woody debris increased, and leaf litter depth decreased. Fewer changes occurred following the midstory removal stage of a shelterwood harvest. Eastern chipmunks (Tamias striatus) and white-footed mice (Peromyscus leucopus) were positively correlated with woody vegetation cover and coarse woody debris, and short-taile...

Small Mammal Habitat Use within Restored Riparian Habitats Adjacent to Channelized Streams in Mississippi

Riparian zones of channelized agricultural streams in northwestern Mississippi typically consist of narrow vegetative corridors low in habitat diversity and lacking riparian wetlands. Land clearing practices and stream channelization have led to the development of gully erosion and further fragmentation of these degraded riparian zones. Currently, installation of a gully erosion control structure (drop pipe) at the riparian zone-agricultural field interface leads to the incidental establishment of four riparian habitat types that differ in habitat area, vegetative structure, and pool size. Small mammals were sampled within four sites of each habitat type from June 1994 to July 1995. Small mammal diversity, abundance, and hispid cotton rat (Sigmodon hispidus) weight were the least within smallest Type I habitats with the least vegetative structural diversity and were the greatest within the larger Type II, III, or IV habitats having greater vegetative structural diversity and pool size. Small mammal diversity and abundance were the least in the summer 1994, increased in the fall 1994, and then declined later in our study. Hispid cotton rat abundance was the least in summer 1994, winter 1994, and spring 1995 and was the greatest in fall 1994 and summer 1995. Our results suggest that modifying the drop pipe installation design to facilitate the development of larger riparian habitats with greater vegetative structural diversity will provide the greatest benefits for small mammals.

Responses of two species of heathland rodents to habitat manipulation: Vegetation density thresholds and the habitat accommodation model

AbstractThe abundance of two native rodent species, Rattus lutreolus and Pseudomys gracilicaudatus, has been shown to correlate with vegetation density in coastal wet heath. Fox's habitat accommodation model relates relative abundances of such small mammal species to heathland vegetation regeneration following disturbance. Implicit in the model is recognition that it is successional changes in vegetation, not time per se, that drives the responses of small mammal species along a regeneration axis. Using a brush‐cutter we deliberately removed approximately 85% of vegetation around trapping stations and recorded significant reductions in the abundance of both P. gracilicaudatus (an earlier‐stage colonizing species) and R. lutreolus (a late seral‐stage species). A significant decrease in the abundance of only the latter had been demonstrated previously when 60–70% of the vegetation had been removed. Following the brush‐cutting both species re‐entered the mammalian secondary succession at different times, first P. gracilicaudatus followed by R. lutreolus after the vegetation cover thresholds of each species had been reached. The impact of this habitat manipulation experiment was to produce a retrogression of the small mammal succession, experimentally demonstrating causality between changes in vegetation density and subsequent small mammal habitat use.