Niche Estimation Above and Below the Species Level

Smith, Adam B.; Godsoe, William; Rodríguez‐Sánchez, Francisco; Wang, Hsiao‐Hsuan; Warren, Dan L.

doi:10.1016/j.tree.2018.10.012

Cited by 149 publications

(159 citation statements)

References 101 publications

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“…Although our predictions at the margins of the distribution of widespread species are consistent with these suggestions, the integration of dispersal constraints also showed an opposite pattern if the different populations of the species are locally adapted but not able to disperse (Valladares et al, 2014). It will contribute to increasing our ability to predict future shifts in species distributions and their resilience under climate change (Peterson et al, 2019;Smith et al, 2019). We provide a tool to filter species for which further information should be collected to document processes underlying potential local adaptation, adaptive plasticity and dispersal abilities.…”

Section: Ta B L Esupporting

confidence: 72%

“…However, it has been shown that there can be important geographical intraspecific variation in the sensitivity and response to changing climate conditions (Mills et al, 2017;Nice et al, 2019;Peterson, Doak, & Morris, 2019). Standard niche-based models may, therefore, incorrectly assess the full range of suitable climate conditions for the species and may produce inaccurate or even wrong predictions of distribution shifts (Hällfors et al, 2016;Nice et al, 2019;Peterson et al, 2019;Smith, Godsoe, Rodríguez-Sánchez, Wang, & Warren, 2019;Valladares et al, 2014). Díaz-Almeyda et al, 2017;Malyshev et al, 2016) and arises from local adaptation or adaptive plasticity along the gradient of climate conditions (Macdonald, Llewelyn, & Phillips, 2018;Moran et al, 2016;Vargas et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…Alternative approaches that integrate basic information about mechanisms into niche-based models have recently been developed (Diniz-Filho et al, 2019;Gotelli & Stanton-Geddes, 2015). With some of these approaches, the distribution range of a species is first split into distinct entities (hereafter 'partitions') based either on evolutionary lineages or on phenotypic traits that are assumed to correlate with different responses to local climate conditions (Hällfors et al, 2016;Lecocq, Harpke, Rasmont, & Schweiger, 2019;Smith et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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A novel tool to assess the effect of intraspecific spatial niche variation on species distribution shifts under climate change

Martin

Dyck

Legendre

et al. 2019

Global Ecol Biogeogr

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Aim: Niche-based models often ignore spatial variation in the climatic niche of a species across its occupied range and the related variation in the response to changing climate conditions. This assumption may lead to inaccurate predictions of species distribution shifts under climate change. Models have been developed to address this issue, but most of them depend upon prior knowledge on evolutionary lineages, phenotypic traits or ecological processes underlying local adaptation or adaptive plasticity. As such information is often lacking, these models are not frequently used to predict distribution shifts for many species. This limits our ability to explore general patterns of change across species.Innovation: Here, we propose a modelling framework that can be applied across a large sample of species to assess their distribution shifts under future climate while exploring the effect of intraspecific spatial variation in the response to climate conditions. The proposed approach does not require a detailed understanding of the processes underlying such variation. The geographical distribution of a species is split into spatial subsets along the gradient of occupied climate conditions. These subsets are considered as proxies for intraspecific spatial niche variation. Local models are built with each subset and their predictions are assembled across the study area | 591 MARTIN eT Al.

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Section: Ta B L Esupporting

confidence: 72%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A novel tool to assess the effect of intraspecific spatial niche variation on species distribution shifts under climate change

Martin

Dyck

Legendre

et al. 2019

Global Ecol Biogeogr

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“…Many investigators are currently developing methods that incorporate more biological and statistical realism into the SDM process, including the integration of physiological and trait data (Pollock et al, 2018) and explicit models of bias (Robinson, Ruiz-Gutierrez, & Fink, 2018), dispersal (Zurell, 2017), plasticity (Bush et al, 2016) and evolutionary history (Smith, Godsoe, Rodriguez-Sanchez, Wang, & Warren, 2019). Many investigators are currently developing methods that incorporate more biological and statistical realism into the SDM process, including the integration of physiological and trait data (Pollock et al, 2018) and explicit models of bias (Robinson, Ruiz-Gutierrez, & Fink, 2018), dispersal (Zurell, 2017), plasticity (Bush et al, 2016) and evolutionary history (Smith, Godsoe, Rodriguez-Sanchez, Wang, & Warren, 2019).…”

Section: Concluding Remarks and Future Directionsmentioning

confidence: 99%

Evaluating presence‐only species distribution models with discrimination accuracy is uninformative for many applications

