scholarly journals Species versus within-species niches: a multi-modelling approach to assess range size of a spring-dwelling amphibian

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Forough Goudarzi ◽  
Mahmoud-Reza Hemami ◽  
Mansoureh Malekian ◽  
Sima Fakheran ◽  
Fernando Martínez-Freiría
Keyword(s):  
Species Distribution ◽  
Conservation Status ◽  
Species Conservation ◽  
Landscape Scale ◽  
Species Level ◽  
Environmental Data ◽  
Similar Species ◽  
Fine Scale ◽  
Distribution Models ◽  
Area Of Occupancy

AbstractSpecies Distribution Models (SDMs) can be used to estimate potential geographic ranges and derive indices to assess species conservation status. However, habitat-specialist species require fine-scale range estimates that reflect resource dependency. Furthermore, local adaptation of intraspecific lineages to distinct environmental conditions across ranges have frequently been neglected in SDMs. Here, we propose a multi-stage SDM approach to estimate the distributional range and potential area of occupancy (pAOO) of Neurergus kaiseri, a spring-dwelling amphibian with two climatically-divergent evolutionary lineages. We integrate both broad-scale climatic variables and fine-resolution environmental data to predict the species distribution while examining the performance of lineage-level versus species-level modelling on the estimated pAOO. Predictions of habitat suitability at the landscape scale differed considerably between evolutionary level models. At the landscape scale, spatial predictions derived from lineage-level models showed low overlap and recognised a larger amount of suitable habitats than species-level model. The variable dependency of lineages was different at the landscape scale, but similar at the local scale. Our results highlight the importance of considering fine-scale resolution approaches, as well as intraspecific genetic structure of taxa to estimate pAOO. The flexible procedure presented here can be used as a guideline for estimating pAOO of other similar species.

Very high resolution environmental predictors in species distribution models

2013 ◽  
Vol 38 (1) ◽  
pp. 79-96 ◽  
Author(s):  
Jean-Nicolas Pradervand ◽  
Anne Dubuis ◽  
Loïc Pellissier ◽  
Antoine Guisan ◽  
Christophe Randin
Keyword(s):  
High Resolution ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Environmental Data ◽  
Swiss Alps ◽  
Fine Scale ◽  
Distribution Models ◽  
Model Quality ◽  
Vegetation Height ◽  
Very High

Recent advances in remote sensing technologies have facilitated the generation of very high resolution (VHR) environmental data. Exploratory studies suggested that, if used in species distribution models (SDMs), these data should enable modelling species’ micro-habitats and allow improving predictions for fine-scale biodiversity management. In the present study, we tested the influence, in SDMs, of predictors derived from a VHR digital elevation model (DEM) by comparing the predictive power of models for 239 plant species and their assemblages fitted at six different resolutions in the Swiss Alps. We also tested whether changes of the model quality for a species is related to its functional and ecological characteristics. Refining the resolution only contributed to slight improvement of the models for more than half of the examined species, with the best results obtained at 5 m, but no significant improvement was observed, on average, across all species. Contrary to our expectations, we could not consistently correlate the changes in model performance with species characteristics such as vegetation height. Temperature, the most important variable in the SDMs across the different resolutions, did not contribute any substantial improvement. Our results suggest that improving resolution of topographic data only is not sufficient to improve SDM predictions – and therefore local management – compared to previously used resolutions (here 25 and 100 m). More effort should be dedicated now to conduct finer-scale in-situ environmental measurements (e.g. for temperature, moisture, snow) to obtain improved environmental measurements for fine-scale species mapping and management.

scholarly journals A Robust Prediction Model for Species Distribution Using Bagging Ensembles with Deep Neural Networks

