Climatic curves as predictors in MaxEnt niche modeling

Mapping Intimacies ◽

10.1101/2021.11.08.467713 ◽

2021 ◽

Author(s):

Ondřej Mikula

Keyword(s):

Model Fitting ◽

Niche Modeling ◽

Environmental Niche ◽

Climatic Parameter ◽

Species Occurrence ◽

Niche Modelling ◽

Different Types ◽

Spline Basis ◽

Annual Changes

Environmental niche modelling (ENM) uses different types of variables to predict species occurrence. In widespread use are variables derived from climatic curves, i.e., average annual changes in some climatic parameter. This study shows how to use the climatic curves themselves as ENM predictors. The key step is projection of the curves' constituent variables on a suitable spline basis, which preserves time-ordering of the variables and supports smoothness of predictions. Complexity of the model is controlled by sensible choice of the spline basis, followed by lasso regularization in model fitting.

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Evaluation metrics and validation of presence-only species distribution models based on distributional maps with varying coverage

Scientific Reports ◽

10.1038/s41598-020-80062-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kamil Konowalik ◽

Agata Nosol

Keyword(s):

Ecological Niche Modeling ◽

Niche Modeling ◽

Ecological Niches ◽

Herbarium Specimens ◽

Wide Field ◽

Environmental Niche ◽

Endemic Plant ◽

Distribution Models ◽

Environmental Niche Modeling ◽

Almost All

AbstractWe examine how different datasets, including georeferenced hardcopy maps of different extents and georeferenced herbarium specimens (spanning the range from 100 to 85,000 km2) influence ecological niche modeling. We check 13 of the available environmental niche modeling algorithms, using 30 metrics to score their validity and evaluate which are useful for the selection of the best model. The validation is made using an independent dataset comprised of presences and absences collected in a range-wide field survey of Carpathian endemic plant Leucanthemum rotundifolium (Compositae). Our analysis of models’ predictive performances indicates that almost all datasets may be used for the construction of a species distributional range. Both very local and very general datasets can produce useful predictions, which may be more detailed than the original ranges. Results also highlight the possibility of using the data from manually georeferenced archival sources in reconstructions aimed at establishing species’ ecological niches. We discuss possible applications of those data and associated problems. For the evaluation of models, we suggest employing AUC, MAE, and Bias. We show an example of how AUC and MAE may be combined to select the model with the best performance.

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Ecological analysis and environmental niche modelling of Dactylorhiza hatagirea (D. Don) Soo: A conservation approach for critically endangered medicinal orchid

Saudi Journal of Biological Sciences ◽

10.1016/j.sjbs.2021.01.054 ◽

2021 ◽

Author(s):

Ishfaq Ahmad Wani ◽

Susheel Verma ◽

Shazia Mushtaq ◽

Abdulaziz Abdullah Alsahli ◽

Mohammed Nasser Alyemeni ◽

...

Keyword(s):

Critically Endangered ◽

Environmental Niche ◽

Niche Modelling ◽

Ecological Analysis ◽

Medicinal Orchid

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Climate variability impacts on diversification processes in a biodiversity hotspot: a phylogeography of ancient pseudoscorpions in south-western Australia

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz010 ◽

2019 ◽

Vol 186 (4) ◽

pp. 934-949 ◽

Cited By ~ 1

Author(s):

Danilo Harms ◽

J Dale Roberts ◽

Mark S Harvey

Keyword(s):

Phylogenetic Analyses ◽

Distribution Patterns ◽

Biodiversity Hotspot ◽

Molecular Dating ◽

Environmental Niche ◽

Ecological Niche Models ◽

The South ◽

Niche Modelling ◽

South West ◽

Western Division

Abstract The south-western division of Australia is the only biodiversity hotspot in Australia and is well-known for extreme levels of local endemism. Climate change has been identified as a key threat for flora and fauna, but very few data are presently available to evaluate its impact on invertebrate fauna. Here, we derive a molecular phylogeography for pseudoscorpions of the genus Pseudotyrannochthonius that in the south-west are restricted to regions with the highest rainfall. A dated molecular phylogeny derived from six gene fragments is used for biogeographic reconstruction analyses, spatial mapping, environmental niche-modelling, and to infer putative species. Phylogenetic analyses uncover nine clades with mostly allopatric distributions and often small linear ranges between 0.5 and 130 km. Molecular dating suggests that the origins of contemporary diversity fall into a period of warm/humid Palaeogene climates, but splits in the phylogeny coincide with major environmental shifts, such as significant global cooling during the Middle Miocene. By testing several models of historical biogeography available for the south-west, we determine that Pseudotyrannochthonius is an ancient relict lineage that principally follows a model of allopatric speciation in mesic zone refugia, although there are derivations from this model in that some species are older and distribution patterns more complex than expected. Ecological niche models indicate that drier and warmer future climates will lead to range contraction towards refugia of highest rainfall, probably mimicking past variations that have generated high diversity in these areas. Their conservation management will be crucial for preserving the unique biodiversity heritage of the south-west.

