scholarly journals Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

2021 ◽  
Author(s):  
Holly A. Broadhurst ◽  
Luke M. Gregory ◽  
Emma K. Bleakley ◽  
Joseph C. Perkins ◽  
Jenna V. Lavin ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Dynamics ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Community Diversity ◽  
Individual Species ◽  
Sampling Effort ◽  
Mammal Species ◽  
Terrestrial Mammals ◽  
Β Diversity

AbstractAimFinding more efficient ways to monitor, and estimate the diversity of, mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Yet, most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. In this study, we focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding rivers.LocationSoutheastern EnglandMethodsWe used eDNA metabarcoding on water samples collected along two rivers and a beaver enclosure over two days, targeting terrestrial and semi-aquatic mammals. Mammalian community diversity and composition was assessed based on species richness and β-diversity. Differences between river communities were calculated and partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling.ResultseDNA metabarcoding efficiently detected 25 wild mammal species from five orders in two days of sampling, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorph species) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers.Main conclusionseDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.

Distributional patterning of mammals on the Wessel and English Company Islands, Arnhem Land, Northern Territory, Australia

1999 ◽  
Vol 47 (1) ◽  
pp. 87 ◽  
Author(s):  
J. C. Z. Woinarski ◽  
C. Palmer ◽  
A. Fisher ◽  
K. Brennan ◽  
R. Southgate ◽  
...  
Keyword(s):  
Species Richness ◽  
Rattus Rattus ◽  
Northern Territory ◽  
Capra Hircus ◽  
Individual Species ◽  
Suitable Habitat ◽  
Sampling Effort ◽  
Mammal Species ◽  
Island Size ◽  
Arnhem Land

Eighteen non-marine mammal species (including seven species of bats) were recorded from a total of 49 islands in the Wessel and English Company island chains off north-eastern Arnhem Land, Northern Territory. Most individual species were restricted to, or had higher incidence on, larger islands, and species richness as a whole increased as island size increased. The most notable exception was the semi-aquatic Hydromys chrysogaster, which occurred relatively equitably across island sizes; this species, two bat species and the macropod Petrogale brachyotis were recorded from islands smaller than 10 ha. However, the variation between islands in the number of native terrestrial mammal species was not best predicted by island size, but rather by a combination of sampling effort and altitude (which explained 64% of the deviance in species richness), or altitude and distance to larger land mass (explaining 63% of deviance). Richness–area patterns for individual islands in these chains were reasonably consistent with those of other islands sampled in northern Australia. However, the fauna of the Wessel and English Company groups as a whole was less rich than that of the Pellew and Kimberley islands, and individual islands appeared to have lower species richness than comparable mainland areas. Species that were notably absent or that were recorded from relatively few islands include large macropods, Tachyglossus aculeatus, Antechinus bellus, Phascogale tapoatafa, Sminthopsis spp., Mesembriomys gouldii, Rattus colletti, Leggadina lakedownensis and Pseudomys calabyi. Some of these species may be absent through lack of suitable habitat; others have presumably disappeared since isolation, possibly due to Aboriginal hunting. Richness at the quadrat (50 × 50 m) scale was generally very low. Habitat relationships are described for the 7 species recorded from more than 5 quadrats. At a quadrat-scale, the richness of native mammals was greater on islands larger than 1000 ha than on islands smaller than 1000 ha. Quadrat-scale species richness varied significantly among the islands sampled by the most quadrats (even when the comparison was restricted to either of the two most extensive vegetation types), but this variation was not closely related to either area or altitude. The two most frequently recorded species, the rodents Melomys burtoni and Zyzomys argurus, showed distinct habitat segregation on islands where both were present, but tended to expand their habitat range on islands where only one of the species occurred. The most notable conservation feature of the mammal fauna of the Wessel and English Company Islands is the occurrence of the golden bandicoot, Isoodon auratus, a vulnerable species apparently now extinct on the Northern Territory mainland. Four feral animal species (Rattus rattus, Canis familiaris, Bubalus bubalis and Capra hircus) were recorded from a total of 6 islands.