2021 ◽  
Vol 13 (8) ◽  
pp. 1495
Author(s):  
Jehyeok Rew ◽  
Yongjang Cho ◽  
Eenjun Hwang
Keyword(s):  
Neural Networks ◽  
Species Distribution ◽  
Best Practice ◽  
Deep Neural Networks ◽  
Species Distribution Models ◽  
Species Distribution Model ◽  
Environmental Data ◽  
Distribution Model ◽  
Distribution Models ◽  
Robust Prediction

Species distribution models have been used for various purposes, such as conserving species, discovering potential habitats, and obtaining evolutionary insights by predicting species occurrence. Many statistical and machine-learning-based approaches have been proposed to construct effective species distribution models, but with limited success due to spatial biases in presences and imbalanced presence-absences. We propose a novel species distribution model to address these problems based on bootstrap aggregating (bagging) ensembles of deep neural networks (DNNs). We first generate bootstraps considering presence-absence data on spatial balance to alleviate the bias problem. Then we construct DNNs using environmental data from presence and absence locations, and finally combine these into an ensemble model using three voting methods to improve prediction accuracy. Extensive experiments verified the proposed model’s effectiveness for species in South Korea using crowdsourced observations that have spatial biases. The proposed model achieved more accurate and robust prediction results than the current best practice models.

Combining conservation status and species distribution models for planning assisted colonisation under climate change

2021 ◽  
Author(s):  
Gabriele Casazza ◽  
Thomas Abeli ◽  
Gianluigi Bacchetta ◽  
Davide Dagnino ◽  
Giuseppe Fenu ◽  
...  
Keyword(s):  
Climate Change ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Conservation Status ◽  
Distribution Models

scholarly journals New localities and distribution models inform the conservation status of the endangered lizard Anolis guamuhaya (Squamata: Dactyloidae) in central Cuba

2020 ◽  
Vol 19 (1) ◽  
pp. 13-33
Author(s):  
Tomás M. Rodríguez-Cabrera ◽  
Javier Torres ◽  
Carlos A. Mancina ◽  
Ruben Marrero ◽  
Yasel U. Alfonso ◽  
...  
Keyword(s):  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
New Records ◽  
Global Climate ◽  
Conservation Status ◽  
Niche Modeling ◽  
Distribution Models ◽  
Area Of Occupancy ◽  
New Localities ◽  
Iucn Criteria

New localities and distribution models inform the conservation status of the endangered lizard Anolis guamuhaya (Squamata: Dactyloidae) from central Cuba. Anolis guamuhaya is known from seven localities restricted to the Guamuhaya Massif in central Cuba and is always associated with mountane ecosystems above 300 m a.s.l. Previous evaluations of the conservation status of the species based on the estimated number of mature individuals have categorized the anole as Endangered. Eight new records of A. guamuhaya are provided here. These double the number of known localities, and two represent the first records of the species in lowland areas, apart from the Guamuhaya Massif. The new records extend the elevational range of the species from 15 m to above 1000 m. We used ecological niche modeling based on all of the locality records, along with what we considered the most appropriate IUCN criteria according to the available information (Criterion B) to reevaluate the conservation status of the species. These new records of A. guamuhaya increase its area of occupancy up to a total of 60 km2 , and its extent of occurrence up to 648 km2 . Despite this increase in geographic range, the species meets the IUCN criteria in the category of Endangered. We used ecological niche modeling to predict possible trends for the species under differing scenarios of global climate change, all of which portend a drastic reduction in area climatically suitable for A. guamuhaya.

Examining Local Transferability of Predictive Species Distribution Models for Invasive Plants: An Example with Cogongrass (Imperata cylindrica)

2011 ◽  
Vol 4 (4) ◽  
pp. 390-401 ◽  
Author(s):  
Gary N. Ervin ◽  
D. Christopher Holly
Keyword(s):  
Invasive Species ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Imperata Cylindrica ◽  
Environmental Data ◽  
Training Data ◽  
Distribution Data ◽  
Strongly Correlated ◽  
Distribution Models ◽  
Tree Canopy Cover