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Understanding biogeographical patterns in the western Balkan Peninsula using environmental niche modelling and geostatistics in polymorphic Edraianthus tenuifolius

AoB Plants ◽

10.1093/aobpla/ply064 ◽

2018 ◽

Cited By ~ 4

Author(s):

Peter Glasnović ◽

Martina Temunović ◽

Dmitar Lakušić ◽

Tamara Rakić ◽

Valentina Brečko Grubar ◽

...

Keyword(s):

Balkan Peninsula ◽

Environmental Niche ◽

Niche Modelling

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Niche conservatism predominates in adaptive radiation: comparing the diversification of Hawaiian arthropods using ecological niche modelling

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz023 ◽

2019 ◽

Vol 127 (2) ◽

pp. 479-492 ◽

Cited By ~ 2

Author(s):

Anna E Hiller ◽

Michelle S Koo ◽

Kari R Goodman ◽

Kerry L Shaw ◽

Patrick M O’Grady ◽

...

Keyword(s):

Adaptive Radiation ◽

Phylogenetic Signal ◽

Niche Overlap ◽

Oceanic Islands ◽

Niche Conservatism ◽

Environmental Niche ◽

Niche Modelling ◽

Closely Related Species ◽

Species Comparisons

Abstract The role of the environmental niche in fostering ecological divergence during adaptive radiation remains enigmatic. In this study, we examine the interplay between environmental niche divergence and conservatism in the context of adaptive radiation on oceanic islands, by characterizing the niche breadth of four Hawaiian arthropod radiations: Tetragnatha spiders (Tetragnathidae Latreille, 1804), Laupala crickets (Gryllidae Otte, 1994), a clade of Drosophila flies (Drosophilidae Fallén, 1823) and Nesosydne planthoppers (Delphacidae Kirkaldy, 1907). We assembled occurrence datasets for the four lineages, modelled their distributions and quantified niche overlap. All four groups occupy the islands in distinct ways, highlighting the contrasting axes of diversification for different lineages. Laupala and Nesosydne have opposite environmental niche extents (broad and narrow, respectively), whereas Tetragnatha and Drosophila share relatively intermediate tolerances. Temperature constrains the distributions of all four radiations. Tests of phylogenetic signal suggest that, for Tetragnatha and Drosophila, closely related species exhibit similar environmental niches; thus, diversification is associated with niche conservatism. Sister species comparisons also show that populations often retain similar environmental tolerances, although exceptions do occur. Results imply that diversification does not occur through ecological speciation; instead, adaptive radiation occurs largely within a single environment.

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Assessing the status of critically endangered Kondana soft-furred rat (Millardia kondana) using integrative taxonomy: combining evidence from morphological, molecular and environmental niche modeling

Mammalia ◽

10.1515/mammalia-2019-0056 ◽

2020 ◽

Vol 84 (4) ◽

pp. 392-406

Author(s):

Sameer B. Bajaru ◽

Aparna Lajmi ◽

Ranjit Manakadan ◽

Amol R. Kulavmode ◽

Uma Ramakrishnan

Keyword(s):

Taxonomic Status ◽

Niche Modeling ◽

Critically Endangered ◽

Morphological Data ◽

Integrative Approach ◽

Environmental Niche ◽

Sister Relationship ◽

Environmental Niche Modeling ◽

Precipitation Seasonality ◽

Significant Difference

AbstractKondana soft-furred rat is a critically endangered (CR) species, known from a single locality – Sinhgad in the northern Western Ghats, India. However, the taxonomic status of this species is uncertain due to its close resemblance to the widely distributed soft-furred field rat Millardia meltada, which has serious implications on the conservation status of Millardia kondana. In this study, we assessed the current taxonomic status of M. kondana through an integrative approach combining morphological, molecular and environmental niche modeling analyses. We collected morphological data from the specimens around Sinhgad as well as preserved specimens in the museum. Both morphological and two-dimensional (2D) morphometrical analyses showed a significant difference between M. kondana and M. meltada. Molecular phylogeny based on cytochrome b gene revealed a sister relationship between M. kondana and M. meltada, and both species form distinct well-supported monophyletic clades. Niche modeling also predicted niche segregation between the two species: M. kondana preferred areas with a high elevation and precipitation seasonality while M. meltada favored regions with a low elevation and precipitation. We confirmed that M. kondana is taxonomically distinct from M. meltada, and based on our estimates of its occurrence and occupancy, M. kondana continues to be treated as CR until further detailed investigations.