Warren

Matzke

Iglesias

2019

Journal of Biogeography

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Aim Species distribution models are used across evolution, ecology, conservation and epidemiology to make critical decisions and study biological phenomena, often in cases where experimental approaches are intractable. Choices regarding optimal models, methods and data are typically made based on discrimination accuracy: a model's ability to predict subsets of species occurrence data that were withheld during model construction. However, empirical applications of these models often involve making biological inferences based on continuous estimates of relative habitat suitability as a function of environmental predictor variables. We term the reliability of these biological inferences ‘functional accuracy.’ We explore the link between discrimination accuracy and functional accuracy. Methods Using a simulation approach we investigate whether models that make good predictions of species distributions correctly infer the underlying relationship between environmental predictors and the suitability of habitat. Results We demonstrate that discrimination accuracy is only informative when models are simple and similar in structure to the true niche, or when data partitioning is geographically structured. However, the utility of discrimination accuracy for selecting models with high functional accuracy was low in all cases. Main conclusions These results suggest that many empirical studies and decisions are based on criteria that are unrelated to models’ usefulness for their intended purpose. We argue that empirical modelling studies need to place significantly more emphasis on biological insight into the plausibility of models, and that the current approach of maximizing discrimination accuracy at the expense of other considerations is detrimental to both the empirical and methodological literature in this active field. Finally, we argue that future development of the field must include an increased emphasis on simulation; methodological studies based on ability to predict withheld occurrence data may be largely uninformative about best practices for applications where interpretation of models relies on estimating ecological processes, and will unduly penalize more biologically informative modelling approaches.

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“…For this purpose, we followed Smith et al (2019) to test for variations in niches by creating separate ENMs for each subspecies to best capture environmental relationships using environmental covariates and occurrence data to construct ENMs for each subspecies based on maximum entropy (Phillips et al 2004(Phillips et al , 2006. In this study, we addressed the question of whether the members of this complex (with the exception of E. l. meridae, for which only a single specimen was available) diverged with regard to their niches to explore the potential role of niche conservatism in their radiation.…”

Section: Introductionmentioning

confidence: 99%

Niches and radiations: a case study on the Andean sapphire‐vented puffleg Eriocnemis luciani and coppery‐naped puffleg E. sapphiropygia (Aves, Trochilidae)

Ramoni‐Perazzi

Schuchmann

Weller

et al. 2020

Journal of Avian Biology

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The interaction between ecology and evolution, particularly with regard to speciation processes, remains a main topic of scientific research. Andean hummingbirds have undergone a remarkable radiation, with many species exhibiting patchy distributions and, in some cases, taxonomic controversy. An example is the sapphire-vented puffleg Eriocnemis luciani; ssp. baptistae, luciani and meridae, which some authors merge with the coppery-naped puffleg E. sapphiropygia; ssp. catharina and sapphiropygia. Each group is distributed either north or south from the Huancabamba Depression, the major biogeographical barrier within the tropical Andes. We investigated whether these subspecies share some niche characteristics despite their geographical separation and determined their meaning in the context of the speciation process of trochilids in the tropical Andes. For each subspecies, we performed geographical predictions and paired tests of niche conservatism in environmental space. Geographical predictions included separate regions for subspecies catharina and sapphiropygia, while the predicted regions for subspecies luciani and baptistae greatly overlapped. The E. l. luciani model predicted a single pixel near to the potential area of E. l. meridae, known only from a unique, old record. Subspecies luciani and baptistae exhibited the greatest niche overlap among the pairs of taxa for most variables. However, our results clearly indicated niche divergence for the four members of the E. luciani-sapphiropygia complex, independent of the similarities or slight dissimilarities in their respective backgrounds, indicating that other forces in addition to variation in environmental parameters, such as natural selection or genetic drift, are driving the radiation of these hummingbirds. This finding coincides with the unusually high speciation rates reported for Andean hummingbirds. Thus, the currently accepted taxonomy within the E. lucianisapphiropygia complex may be even more convoluted than indicated by previous studies. Hence, the results of our study are a wakeup call to include the exploration of lineage diversification in biodiversity-related efforts.Niches and radiations: a case study on the Andean sapphire-vented puffleg Eriocnemis luciani and coppery-naped puffleg E. sapphiropygia (Aves, Trochilidae)

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Niche Estimation Above and Below the Species Level

Cited by 149 publications

References 101 publications

A novel tool to assess the effect of intraspecific spatial niche variation on species distribution shifts under climate change

A novel tool to assess the effect of intraspecific spatial niche variation on species distribution shifts under climate change

Evaluating presence‐only species distribution models with discrimination accuracy is uninformative for many applications

Niches and radiations: a case study on the Andean sapphire‐vented puffleg Eriocnemis luciani and coppery‐naped puffleg E. sapphiropygia (Aves, Trochilidae)

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