AbstractSpecies distribution modeling is a tool that is gaining widespread use in the projection of future distributions of invasive species and has important potential as a tool for monitoring invasive species spread. However, the transferability of models from one area to another has been inadequately investigated. This study aimed to determine the degree to which species distribution models (SDMs) for cogongrass, developed with distribution data from Mississippi (USA), could be applied to a similar area in neighboring Alabama. Cogongrass distribution data collected in Mississippi were used to train an SDM that was then tested for accuracy and transferability with cogongrass distribution data collected by a forest management company in Alabama. Analyses indicated the SDM had a relatively high predictive ability within the region of the training data but had poor transferability to the Alabama data. Analysis of the Alabama data, via independent SDM development, indicated that predicted cogongrass distribution in Alabama was more strongly correlated with soil variables than was the case in Mississippi, where the SDM was most strongly correlated with tree canopy cover. Results suggest that model transferability is influenced strongly by (1) data collection methods, (2) landscape context of the survey data, and (3) variations in qualitative aspects of environmental data used in model development.

Is the Carpentarian Rock-rat Zyzomys palatalis critically endangered?

2006 ◽  
Vol 12 (2) ◽  
pp. 134 ◽  
Author(s):  
David M. J. S. Bowman ◽  
Daniel L McIntyre ◽  
Barry W. Brook
Keyword(s):  
Conservation Status ◽  
Species Conservation ◽  
Population Viability Analysis ◽  
Critically Endangered ◽  
Isolated Populations ◽  
Forest Habitat ◽  
Viability Analysis ◽  
Area Of Occupancy ◽  
Closed Forest ◽  
Minimum Number

The Carpentarian Rock-rat Zyzomys palatalis is a rare conilurine rodent with a global distribution restricted to a small area of sandstone escarpments in the Gulf of Carpentaria region of the Northern Territory. Previous assessments of its World Conservation Union (IUCN) status in 1996 had classified the species as Critically Endangered based on the restricted area of occupancy and a putative decline in the extent and quality of its closed forest habitat due to uncontrolled landscape fires. A later population viability analysis confirmed that habitat loss was potentially the single most important threatening process. Here we argue that the species should be reclassified as Vulnerable, on the basis of the following new evidence: (1) the assumption that it was a closed forest specialist was not supported by a radiotracking study, which showed that on average 43% of an individual's monitored time was spent in the forest-savannah margin, and (2) analysis of repeat historical aerial photography has shown that the core closed forest habitat has in fact increased by 36% over the last 50 years. This has lead to an increase of 140 in the minimum number of equivalent Z. paJatalis territories, from 387 to 587, when home range overlaps and utilization of the savannah margins are considered. Reclassification of the species' conservation status should be accompanied with: (i) genetic studies of relatedness between isolated populations; (ii) monitoring and maintenance of the integrity of the landscapes, including creeklines that connect patches; and (iii) consideration of the introduction of captive bred specimens into an adjacent unoccupied fragments.

scholarly journals New island record and conservation status of Puerto Rican Bank endemic plant species, Ruehssia woodburyana (Acev.-Rodr.) Goyder, comb. nov., formally transferred from Marsdenia

2020 ◽  
Vol 8 ◽  
Author(s):  
Sara Bárrios ◽  
José Sustache ◽  
David Goyder ◽  
Martin Hamilton
Keyword(s):  
Forest Fires ◽  
Conservation Status ◽  
Species Conservation ◽  
Virgin Islands ◽  
Ex Situ ◽  
Suitable Habitat ◽  
Endemic Plant ◽  
Conservation Action ◽  
British Virgin Islands ◽  
Area Of Occupancy