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Circum-Mediterranean phylogeography of a bat coupled with past environmental niche modeling: A new paradigm for the recolonization of Europe?

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2016.03.024 ◽

2016 ◽

Vol 99 ◽

pp. 323-336 ◽

Cited By ~ 12

Author(s):

Raşit Bilgin ◽

Kanat Gürün ◽

Hugo Rebelo ◽

Sebastien J. Puechmaille ◽

Öncü Maracı ◽

...

Keyword(s):

Niche Modeling ◽

Environmental Niche ◽

New Paradigm ◽

Environmental Niche Modeling

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Using environmental niche modelling to investigate abiotic predictors of crocodilian attacks on people

Oryx ◽

10.1017/s0030605319000681 ◽

2020 ◽

Vol 54 (5) ◽

pp. 639-647

Author(s):

George Powell ◽

Thomas M. M. Versluys ◽

Jessica J. Williams ◽

Sonia Tiedt ◽

Simon Pooley

Keyword(s):

Human Life ◽

Seasonal Pattern ◽

Alligator Mississippiensis ◽

Effect Of Temperature ◽

Environmental Niche ◽

Niche Modelling ◽

Human Safety ◽

Hunting Behaviour ◽

The Tropics ◽

The Relationship

AbstractCrocodilians are distributed widely through the tropics and subtropics, and several species pose a substantial threat to human life. This has important implications for human safety and crocodilian conservation. Understanding the drivers of crocodilian attacks on people could help minimize future attacks and inform conflict management. Crocodilian attacks follow a seasonal pattern in many regions, but there has been limited analysis of the relationship between attack occurrence and fine-scale contemporaneous environmental conditions. We use methods from environmental niche modelling to explore the relationships between attacks on people and abiotic predictors at a daily temporal resolution for the Nile crocodile Crocodylus niloticus in South Africa and Eswatini (formerly Swaziland), and the American alligator Alligator mississippiensis in Florida, USA. Our results indicate that ambient daily temperature is the most important abiotic temporal predictor of attack occurrence for both species, with attack likelihood increasing markedly when mean daily temperatures exceed 18 °C and peaking at 28 °C. It is likely that this relationship is explained partially by human propensity to spend time in and around water in warmer weather but also by the effect of temperature on crocodilian hunting behaviour and physiology, especially the ability to digest food. We discuss the potential of our findings to contribute to the management of crocodilians, with benefits for both human safety and conservation, and the application of environmental niche modelling for understanding human–wildlife conflicts involving both ectotherms and endotherms.

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PaleoENM: applying ecological niche modeling to the fossil record

Paleobiology ◽

10.1017/pab.2014.19 ◽

2015 ◽

Vol 41 (2) ◽

pp. 226-244 ◽

Cited By ~ 22

Author(s):

Corinne E. Myers ◽

Alycia L. Stigall ◽

Bruce S. Lieberman

Keyword(s):

Best Practices ◽

Fossil Record ◽

Ecological Niche ◽

Ecological Niche Modeling ◽

Niche Modeling ◽

Data Sets ◽

Species Occurrence ◽

Deep Time ◽

Environmental Suitability ◽

Species Occurrences

AbstractEcological niche modeling (ENM) is a quantitative approach to predict species’ abiotic requirements. It is a correlative technique, requiring geographically explicit information on species occurrences and the suites of environmental conditions experienced at each occurrence point. The output of these models is a set of environmental suitability rules that can be projected geographically and through time to test biogeographic, ecologic, and evolutionary hypotheses. Although developed by biologists and used extensively in the modern, ENM is in its early stages of application to the deep-time fossil record (hence PaleoENM). In part its limited use in the fossil record thus far reflects the methodological challenge of constructing paleoenvironmental layers needed for PaleoENM analysis, whereas in the modern these layers are available from large public databases (e.g., WorldClim). This paper provides a contextual and methodological framework for appropriately applying PaleoENM, including best practices for developing species occurrence and paleoenvironmental data sets for PaleoENM analyses.

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