scholarly journals Estimates of Species Richness and Composition Depend on Detection Method in Assemblages of Terrestrial Mammals

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 186
Author(s):  
Bruno D. Suárez-Tangil ◽  
Alejandro Rodríguez
Keyword(s):  
Species Richness ◽  
Species Composition ◽  
Spatial Scales ◽  
Camera Traps ◽  
Survey Method ◽  
Sampling Effort ◽  
Method Performance ◽  
Terrestrial Mammals ◽  
Mediterranean Landscapes ◽  
The Impact

Detecting rapid changes in mammal composition at large spatial scales requires efficient detection methods. Many studies estimate species composition with a single survey method without asking whether that particular method optimises detection for all occurring species and yields reliable community-level indices. We explore the implications of between-method differences in efficiency, consistency, and sampling effort for the basic characterisation of assemblages of medium to large mammals in a region with three contrasted Mediterranean landscapes. We assessed differences between camera traps, scent stations, scat surveys, and track surveys. Using track surveys, we detected all species present in the regional pool (13) and obtained the most accurate description of local species richness and composition with the lowest sampling effort (16 sampling units and 2 survey sessions at most). Had we chosen camera traps, scent stations, or scat surveys as the only survey method, we would have underestimated species richness (9, 11, and 12 species, respectively) and misrepresented species composition in varying degrees. Preliminary studies of method performance inform whether single or multiple survey methods are needed and eventually which single method might be most appropriate. Without such a formal assessment current practices may produce unreliable and incomplete species inventories, ultimately leading to incorrect conclusions about the impact of human activity on mammal communities.

Performance of individual species as indicators for large mammal species richness in Northern Tanzania

2015 ◽  
Vol 53 ◽  
pp. 70-77 ◽  
Author(s):  
Christian Kiffner ◽  
Michael Albertini ◽  
Alena Ede ◽  
Brenna Donnellan ◽  
Nathan Hahn ◽  
...  
Keyword(s):  
Species Richness ◽  
Individual Species ◽  
Mammal Species ◽  
Large Mammal ◽  
Northern Tanzania

scholarly journals Edge effects and landscape matrix use by a small mammal community in fragments of semideciduous submontane forest in Mato Grosso, Brazil

2008 ◽  
Vol 68 (4) ◽  
pp. 703-710 ◽  
Author(s):  
M. Santos-Filho ◽  
DJ. da Silva ◽  
TM. Sanaiotti
Keyword(s):  
Species Richness ◽  
Small Mammal ◽  
Species Number ◽  
Sampling Effort ◽  
Similar Species ◽  
Species Accumulation Curves ◽  
Mammal Species ◽  
Mato Grosso ◽  
Species Accumulation ◽  
Species Richness And Abundance

A community of small mammals was studied in seasonal semideciduous submontane forest in the state of Mato Grosso, Brazil. This study evaluated the use of edge and matrix pasture, by different small mammal species. Overall, 31 areas were studied, with a total sampling effort of 33,800 trap x nights. Only seven of the 25 species captured in the study sites were able to use the pasture matrix; we classified these species as generalists. Fourteen species were found to be intermediate in habits, being able to use forest edges. We found only four species habitat specialists, occurring only on transect lines in the interior of the fragment, at least 150 m from the edge. Transects located in the pasture matrix and 50 m from the edge had significantly lower species richness and abundance than transects located in the fragment edge or in the interior of the fragment. All transects located within the fragment had similar species richness and abundance, but transects located 50 m from the edge had slightly lower, but non-significant, species richness than transects located 100 m apart from edges. Rarefaction curves demonstrated that only medium-sized fragments (100 300 ha) reached an asymptote of species accumulation. The other areas require further sampling, or more sampling transect, before species accumulation curves stabilize, due to a continued increase in species number.

scholarly journals Agricultural expansion in African savannas – effects on diversity and composition of trees and mammals