Thought to be endemic to the Commonwealth of Puerto Rico, Ruehssia woodburyana (Apocynaceae) was recently discovered at a single location on Norman Island in the British Virgin Islands. Despite an increase in the extent of occurrence and area of occupancy, this species meta-population is very limited with a total of 37 individuals known in the wild. The largest subpopulation, on Mona Island, has only 26 individuals. The species suitable habitat is experiencing a continuing decline due to urban development, grazing by feral ungulates and human-induced forest fires. Conservation action is urgently needed and should be directed towards establishing genetically representative ex situ collections, such as seed for long term storage and live material for propagation. This species is evaluated as Critically Endangered (CR), based on Criteria C2a(i)+D, according to the IUCN Red List Categories and Criteria (version 3.1) and guidelines (Subcommittee IUCN Standards and Petitions 2016). Extensive and regular surveys to the region enable the discovery of new plant records for different countries and islands. In this paper, we record a new island record for Ruehssia woodburyana on Norman Island, in the British Virgin Islands and discuss the species conservation status. Marsdenia woodburyana is transferred to the genus Ruehssia to reflect the resurrection of that genus for species of Marsdenia native to the New World.

scholarly journals Trends and gaps in the use of citizen science derived data as input for species distribution models: A quantitative review

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0234587
Author(s):  
Mariano J. Feldman ◽  
Louis Imbeau ◽  
Philippe Marchand ◽  
Marc J. Mazerolle ◽  
Marcel Darveau ◽  
...  
Keyword(s):  
Citizen Science ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Spatial Scales ◽  
Species Conservation ◽  
Innovative Technology ◽  
Data Types ◽  
Species Occurrence ◽  
Distribution Models ◽  
Digital Platforms

Citizen science (CS) currently refers to the participation of non-scientist volunteers in any discipline of conventional scientific research. Over the last two decades, nature-based CS has flourished due to innovative technology, novel devices, and widespread digital platforms used to collect and classify species occurrence data. For scientists, CS offers a low-cost approach of collecting species occurrence information at large spatial scales that otherwise would be prohibitively expensive. We examined the trends and gaps linked to the use of CS as a source of data for species distribution models (SDMs), in order to propose guidelines and highlight solutions. We conducted a quantitative literature review of 207 peer-reviewed articles to measure how the representation of different taxa, regions, and data types have changed in SDM publications since the 2010s. Our review shows that the number of papers using CS for SDMs has increased at approximately double the rate of the overall number of SDM papers. However, disparities in taxonomic and geographic coverage remain in studies using CS. Western Europe and North America were the regions with the most coverage (73%). Papers on birds (49%) and mammals (19.3%) outnumbered other taxa. Among invertebrates, flying insects including Lepidoptera, Odonata and Hymenoptera received the most attention. Discrepancies between research interest and availability of data were as especially important for amphibians, reptiles and fishes. Compared to studies on animal taxa, papers on plants using CS data remain rare. Although the aims and scope of papers are diverse, species conservation remained the central theme of SDM using CS data. We present examples of the use of CS and highlight recommendations to motivate further research, such as combining multiple data sources and promoting local and traditional knowledge. We hope our findings will strengthen citizen-researchers partnerships to better inform SDMs, especially for less-studied taxa and regions. Researchers stand to benefit from the large quantity of data available from CS sources to improve global predictions of species distributions.

scholarly journals Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8059 ◽  
Author(s):  
Benjamin M. Marshall ◽  
Colin T. Strine
Keyword(s):  
Social Media ◽  
North America ◽  
South America ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Conservation Status ◽  
Model Performance ◽  
Distribution Models ◽  
Occurrence Data ◽  
Occurrence Records

A species’ distribution provides fundamental information on: climatic niche, biogeography, and conservation status. Species distribution models often use occurrence records from biodiversity databases, subject to spatial and taxonomic biases. Deficiencies in occurrence data can lead to incomplete species distribution estimates. We can incorporate other data sources to supplement occurrence datasets. The general public is creating (via GPS-enabled cameras to photograph wildlife) incidental occurrence records that may present an opportunity to improve species distribution models. We investigated (1) occurrence data of a cryptic group of animals: non-marine snakes, in a biodiversity database (Global Biodiversity Information Facility (GBIF)) and determined (2) whether incidental occurrence records extracted from geo-tagged social media images (Flickr) could improve distribution models for 18 tropical snake species. We provide R code to search for and extract data from images using Flickr’s API. We show the biodiversity database’s 302,386 records disproportionately originate from North America, Europe and Oceania (250,063, 82.7%), with substantial gaps in tropical areas that host the highest snake diversity. North America, Europe and Oceania averaged several hundred records per species; whereas Asia, Africa and South America averaged less than 35 per species. Occurrence density showed similar patterns; Asia, Africa and South America have roughly ten-fold fewer records per 100 km2than other regions. Social media provided 44,687 potential records. However, including them in distribution models only marginally impacted niche estimations; niche overlap indices were consistently over 0.9. Similarly, we show negligible differences in Maxent model performance between models trained using GBIF-only and Flickr-supplemented datasets. Model performance appeared dependent on species, rather than number of occurrences or training dataset. We suggest that for tropical snakes, accessible social media currently fails to deliver appreciable benefits for estimating species distributions; but due to the variation between species and the rapid growth in social media data, may still be worth considering in future contexts.

scholarly journals An estimate of the area of occupancy and population size of Brachycephalus tridactylus (Anura: Brachycephalidae) to reassess its conservation status, with a proposal for conservation measures

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12687
Author(s):  
Marcos R. Bornschein ◽  
Júnior Nadaline ◽  
Luiz Fernando Ribeiro ◽  
Giovanna Sandretti-Silva ◽  
Maria Fernanda Ferreira Rivas ◽  
...  
Keyword(s):  
New Species ◽  
Population Size ◽  
Conservation Status ◽  
Species Conservation ◽  
Type Locality ◽  
Area Of Occupancy ◽  
Conservation Measures ◽  
New Localities ◽  
Species Population ◽  
Surrounding Areas

Background We are experiencing a global crisis in conservation, which has led to the prioritization of targets, such as nations, regions, and animal groups, which are necessary while resources are disputed. Brazil is a priority not only because of its megadiversity, high rates of endemism, and frequent descriptions of new species but also because of its high levels of deforestation. Among the species groups prioritized for conservation is the anurans (Amphibia: Anura), the population of which is severely declining. One group of anurans is the genus Brachycephalus, which includes 37 endemic species in the Brazilian Atlantic Rainforest. Some of these species have highly restricted distributions (<100 ha). Thirty new species have been described since 2000, and 55.3% of all species are threatened with extinction. Brachycephalus tridactylus was only recently described and remains restricted to its type locality. Because of its reduced geographical distribution (0.41 km2), it has been proposed to be considered as Vulnerable. The objective of this study is to reevaluate the conservation status of Brachycephalus tridactylus and propose conservation measures. Methods We searched for new populations during 2016–2020, evaluated in loco impacts and potential impacts on the species’ population, and performed an analysis of the density of this population and estimated its size. International Union for Conservation of Nature (IUCN) criteria were used to assess the conservation status of the species. Results We recorded the species in seven new localities (from 715–1,140 m above sea level) in the state of São Paulo up to 33 km from the type locality of the species (in state of Paraná). We estimated the area of occupancy as 148.44 km2, densities as one calling male per 4.05 m2 and 130.00 m2, and a total population size of 4,429,722 adult individuals. Based on our finding, we proposed three lines of management: (1) formation of fire brigades, (2) management of residents’ mules in the conservation unit and surrounding areas, and (3) management of degraded areas. We recommend changing the species’ conservation status from Vulnerable to Endangered because of its fragmented distribution and decline in the area of occupancy and in the quality of its habitat. Our results have expanded the species previous geographic distribution and delimited areas without previous records. Our estimates of population density and size are in accordance with those verified for congeners. The conservation of this species benefits the environments and other species that inhabit them, being, therefore, strategic for receiving conservation actions that will spread throughout the ecosystem.

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