2021 ◽  
Author(s):  
Hemant Tripathi ◽  
Emily Woollen ◽  
Mariana Carvalho ◽  
Catherine Parr ◽  
Casey Ryan
Keyword(s):  
Land Use ◽  
Species Richness ◽  
Land Use Change ◽  
Biodiversity Loss ◽  
Small Scale ◽  
Agricultural Expansion ◽  
Miombo Woodlands ◽  
Mammal Species ◽  
Β Diversity ◽  
Impact On Biodiversity

Abstract Land use change (LUC) is the leading cause of biodiversity loss worldwide. However, the global understanding of LUC's impact on biodiversity is mainly based on comparisons of land use endpoints (habitat vs non-habitat) in forest ecosystems. Hence, it may not generalise to savannas, which are ecologically distinct from forests, as they are inherently patchy, and disturbance adapted. Endpoint comparisons also cannot inform the management of intermediate mosaic landscapes. We aim to address these gaps by investigating species- and community-level responses of mammals and trees along a gradient of small scale agricultural expansion in the miombo woodlands of northern Mozambique. Thus, the case study represents the most common pathway of LUC and biodiversity change in the world's largest savanna. Tree abundance, mammal occupancy, and tree- and mammal-species richness showed a non-linear relationship with agricultural expansion (characterised by the Land Division Index, LDI). These occurrence and diversity metrics increased at intermediate LDI (0.3 to 0.7), started decreasing beyond LDI > 0.7, and underwent high levels of decline at extreme levels of agricultural expansion (LDI > 0.9). Despite similarities in species richness responses, the two taxonomic groups showed contrasting β-diversity patterns in response to increasing LDI: increased dissimilarity among tree communities (heterogenisation) and high similarity among mammals (homogenisation). Our analysis along a gradient of landscape-scale land use intensification allows a novel understanding of the impacts of different levels of land conversion, which can help guide land use and restoration policy. Biodiversity loss in this miombo landscape was lower than would be inferred from existing global syntheses of biodiversity-land use relations for Africa or the tropics, probably because such syntheses take a fully converted landscape as the endpoint. As, currently, most African savanna landscapes are a mosaic of savanna habitats and small scale agriculture, biodiversity loss is probably lower than in current global estimates, albeit with a trend towards further conversion. However, at extreme levels of land use change (LDI > 0.9 or < 15% habitat cover) miombo biodiversity appears to be more sensitive to LUC than inferred from the meta-analyses. To mitigate the worst effects of land use on biodiversity, our results suggest that miombo landscapes should retain > 25% habitat cover and avoid LDI > 0.75 – after which species richness of both groups begin to decline. Our findings indicate that tree diversity may be easier to restore from natural restoration than mammal diversity, which became spatially homogeneous.

Incorporating local habitat heterogeneity and productivity measures when modelling vertebrate richness

2019 ◽  
Vol 47 (1) ◽  
pp. 7-14 ◽  
Author(s):  
W Justin Cooper ◽  
William J McShea ◽  
David A Luther ◽  
Tavis Forrester
Keyword(s):  
Species Richness ◽  
Habitat Heterogeneity ◽  
Spatial Scales ◽  
Model Performance ◽  
Remotely Sensed ◽  
Habitat Characteristics ◽  
Measurement Scale ◽  
Terrestrial Mammals ◽  
Declining Species ◽  
Monitoring Technologies

SummaryDeclining species richness is a global concern; however, the coarse-scale metrics used at regional or landscape levels might not accurately represent the important habitat characteristics needed to estimate species richness. Currently, there exists a lack of knowledge with regard to the spatial extent necessary to correlate remotely sensed habitat metrics to species richness and animal surveys. We provide a protocol for determining the best scale to use when merging remotely sensed habitat and animal survey data as a step towards improving estimates of vertebrate species richness on broad scales. We test the relative importance of fine-resolution habitat heterogeneity and productivity metrics at multiple spatial scales as predictors of species richness for birds, frogs and mammals using a Bayesian approach and a combination of passive monitoring technologies. Model performance was different for each taxonomic group and dependent on the scale at which habitat heterogeneity and productivity were measured. Optimal scales included a 20-m radius for bats and frogs, an 80-m radius for birds and a 180-m radius for terrestrial mammals. Our results indicate that optimal scales do exist when merging remotely sensed habitat measures with ground-based surveys, but they differ between vertebrate groups. Additionally, the selection of a measurement scale is highly influential to our understanding of the relationships between species richness and habitat characteristics.

Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques

2010 ◽  
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Community Ecology ◽  
Community Dynamics ◽  
Spatial Scales ◽  
River Mouth ◽  
Extrinsic Factors ◽  
Local Species Richness ◽  
Community Convergence ◽  
Local Filters

<em>Abstract</em>.—Community ecology increasingly seeks to integrate the influences of regional and historical processes with species interactions within local habitats. This broadened perspective is largely based on comparative approaches that employ “natural experiments” to identify factors shaping community structure. Because coastal rivers are separated from one another by insurmountable barriers (oceans or land), freshwater fishes are particularly well suited for comparative analyses of factors that influence fish community organization. In this chapter, we review how this comparative approach shed light on large-scale biodiversity gradients, community saturation, community convergence, density compensation, and the role of intrinsic and extrinsic factors in community dynamics. The main factors (e.g., river mouth discharge and history) empirically related to species richness of a river are well identified, and metacommunity ecology provides a fruitful conceptual framework for understanding how regional (river) species richness translates into local species richness. Much work remains to identify factors explaining differences among whole river basin assemblages with regard to ecological traits (e.g., trophic status and life history) composition and to assess whether trait-related environmental and biotic local filters act similarly over large spatial scales. One important conclusion that can be drawn from the studies reviewed here is that history cannot be neglected whatever the scale of investigation (global, river, or site). A second conclusion is that historical effects are not strong enough to blur the occurrence of qualitatively repeatable patterns of community structure over large spatial scale, which is encouraging because it suggests development of general predictive models of community structure is an attainable goal.

scholarly journals Variation of plant species richness at different spatial scales

2018 ◽  
Vol 11 ◽  
pp. 49-62 ◽  
Author(s):  
Khem Raj Bhattarai
Keyword(s):  
Species Richness ◽  
Spatial Scales ◽  
Local Scale ◽  
Explanatory Variables ◽  
Local Species Richness ◽  
Β Diversity ◽  
Historical Processes ◽  
Α Diversity ◽  
Local Species ◽  
Broad Scale

 It is now realized that the variation in species richness is influenced by spatial and temporal scales. Pattern and scale are a central focus in ecology and biogeography. The species richness relationship depends on the scale of study and their correlated factors. The broad objective of this review is to elucidate how different scales are correlated with different explanatory variables to generate patterns of species richness. Addressing the problem of scale has both fundamental and applied importance in understanding variation in species richness along gradients. The understanding of pattern, its causes, and consequences is central to our understanding of processes such as succession, community development, and the spread and persistence of species. According to the hierarchical theory of species diversity there are mainly three categories of scales: local, landscape and regional. The local species richness or α-diversity is the diversity of individual stands. The β-diversity or species change is turnover between two elevational bands or between two plots or two sites. The regional or γ-diversity is the total richness of whole mountains or study systems and it has a combined influence from α- and β-diversity. The local species richness is affected by both local-scale processes (e.g., internal interactions) and broad-scale processes (e.g., evolutionary). Different explanatory variables according to the scales of study are necessary to explain variation at different spatial scales. Local factors (e.g., disturbance, grazing and tree cover) have been used to detect variation at a local scale. Generally, topographical factors are used to detect variation in species richness at a landscape scale; whereas climate, water-energy dynamics and historical processes are used to detect variation at a regional scale. However, it is not easy to separate strictly one scale from other because there is no clear boundary between them. The study of the whole elevation gradient from tropical to alpine zone or long latitude is a broad-scale study. The intermediate scale is a study on a local mountain, which covers the subtropical to warm temperate zones. To explain patterns of species richness, a pluralistic body of hypotheses, which incorporates historical, biological and climatic factors, is needed. This is depicted by the strong relationship between climate, biological interactions, and historical processes in influencing variation in species richness at different spatial scales.Botanica Orientalis – Journal of Plant Science (2017) 11: 49–62

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